diff --git a/docs/.static/exomiser-logo_white-banner.png b/docs/.static/exomiser-logo_white-banner.png new file mode 100644 index 000000000..f378cab4d Binary files /dev/null and b/docs/.static/exomiser-logo_white-banner.png differ diff --git a/docs/acmg_assignment.rst b/docs/acmg_assignment.rst new file mode 100644 index 000000000..64916fd7b --- /dev/null +++ b/docs/acmg_assignment.rst @@ -0,0 +1,245 @@ +.. _acmg_assignment: + +=============== +ACMG Assignment +=============== + +Starting with version 13.1.0, Exomiser performs a partial categorisation of the variants contributing to the gene +score for a mode of inheritance using the ACMG/AMP `Standards and guidelines for the interpretation of sequence +variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association +for Molecular Pathology `_. The criteria are assigned and combined according to the +`UK ACGS 2020 guidelines `_. + +It is important to be aware that these scores are not a substitute for manual assignment by a qualified clinical geneticist +or clinician - The scores displayed utilise the data found in the Exomiser database and are a subset of the possible +criteria by which to assess a variant. Nonetheless, in our benchmarking on the returned cases from the 100K Genomes Project, +restricting to variants with these automated P/LP classifications increases precision (positive predictive value) markedly +without excluding many real diagnoses. For example, on a cohort of 742 solved cases where the top 5 Exomiser candidates +were considered, including the P/LP criteria increased precision 3.8-fold from 15% to 57% with only a small drop in the +recall of the diagnoses from 94% to 83%. An even larger 5.7-fold increase of precision from 3% to 17% was observed when +considering a larger cohort of 31k cases where only 17% had received a positive diagnosis (again with a modest drop in +recall from 91% to 75%). + +Exomiser is capable of assigning the following ACMG categories: + +Computational and Predictive Data +================================= +PVS1 +---- +Variants must have a predicted loss of function effect, be in a gene with known disease associations and have a gene +constraint LOF O/E < 0.7635 (gnomAD 2.1.1) to suggest that a gene is LoF intolerant. Variants not predicted to lead to +NMD (those located in the last exon) will have the modifier downgraded to Strong. + +PM4 +--- +Stop-loss and in-frame insertions or deletions, not previously assigned a `PVS1` criterion are assigned `PM4`. + +PP3 / BP4 +--------- +If REVEL is chosen as a pathogenicity predictor for missense variants, `PP3` and `BP4` are assigned using the modifiers +according to table 2 of `Evidence-based calibration of computational tools for missense variant pathogenicity classification +and ClinGen recommendations for clinical use of PP3/BP4 criteria `_. +Note that this suggests the use of modifiers up to Strong in the case of pathogenic or Very Strong in the case of benign predictions. +Otherwise, an ensemble-based approach will be used for other pathogenicity predictors as per the original 215 guidelines. +It should be noted we found better performance using the REVEL-based approach when testing against the 100K genomes data. + +Segregation Data +================ +BS4 +--- +If a pedigree with two or more members, including the proband is provided, Exomiser will assign `BS4` for variants not +segregating with affected members of the family. + +De novo Data +=========== + +PS2 +--- +Exomiser assigns the `PS2` criterion for variants compatible with a dominant mode of inheritance, with a pedigree containing +at least two ancestors of the proband, none of whom are affected and none of whom share the same allele as the proband. + +Population Data +=============== +BA1 +--- +Given Exomiser will filter out alleles with an allele frequency of >= 2.0%, this is unlikely to be seen. However, alleles +with a maximum frequency >= 5.0% in the frequency sources specified will be assigned the `BA1` criterion. + +PM2 +--- +Alleles not present in the ESP, ExAC and 1000 Genomes data sets (i.e. the allele must be absent from all three) are +assigned the `PM2` criterion. + +Allelic Data +============ +PM3 / BP2 +--------- +If Exomiser is provided with a phased VCF and a variant is found to be *in-trans* with a ClinVar Pathogenic variant and +associated with a recessive disorder, the `PM3` criterion will be applied. However, in cases where variant is being +considered for a recessive disorder and is *in-cis* or a dominant disorder and *in-trans* with another pathogenic variant +the `BP2` criterion is applied. + + +Phenotype +========= +PP4 +--- +Given Exomiser's focus on phenotype-driven variant prioritisation, variants in a gene associated with a disorder with a +phenotype match score > 0.6 to the patient's phenotype are assigned the `PP4` criterion at the Moderate, rather than +Supporting level. + +Clinical +======== +PP5 / BP6 +-------- +If a variant is previously reported as P/LP in ClinVar with a 1-start rating, it will be assigned `PP5`, those with >= 2 +stars (multiple submitters, criteria provided, no conflicts / reviewed by expert panel / practice guideline) will be +assigned a Strong level. Conversely, if the variant is previously reported as B/LB it will be assigned `BP6` with the same +modification criteria. Typically these P/LP variants will be in the Exomiser ClinVar 'whitelist', and will have +a very high variant score irrespective of the predicted variant effect and always survive any filtering criteria. + + +Transcript Selection +==================== + +Transcripts will be selected using the most deleterious predicted variant effect from `Jannovar `_ +according to the `transcript-source` property set in the `application.properties`. We recommend using the Ensembl +transcript datasource as the Exomiser build uses the GENCODE basic set of transcripts. Future versions should use MANE transcripts. + +ACMG assignments will be reported for a variant on a transcript consistent with a particular mode of inheritance in +conjunction with a disorder, the assigned criteria with any modifiers and the final classification e.g. + +.. parsed-literal:: + + 1-12335-A-T, NC_000001.10:g.12335A>T, GENE1(ENST12345678):c.2346A>T:p.1234A>-, PATHOGENIC, [PVS1, PS1, PP4_Strong], Disease (OMIM:12345), AUTOSOMAL_DOMINANT + + +.. code-block:: json + + "acmgAssignments": [ + { + "variantEvaluation": { + "genomeAssembly": "HG19", + "contigName": "10", + "start": 123256215, + "end": 123256215, + "ref": "T", + "alt": "G", + "type": "SNV", + "length": 1, + "phredScore": 100, + "variantEffect": "MISSENSE_VARIANT", + "whiteListed": true, + "filterStatus": "PASSED", + "contributesToGeneScore": true, + "variantScore": 1, + "frequencyScore": 1, + "pathogenicityScore": 1, + "predictedPathogenic": true, + "passedFilterTypes": [ + "FAILED_VARIANT_FILTER", + "PATHOGENICITY_FILTER", + "FREQUENCY_FILTER", + "VARIANT_EFFECT_FILTER", + "INHERITANCE_FILTER" + ], + "frequencyData": { + "rsId": "rs121918506", + "score": 1 + }, + "pathogenicityData": { + "clinVarData": { + "alleleId": "28333", + "primaryInterpretation": "LIKELY_PATHOGENIC", + "reviewStatus": "criteria provided, single submitter" + }, + "score": 0.965, + "predictedPathogenicityScores": [ + { + "source": "REVEL", + "score": 0.965 + }, + { + "source": "MVP", + "score": 0.9517972 + } + ], + "mostPathogenicScore": { + "source": "REVEL", + "score": 0.965 + } + }, + "compatibleInheritanceModes": [ + "AUTOSOMAL_DOMINANT" + ], + "contributingInheritanceModes": [ + "AUTOSOMAL_DOMINANT" + ], + "transcriptAnnotations": [ + { + "variantEffect": "MISSENSE_VARIANT", + "geneSymbol": "FGFR2", + "accession": "ENST00000346997.2", + "hgvsGenomic": "g.12278533A>C", + "hgvsCdna": "c.1688A>C", + "hgvsProtein": "p.(Glu563Ala)", + "rankType": "EXON", + "rank": 12, + "rankTotal": 17 + }, + { + "variantEffect": "MISSENSE_VARIANT", + "geneSymbol": "FGFR2", + "accession": "ENST00000351936.6", + "hgvsGenomic": "g.12278533A>C", + "hgvsCdna": "c.1688A>C", + "hgvsProtein": "p.(Glu563Ala)", + "rankType": "EXON", + "rank": 13, + "rankTotal": 18 + } + ] + }, + "geneIdentifier": { + "geneId": "ENSG00000066468", + "geneSymbol": "FGFR2", + "hgncId": "HGNC:3689", + "hgncSymbol": "FGFR2", + "entrezId": "2263", + "ensemblId": "ENSG00000066468", + "ucscId": "uc057wle.1" + }, + "modeOfInheritance": "AUTOSOMAL_DOMINANT", + "disease": { + "diseaseId": "OMIM:123150", + "diseaseName": "Jackson-Weiss syndrome", + "associatedGeneId": 2263, + "diseaseType": "DISEASE", + "inheritanceMode": "AUTOSOMAL_DOMINANT", + "phenotypeIds": [ + "HP:0000006", + "HP:0000272", + "HP:0001363", + "HP:0001783", + "HP:0004691", + "HP:0008080", + "HP:0008122", + "HP:0010055", + "HP:0010743", + "HP:0011800" + ], + "id": "OMIM:123150", + "associatedGeneSymbol": "FGFR2" + }, + "acmgEvidence": { + "evidence": { + "PM2": "MODERATE", + "PP3": "STRONG", + "PP4": "SUPPORTING", + "PP5": "SUPPORTING" + } + }, + "acmgClassification": "LIKELY_PATHOGENIC" + } + ] + } \ No newline at end of file diff --git a/docs/advanced_analysis.rst b/docs/advanced_analysis.rst new file mode 100644 index 000000000..1a58ac646 --- /dev/null +++ b/docs/advanced_analysis.rst @@ -0,0 +1,620 @@ +=============================== +Analysis/Job File Configuration +=============================== + +Exomiser analyses are defined using a `yml format `_ configuration file(s). Examples can be found in +the unpacked exomiser-cli-|version|/examples/ directory. Here you will find a mixture of samples, jobs, analyses, +outputOptions, phenopackets, phenopacket family, vcf and ped files. + +.. _job: + +Job +~~~ + +An Exomiser :ref:`job` contains three sections: + + - :ref:`sample` or `phenopacket `_ + - :ref:`preset` or :ref:`analysis` + - :ref:`outputOptions` + + +These fields define all the input data, analysis steps and output requirements for a complete Exomiser analysis. They can +be used as a record of how a sample was analysed. Alternatively the various sections can all be defined at runtime using +the CLI arguments as explained in the :ref:`inputandoptions` section. + +which defines run mode, :ref:`filters` and :ref:`prioritisers`, and the :ref:`output options` section that defines the output format, +output file and number of results that should be returned. Each of these sections can be defined independently on the +command line or provided as a single file as shown in the `job`_ section. + +.. literalinclude:: ../exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml + :language: yaml + + +.. _sample: + +Sample +~~~~~~ + +It is recommended to provide Exomiser the input sample as in `Phenopacket `_ format. +Exomiser will accept this in either JSON or YAML format. + +probandId: +---------- + +hpoIds: +------- +Input of the HPO identifiers/terms. You can select them using the `HPO browser `_. Input must be in +array format. Terms are comma separated and delimited by single quotes. For example `['HP:0001156', 'HP:0001363', 'HP:0011304', 'HP:0010055']`. +It is *critical* that these are as detailed as possible and describe the observed phenotypes as fully and precisely as +possible. These are used by the phenotype matching algorithms and will heavily influence the outcome of an analysis. + +vcf: +---- +The variant file in `VCF format `_. There can be variants of multiple samples from +one family in the file. + +ped: +---- +If you have multiple samples as input you have to define the pedigree using the `ped format `_. +It is important that you correctly define affected and unaffected individuals. If you use ``X_RECESSIVE`` as mode of inheritance +be sure that the sex is correct (unknown is also fine). + + +.. _preset: + +Preset +~~~~~~ + +.. code-block:: yaml + + # one of EXOME or GENOME. GENOME will require REMM to be available. Default is EXOME. + preset: EXOME + + + +.. _analysis: + +Analysis +~~~~~~~~~ + +The analysis shown below is equivalent to the ``--preset exome`` argument or adding + +.. code-block:: yaml + + preset: EXOME + +to an Exomiser job file. In most cases it is recommended to use the default presets as these have been thoroughly +tested on the `UK 100,000 genome rare-disease cohort `_. In case the user +requires anything different, it is possible to manually define the data sources and steps in an Exomiser analysis. + + +.. code-block:: yaml + + --- + analysisMode: PASS_ONLY + inheritanceModes: { + AUTOSOMAL_DOMINANT: 0.1, + AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, + AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, + X_DOMINANT: 0.1, + X_RECESSIVE_HOM_ALT: 0.1, + X_RECESSIVE_COMP_HET: 2.0, + MITOCHONDRIAL: 0.2 + } + frequencySources: [ + THOUSAND_GENOMES, + TOPMED, + UK10K, + + ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + + EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + EXAC_OTHER, + + GNOMAD_E_AFR, + GNOMAD_E_AMR, + # GNOMAD_E_ASJ, + GNOMAD_E_EAS, + GNOMAD_E_FIN, + GNOMAD_E_NFE, + GNOMAD_E_OTH, + GNOMAD_E_SAS, + + GNOMAD_G_AFR, + GNOMAD_G_AMR, + # GNOMAD_G_ASJ, + GNOMAD_G_EAS, + GNOMAD_G_FIN, + GNOMAD_G_NFE, + GNOMAD_G_OTH, + GNOMAD_G_SAS + ] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP ] + #this is the standard exomiser order. + steps: [ + failedVariantFilter: { }, + variantEffectFilter: { + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + NON_CODING_TRANSCRIPT_INTRON_VARIANT, + CODING_TRANSCRIPT_INTRON_VARIANT, + UPSTREAM_GENE_VARIANT, + DOWNSTREAM_GENE_VARIANT, + INTERGENIC_VARIANT, + REGULATORY_REGION_VARIANT + ] + }, + frequencyFilter: { maxFrequency: 2.0 }, + pathogenicityFilter: { keepNonPathogenic: true }, + inheritanceFilter: { }, + omimPrioritiser: { }, + hiPhivePrioritiser: { } + ] + + + +analysisMode: +------------- +Can be ``FULL`` or ``PASS_ONLY``. We highly recommend ``PASS_ONLY`` on genomes for because of memory issues. It will only +keep variants that passes all filters. ``FULL`` will keep all variants, using the most memory and requiring the most time, +but it can be useful for troubleshooting why a particular variant of interest might not have been returned in the results +of an analysis. + +.. code-block:: yaml + + analysisMode: PASS_ONLY + + +inheritanceModes: +------------------ +Can be ``AUTOSOMAL_DOMINANT``, ``AUTOSOMAL_RECESSIVE``, ``X_RECESSIVE`` or ``UNDEFINED``. This is a functionality of Jannovar. +See its `inheritance documentation `_ for further information. + +.. code-block:: yaml + + # These are the default settings, with values representing the maximum minor allele frequency in percent (%) permitted for an + # allele to be considered as a causative candidate under that mode of inheritance. + # If you just want to analyse a sample under a single inheritance mode, delete/comment-out the others. For AUTOSOMAL_RECESSIVE + # or X_RECESSIVE ensure *both* relevant HOM_ALT and COMP_HET modes are present. + # In cases where you do not want any cut-offs applied an empty map should be used e.g. inheritanceModes: {} + inheritanceModes: { + AUTOSOMAL_DOMINANT: 0.1, + AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, + AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, + X_DOMINANT: 0.1, + X_RECESSIVE_HOM_ALT: 0.1, + X_RECESSIVE_COMP_HET: 2.0, + MITOCHONDRIAL: 0.2 + } + + +.. _frequencysources: + +frequencySources: +----------------- + +Here you can specify which variant frequency databases you want to use. You can add multiple databases using the same +array format as the HPO IDs. + +The data sources used are from `1000 genomes `_ (via DBSNP), `DBSNP `_, +`ESP `_, `ExAC, gnomAD exomes and gnomAD genomes `_, +`UK10K `_ (via DBSNP), `TOPMed `_ (via DBSNP). + +DBSNP: + ``THOUSAND_GENOMES``, + ``UK10K``, + ``TOPMED`` + +ESP: + ``ESP_AFRICAN_AMERICAN``, ``ESP_EUROPEAN_AMERICAN``, ``ESP_ALL`` + +ExAC: + ``EXAC_AFRICAN_INC_AFRICAN_AMERICAN``, + ``EXAC_AMERICAN``, + ``EXAC_SOUTH_ASIAN``, + ``EXAC_EAST_ASIAN``, + ``EXAC_FINNISH``, + ``EXAC_NON_FINNISH_EUROPEAN``, + ``EXAC_OTHER`` + +gnomAD exomes: + ``GNOMAD_E_AFR``, + ``GNOMAD_E_AMR``, + ``GNOMAD_E_ASJ``, + ``GNOMAD_E_EAS``, + ``GNOMAD_E_FIN``, + ``GNOMAD_E_NFE``, + ``GNOMAD_E_OTH``, + ``GNOMAD_E_SAS``, + +gnomAD genomes: + ``GNOMAD_G_AFR``, + ``GNOMAD_G_AMR``, + ``GNOMAD_G_ASJ``, + ``GNOMAD_G_EAS``, + ``GNOMAD_G_FIN``, + ``GNOMAD_G_NFE``, + ``GNOMAD_G_OTH``, + ``GNOMAD_G_SAS`` + +We recommend using all databases if the proband population background is unknown, although removing the ``GNOMAD_E_ASJ`` and ``GNOMAD_G_ASJ``, unless your proband is +known to come from an Ashkenazi population e.g. + +.. code-block:: yaml + + frequencySources: [ + THOUSAND_GENOMES, + TOPMED, + UK10K, + + ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + + EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + EXAC_OTHER, + + GNOMAD_E_AFR, + GNOMAD_E_AMR, + # GNOMAD_E_ASJ, + GNOMAD_E_EAS, + GNOMAD_E_FIN, + GNOMAD_E_NFE, + GNOMAD_E_OTH, + GNOMAD_E_SAS, + + GNOMAD_G_AFR, + GNOMAD_G_AMR, + # GNOMAD_G_ASJ, + GNOMAD_G_EAS, + GNOMAD_G_FIN, + GNOMAD_G_NFE, + GNOMAD_G_OTH, + GNOMAD_G_SAS + ] + + +.. _pathogenicitysources: + +pathogenicitySources: +--------------------- +Possible pathogenicitySources: ``POLYPHEN``, ``MUTATION_TASTER``, ``SIFT``, ``REVEL``, ``MVP``, ``CADD``, ``REMM``. ``REMM`` is trained on +non-coding regulatory regions. **WARNING** if you enable ``CADD``, ensure that you have downloaded and installed the CADD +tabix files and updated their location in the ``application.properties`` (see :ref:`cadd-install`). Exomiser will not run +without this. + +We recommend using either ``[REVEL, MVP]`` **OR** ``[POLYPHEN, MUTATION_TASTER, SIFT]`` as REVEL and MVP are newer +predictors which have been shown to have better performance and are more nuanced. Mixing them with the Polyphen2, +MutationTaster or SIFT will give worse performance. + +.. code-block:: yaml + + pathogenicitySources: [REVEL, MVP, REMM] + + +.. _steps: + +steps +----- +This section instructs exomiser which analysis steps should be run and with which criteria. **_n.b._ the order in which the steps are declared is important** +- exomiser will run them in the order declared, although certain optimisations will happen automatically. We recommend +using the [standard settings](../example/test-analysis-genome) for genome wide analysis as these have been optimised for +both speed and memory performance. Nonetheless all steps are optional. Being an array of steps, this section must be +enclosed in square brackets. Steps are comma separated and written in hash format *name: {options}*. **All steps are optional** +- comment them out or delete them if you do not want to use them. + +Analysis steps are defined in terms of :ref:`variant filters`, :ref:`gene filters` or +:ref:`prioritisers`. The :ref:`inheritanceFilter` and :ref:`omimPrioritiser` are both somewhat anomalous as they +operate on genes but also require the variants to have already been filtered. The optimiser will ensure that these are +run at the correct time if they have been incorrectly placed. + +Using these it is possible to create artificial exomes, define gene panels or only examine specific regions, for example. + +.. _variantfilters: + +Variant filters +............... + +These operate on variants and will produce a pass or fail result for each variant run through the filter. + +failedVariantFilter: +............... +Removes variants which are not marked as `PASS` or `.` in the VCF file. This is a highly recommended filter which will +remove a lot of noise. + +.. code-block:: yaml + + failedVariantFilter: {} + + +qualityFilter: +............... +Removes variants with VCF `QUAL` scores lower than the given `minQuality`. + +.. code-block:: yaml + + qualityFilter: {minQuality: 50.0} + + +intervalFilter: +............... +Defines an interval of interest. Only variants within this interval will be passed. Currently only single intervals are +possible. + +.. code-block:: yaml + + intervalFilter: {interval: 'chr10:123256200-123256300'} + + +geneIdFilter: +............. +You can define `entrez-gene-ids `_ for genes of interest. Only variants associated with +these genes will be analyzed. + +.. code-block:: yaml + + geneIdFilter: {geneIds: [12345, 34567, 98765]} + + +variantEffectFilter: +.................... +If you are interested only in specific functional classes of variants you can define a set of classes you want to remove +from the output. Variant effects are generated by `Jannovar `_. Jannovar uses +`Sequence Ontology (SO) `_ terms and are listed in their `manual `_. + +.. code-block:: yaml + + variantEffectFilter: {remove: [SYNONYMOUS_VARIANT]} + + +regulatoryFeatureFilter: +........................ +If included it removes all non-regulatory, non-coding variants over 20Kb from a known gene. Intergenic and upstream +variants in known enhancer regions over 20kb from a known gene are associated with genes in their TAD and not effected +by this filter. This is an important filter to include when analysing whole-genome data. + +.. code-block:: yaml + + regulatoryFeatureFilter: {} + + +knownVariantFilter: +................... +Removes variants represented in the databases set in the :ref:`frequencySources` section. E.g. if you define + +.. code-block:: yaml + + frequencySources: [THOUSAND_GENOMES] + + +every variant with an RS number will be removed. Variants without an RSid will be removed/failed if they are represented +in any database defined in the :ref:`frequencySources` section. We do not recommend this option on recessive diseases. + +.. code-block:: yaml + + knownVariantFilter: {} + + +.. _frequencyfilter: + +frequencyFilter: +................ +Frequency cutoff of a variant **in percent**. Frequencies are derived from the databases defined in the :ref:`frequencySources` +section. We recommend a value below 5.0 % depending on the disease. Variants will be removed/failed if they have a +frequency higher than the stated percentage in any database defined in the :ref:`frequencySources` section. +_n.b_ Not defining this filter will result in all variants having no frequency data, even if the :ref:`frequencySources` +contains values. + +.. code-block:: yaml + + frequencyFilter: {maxFrequency: 1.0} + + +.. _pathogenicityfilter: + +pathogenicityFilter: +.................... +Will apply the pathogenicity scores defined in the :ref:`pathogenicitySources` section to variants. +If the ``keepNonPathogenic`` field is set to ``true`` then all variants will be kept. Setting this to ``false`` will set +the filter to fail non-missense variants with pathogenicity scores lower than a score cutoff of 0.5. +This filter is meant to be quite permissive and we recommend it be set to true. + +.. code-block:: yaml + + pathogenicityFilter: {keepNonPathogenic: true} + + +.. _genefilters: + +Gene filters +............ +These act at the gene-level and therefore may also refer to the variants associated with the gene. As a rule this is +discouraged, although is broken by the inheritanceFiler. + +priorityScoreFilter: +.................... +Running the prioritizer followed by a priorityScoreFilter will remove genes which are least likely to contribute to the +phenotype defined in hpoIds, this will dramatically reduce the time and memory required to analyze a genome. 0.501 +is a good compromise to select good phenotype matches and the best protein-protein interactions hits using the hiPhive +prioritiser. PriorityType can be one of ``HIPHIVE_PRIORITY``, ``PHIVE_PRIORITY``, ``PHENIX_PRIORITY``, ``OMIM_PRIORITY``, ``EXOMEWALKER_PRIORITY``. + +.. code-block:: yaml + + priorityScoreFilter: {priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501} + + +.. _inheritancefilter: + +inheritanceFilter: +.................. +**inheritanceFilter** and **omimPrioritiser** should always run AFTER all other filters have completed. They will analyze +genes according to the specified **modeOfInheritance** above. If set to ``UNDEFINED`` no filtering will be done. +You can read more in the `Jannovar inheritance documentation `_ how exactly this filter works. + +.. code-block:: yaml + + inheritanceFilter: {} + + +.. _prioritisers: + +Prioritisers +............ + +These work on the gene-level and will produce the semantic-similarity scores for how well a gene matches the sample's HPO +profile. We recommend using a combination of the :ref:`OMIM` and :ref:`hiPHIVE` prioritisers **only**. These have been tested +on the UK's `100,000 genomes pilot project on rare disease diagnoses `_. +Using other prioritisers may miss diagnoses as the data could be out of date or the algorithm's effectiveness may have +been superseded. They are retained for historical interest. + +.. _omimprioritiser: + +omimPrioritiser: +................. +**inheritanceFilter** and **omimPrioritiser** should always run AFTER all other filters have completed. Other prioritisers: +Only combine **omimPrioritiser** with one of the next filters. The OMIM prioritiser adds known disease information from +OMIM to genes including the inheritance mode and then checks this inheritance mode with the compatible inheritance modes +of the gene. Genes with incompatible modes will have their scores halved. + +.. code-block:: yaml + + omimPrioritiser: {} + + +.. _hiphiveprioritiser: + +hiPhivePrioritiser: +................... +Scores genes using phenotype comparisons to human, mouse and fish involving disruption of the gene or nearby genes in the +interactome using a random walk. + +See the `hiPHIVE publication `_ for details. + + +.. code-block:: yaml + + # Using the default + hiPhivePrioritiser: {} + + +is the same as + +.. code-block:: yaml + + hiPhivePrioritiser: {runParams: 'human, mouse, fish, ppi'} + + +It is possible to only run comparisons agains a given organism/set of organisms ``human,mouse,fish`` and include/exclude +protein-protein interaction proximities ``ppi``. e.g. only using human and mouse data - + +.. code-block:: yaml + + hiPhivePrioritiser: {runParams: 'human,mouse'} + + +phenixPrioritiser: +.................. +Scores genes using phenotype comparisons to known human disease genes. See the `PhenIX publication `_ for details. + +.. code-block:: yaml + + phenixPrioritiser: {} + + +phivePrioritiser: +................. + +Scores genes using phenotype comparisons to mice with disruption of the gene. This is equivalent to running ``hiPhivePrioritiser: {runParams: 'mouse'}``. +See the `PHIVE publication `_ for details. + +.. code-block:: yaml + + phivePrioritiser: {} + + + +exomeWalkerPrioritiser: +....................... +Scores genes by proximity in interactome to the seed genes. Gene identifiers are required to be genbank identifiers. +See the `ExomeWalker publication `_ for details. + +.. code-block:: yaml + + exomeWalkerPrioritiser: {seedGeneIds: [11111, 22222, 33333]} + + +.. _outputoptions: + +Output options +~~~~~~~~~~~~~~ + +When specified as part of a command-line argument, the file should be a properly formed YAML object: + +.. code-block:: yaml + + # Exomiser outputOptions + --- + outputContributingVariantsOnly: true + numGenes: 20 + minExomiserGeneScore: 0.7 + outputPrefix: /analyses/sample-12345/sample-12345 + outputFormats: [HTML, JSON] + + +When included as part of an exomiser :ref:`job` the fields are inlined in the ``exomiser-job.yaml`` file like so: + +.. code-block:: yaml + + # other analysis and sample options above + outputOptions: + outputContributingVariantsOnly: true + numGenes: 20 + minExomiserGeneScore: 0.7 + outputPrefix: /analyses/sample-12345/sample-12345 + outputFormats: [HTML, JSON] + + +outputContributingVariantsOnly: +------------------------------- +Can be ``true`` or ``false``. Setting this to ``true`` will make the ``TSV_VARIANT`` and ``VCF`` output file only contain +**PASS** variants which contribute to the gene score. Defaults to ``true``. + +numGenes: +--------- +Maximum number of genes listed in the results. If set to ``0`` all are listed. In most cases a limit of ``50`` is more +than adequate as typically a good result will be found in the top 5. Not enabled by +default. + +minExomiserGeneScore +-------------------- +The mimimum gene (combined phenotype and variant) score required to be returned. As a rule of thumb scores >= 0.7 are a +good score however, depending on the proband phenotype and the phenotype of best matching condition although it is not a +hard-and-fast number. In our testing 0.7 gave the best performance in terms or recall and sensitivity. Not enabled by +default. + +outputPrefix: +------------- +Specify the path/filename without an extension and this will be added according to the +:ref:`outputFormats` option. If unspecified this will default to the following: +``{exomiserDir}/results/input-vcf-name-exomiser-results.html``. Alternatively, specify a fully qualified path +only. e.g. ``/home/jules/exomes/analysis``. + +.. _outputformats: + +outputFormats: +-------------- +Array to define the output formats. can be ``[TSV-GENE]``, ``[TSV-VARIANT]``, ``[VCF]``, ``JSON`` or ``HTML`` or any +combination like ``[TSV-GENE, TSV-VARIANT, VCF]``. JSON is the most informative output option and suitable for use in +downstream computational analyses or manually queried using something like `jq `_. The +HTML output is most suitable for manual inspection / human use. +Default is ``[JSON, HTML]``. diff --git a/docs/conf.py b/docs/conf.py index eaf4b0b8c..e7d648ed7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,4 +1,39 @@ # -*- coding: utf-8 -*- + +# The Exomiser - A tool to annotate and prioritize genomic variants +# +# Copyright (c) 2016-2022 Queen Mary University of London. +# Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + +# The Exomiser - A tool to annotate and prioritize genomic variants +# +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + # # Configuration file for the Sphinx documentation builder. # @@ -20,13 +55,13 @@ # -- Project information ----------------------------------------------------- project = u'exomiser' -copyright = u'2018, Jules Jacobsen, Damian Smedley, Peter Robinson' +copyright = u'2021, Jules Jacobsen, Damian Smedley, Peter Robinson' author = u'Jules Jacobsen, Damian Smedley, Peter Robinson' # The short X.Y version -version = u'' +version = u'13.1.0' # The full version, including alpha/beta/rc tags -release = u'10.0.0' +release = version # -- General configuration --------------------------------------------------- @@ -76,6 +111,7 @@ # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' +html_logo = '.static/exomiser-logo_white-banner.png' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -129,7 +165,7 @@ # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (master_doc, 'exomiser.tex', u'exomiser Documentation', + (master_doc, 'exomiser.tex', u'Exomiser Documentation', u'Jules Jacobsen, Damian Smedley, Peter Robinson', 'manual'), ] @@ -139,7 +175,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'exomiser', u'exomiser Documentation', + (master_doc, 'exomiser', u'Exomiser Documentation', [author], 1) ] diff --git a/docs/getting_started.rst b/docs/getting_started.rst deleted file mode 100644 index a1c5572b9..000000000 --- a/docs/getting_started.rst +++ /dev/null @@ -1,3 +0,0 @@ -=============== -Getting Started -=============== diff --git a/docs/images/exomiser-html-description-1.svg b/docs/images/exomiser-html-description-1.svg new file mode 100644 index 000000000..41fa207a6 --- /dev/null +++ b/docs/images/exomiser-html-description-1.svg @@ -0,0 +1,693 @@ + +image/svg+xml + List of candidate genes and variants sorted +by descending Exomiser score (0-1) +Human disease evidence including phenotype +similarity score, the matched disease +associated +with +FGFR2 +linked out to +OMIM/ +Orphanet +, and best disease phenotype +matches (right hand side), if any, to each of the +patient phenotypes (left hand side) +Mouse model evidence including phenotype +similarity score, link out to mouse model +associated with ortholog of +FGFR2 +, and best +mouse phenotypes to each of the patient +phenotypes +S +core representing the proximity of +FGFR2 +to +SALL4 +in the +StringDB +protein +- +protein +association network weighted by the disease +phenotype evidence for +SALL4 +Best +disease, +model +organism +and +protein +- +protein interaction evidence for +FGFR2 +’s +involvement in the patient’s phenotypes +Variant, +phenotype and combined +E +xomiser +scores (for the highest +scoring, compatible mode of inheritance if more than one) +S +core representing the proximity of +FGFR2 +to +SALL4 +in the +StringDB +protein +- +protein +association network weighted by the mouse +phenotype evidence for +SALL4 + \ No newline at end of file diff --git a/docs/images/exomiser-html-description-2.svg b/docs/images/exomiser-html-description-2.svg new file mode 100644 index 000000000..d9183b590 --- /dev/null +++ b/docs/images/exomiser-html-description-2.svg @@ -0,0 +1,539 @@ + + + +image/svg+xmlScores and variant evidence for each +compatible mode of inheritance based on the +genotypes of variants left after filtering and +family segregation +All disease matches and phenotypic similarity +scores for this mode of inheritance +Consequence, variant type, genomic position, +genotype and +rsID +for candidate variant +Automated ACMG classification +Clinvar +ACMG classification and evidence (if any) +Score for this variant based on consequence +and/o +r +predicted pathogenicity as well as minor +allele frequency. However, if present in a locally +configured whitelist of known pathogenic +variants, will be flagged and scored as 1 +regardless of this evidence. +Evidence for each variant contributing to this +gene’s candidacy, e.g., two will be displayed for +compound +heterozygous +candidate +s +HGVS transcript annotations +Predicted pathogenicity for missense variants +using configured sources, e.g., REVEL and MVP +Population +specific minor allele frequency data +from configures sources such as +GnomAD + \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 3ab5122ce..87b4cd40f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,28 +17,38 @@ The functional annotation of variants is handled by the Jannovar library and use Variants are prioritised according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, and model organism phenotype data. Predicted pathogenicity data is extracted from the dbNSFP resource. Variant frequency data is taken from the 1000 Genomes, ESP, TOPMed, UK10K, ExAC and gnomAD datasets. Subsets of these frequency and pathogenicity data can be defined to further tune the analysis. Cross-species phenotype comparisons come from our PhenoDigm tool powered by the OWLTools OWLSim algorithm. +.. toctree:: + :caption: Setup and Install + :name: setup + :maxdepth: 3 + :hidden: + + installation .. toctree:: :caption: Running the Exomiser - :name: running-it - :maxdepth: 2 + :name: run + :maxdepth: 3 :hidden: - installation - getting_started + running + input_files_and_options + advanced_analysis + sv_prioritisation .. toctree:: - :caption: Interpretation of Results - :name: whats-it-all-mean - :maxdepth: 2 + :caption: Interpreting Results + :name: results + :maxdepth: 3 :hidden: result_interpretation + acmg_assignment .. toctree:: :caption: Publications :name: publications - :maxdepth: 1 + :maxdepth: 3 :hidden: publications \ No newline at end of file diff --git a/docs/input_files_and_options.rst b/docs/input_files_and_options.rst new file mode 100644 index 000000000..ab8a66d07 --- /dev/null +++ b/docs/input_files_and_options.rst @@ -0,0 +1,190 @@ +.. _inputandoptions: + +======================= +Input Files and Options +======================= + +The Exomiser can be run via simply via a yaml analysis file. The extended cli capability was removed in version 10.0.0 +as this was less capable than the yaml scripts and only supported hg19 exome analysis. Version 13.0.0 introduced a more +flexible input using a `GA4GH Phenopacket `_ (v 1.0) for the sample data with +the ability to specify the input pedigree, VCF and genome assembly independently; user-specified, preset or default +analysis options and a new batch mode. + + +Sample, vcf, assembly, ped +========================== + +It is recommended to provide Exomiser with the input sample as a `Phenopacket `_. +Exomiser will accept this in either JSON or YAML format. The sample is provided using the ``sample`` switch and +the full path to the phenopacket file: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/phenopacket.json + + +Should the phenopacket either not specify a VCF file or specifies a file on another filesystem, the VCF file path can be +provided/overridden using the ``vcf`` switch: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/phenopacket.json --vcf path/to/genome.vcf + + +Exomiser will assume that the vcf file was called using the default assembly (GRCh37 / hg19) but this can be specified +using the ``assembly`` switch: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/phenopacket.json --vcf path/to/genome.vcf --assembly hg19 + + +or for hg38/ GRCh38: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/phenopacket.json --vcf path/to/genome.vcf --assembly hg38 + + +Lastly, when analysing a multi-sample VCF a pedigree is required. This can be provided using a dedicated PED file. This +uses the ``ped`` switch and a full path to the PED file: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/phenopacket.json --vcf path/to/genome.vcf --assembly hg38 --ped path/to/pedigree.ped + + +or the pedigree, proband and family members can be provided as a phenopacket `family `_ message +which can encode the pedigree. + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/family.json --vcf path/to/genome.vcf --assembly hg38 + + +Whatever the input used it is essential that the sample names used for the proband and other family members are consistent between the +pedigree and the sample identifiers used in the VCF file. Exomiser will exit with an error explaining that they do not match. +Examples of these can be found in the `examples` directory of the installation. + + +Preset +====== + +If no ``analysis`` is provided and no preset is specified, Exomiser will default to running the ``exome`` preset analysis. +If you want to run Genomiser, which will analyse non-coding regions of a WGS sample use ``--preset genome``: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample path/to/phenopacket.json --preset genome + + +In order to run a ``genome`` preset you need to first ensure that the REMM score data has been downloaded for the relevant +genome assembly and is enabled in the ``application.properties`` see the :ref:`remm` section. + + +Analysis +======== + +Analysis files contain all possible options for running an analysis including the ability to specify variant frequency +and pathogenicity data sources and the ability to tweak the order that analysis steps are performed. + +See the test-analysis-exome.yml and test-analysis-genome.yml files located in the base install directory for examples. +Details can be found in the :ref:`analysis` section. + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --analysis examples/test-analysis-exome.yml + +These files an also be used to run full-genomes, however they will require substantially more RAM to do so. For example +a 4.4 million variant analysis requires approximately 12GB RAM. However, RAM requirements can be greatly reduced by +setting the analysisMode option to PASS_ONLY. This will also aid your ability to evaluate the results. + +Analyses can be run in batch mode. Simply put the path to each analysis file in the batch file - one file path per line. + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --analysis-batch examples/test-analysis-batch.txt + + +Output +====== + +By default Exomiser will write out any result files to the exomiser-cli-|version|/results sub-directory of the +Exomiser installation directory. Unless specified in the `output.yml` or `outputOptions` section of the analysis YAML +file, Exomiser will write out a `.json` and a `.html` file. These are for machine (JSON) and human (HTML) use. The +filenames will match the input VCF filename. For example + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample examples/pfeiffer-phenopacket.yml --vcf path/to/manuel.vcf.gz + +Would result in two files being output with the filename 'manuel_exomiser' and the '.json' and '.html' extensions: + +.. parsed-literal:: + + exomiser-cli-|version|/results/manuel_exomiser.html + exomiser-cli-|version|/results/manuel_exomiser.json + + +Users requiring more control over their output can use either the ``outputOptions`` section of an analysis file or a +specific output options yaml file. An example of this can be found in the exomiser-cli-|version|/examples/output-options.yml +file: + +.. code-block:: yaml + + --- + outputContributingVariantsOnly: false + #numGenes options: 0 = all or specify a limit e.g. 500 for the first 500 results + numGenes: 10 + minExomiserGeneScore: 0.7 + #outputPrefix options: specify the path/filename without an extension and this will be added + # according to the outputFormats option. If unspecified this will default to the following: + # {exomiserDir}/results/input-vcf-name-exomiser-results.html + # alternatively, specify a fully qualifed path only. e.g. /users/jules/exomes/analysis + outputPrefix: /results/NA12345/NA12345 + #out-format options: HTML, JSON, TSV_GENE, TSV_VARIANT, VCF (default: HTML) + outputFormats: [HTML, JSON, TSV_GENE] + + +This file is passed to Exomiser using the ``--output`` switch: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --sample examples/pfeiffer-phenopacket.yml --vcf path/to/manuel.vcf.gz --output path/to/output-options.yml + + +Batch +===== + +The above commands can be added to a batch file for example in the file exomiser-cli-|version|/examples/test-analysis-batch-commands.txt + +.. parsed-literal:: + + #This is an example analysis batch file to be run using the --analysis-batch command + # + #Each line should specify the path of a single analysis file, either relative to the directory the exomiser + #is being run from or the full system path. It will run any combination of exomiser commands listed using -h or --help. + # + # Original format exomiser analysis containing all the sample and analysis information + --analysis test-analysis-exome.yml + # New preset exome analysis using a v1 phenopacket to submit the phenotype information and adding/overriding the VCF input + --preset exome --sample pfeiffer-phenopacket.yml --vcf Pfeiffer.vcf.gz + # Using the default analysis (exome) with a v1 phenopacket containing the phenotype information and adding/overriding the VCF input + --sample pfeiffer-phenopacket.yml --vcf Pfeiffer.vcf.gz + # Using a user-defined analysis with a v1 phenopacket containing the phenotype information and adding/overriding the VCF input + --analysis preset-exome-analysis.yml --sample pfeiffer-phenopacket.yml --vcf Pfeiffer.vcf.gz + # Using a user-defined analysis with a v1 phenopacket containing the phenotype information and adding/overriding the VCF input + --analysis preset-exome-analysis.yml --sample pfeiffer-phenopacket.yml --vcf Pfeiffer.vcf.gz --output output-options.yml + + +then run using the ``--batch`` command: + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --batch path/to/exomiser-cli-|version|/examples/test-analysis-batch-commands.txt + + +The advantage of this is that a single command will be able to analyse many samples in far less time than starting a new +JVM for each as there will be no start-up penalty after the initial start and the Java JIT compiler will be able to take +advantage of a longer-running process to optimise the runtime code. For maximum throughput on a cluster consider splitting +your batch jobs over multiple nodes. \ No newline at end of file diff --git a/docs/installation.rst b/docs/installation.rst index cd7112b99..e0bd589fa 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -2,14 +2,253 @@ Installation ============ +Software and Hardware requirements +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- Minimum 8/16GB RAM (For an exome analysis of a 30,000 variant sample 4GB RAM should suffice. For a genome analysis of a 4,400,000 variant sample 12GB RAM should suffice.) +- Any 64-bit operating system +- Java 11 or above +- At least 100GB free disk space (SSD preferred for best performance) +- An internet connection is not required to run the Exomiser, although network access will be required if accessing a networked database (optional). +- By default the Exomiser is completely self-contained and is able to run on standard consumer laptops. + Pre-built Binaries -================== +~~~~~~~~~~~~~~~~~~ .. note:: This is the recommended way of installing for normal users. -Pre-built binaries are available from `The Monarch Initiative `_. -Download exomiser-cli-\ |version| \-distribution.zip from `here `_. +Pre-built binaries are available from `The Monarch Initiative `_ or from the Exomiser repository on `GitHub `_. + +Exomiser requires 2-3 data files to be available as well - one for the phenotype data and one for each genome assembly required. + +Windows install +~~~~~~~~~~~~~~~ + +1. Install `7-Zip `_ for unzipping the archive files. The built-in archiving software has issues extracting the zip files. +2. Download the data and distribution files from https://data.monarchinitiative.org/exomiser/latest +3. Extract the distribution files by right-clicking exomiser-cli-|version|-distribution.zip and selecting 7-Zip > Extract Here +4. Extract the data files (e.g. 2109_phenotype.zip, 2109_hg19.zip) by right-clicking the archive and selecting 7-Zip > Extract files... into the exomiser data directory. By default exomiser expects this to be 'exomiser-cli-\ |version|\/data', but this can be changed in the ``application.properties`` +5. cd exomiser-cli-|version| +6. java -Xmx4g -jar exomiser-cli-|version|.jar --analysis examples/test-analysis-exome.yml + +Linux install +~~~~~~~~~~~~~ + +The following shell script should work- + +.. parsed-literal:: + + # download the distribution (won't take long) + wget https://data.monarchinitiative.org/exomiser/latest/exomiser-cli-\ |version|\-distribution.zip + # download the data (this is ~80GB and will take a while). If you only require a single assembly, only download the relevant file. + wget https://data.monarchinitiative.org/exomiser/latest/2202_hg19.zip + wget https://data.monarchinitiative.org/exomiser/latest/2202_hg38.zip + wget https://data.monarchinitiative.org/exomiser/latest/2202_phenotype.zip + + # unzip the distribution and data files - this will create a directory called 'exomiser-cli-|version|' in the current working directory + unzip exomiser-cli-|version|-distribution.zip + unzip 2202_*.zip -d exomiser-cli-|version|/data + + # Check the application.properties are pointing to the correct versions + # exomiser.hg19.data-version=2202 + # exomiser.hg38.data-version=2202 + # exomiser.phenotype.data-version=2202 + + # run a test exome analysis + cd exomiser-cli-|version| + java -Xmx4g -jar exomiser-cli-|version|.jar --analysis examples/test-analysis-exome.yml + + +This script will download, verify and extract the exomiser files and then run the analysis contained in the file 'test-analysis-exome.yml' from the examples sub-directory. This contains a known pathogenic missense variant in the FGFR2 gene. + +.. _remm: + +Genomiser / REMM data +~~~~~~~~~~~~~~~~~~~~~ + +In order to run the Genomiser you will also need to download the REMM data file +from [here](https://zenodo.org/record/4768448). Once downloaded you'll need to add the path to the ReMM.v0.3.1.tsv.gz +file to the ``application.properties`` file. For example if you downloaded the file to the exomiser data directory you +could add the entry like this: + +.. parsed-literal:: + + exomiser.hg19.remm-path=${exomiser.hg19.data-directory}/ReMM.v0.3.1.tsv.gz + +If this step is omitted, the application will throw and error and stop any analysis which defines ``REMM`` in the ``pathogenicitySources`` section of an analysis yml file. + +Having done this, run the analysis like this: + +.. parsed-literal:: + + java -Xmx6g -jar exomiser-cli-|version|.jar --analysis examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml + +This is an analysis for an autosomal recessive 5'UTR variant located in POMP gene on chromosome 13. The phenotype HPO terms are taken from the clinical synopsis of +OMIM #601952 (http://www.omim.org/clinicalSynopsis/601952) + +.. _cadd-install: + +CADD data +~~~~~~~~~ +In order to use CADD you will need to download the CADD data files separately. These can be accessed from https://cadd.gs.washington.edu/download. Exomiser only +requires the file with the score in, not the full annotations. For example, in release v1.4 Exomiser requires both the files `All possible SNVs of GRCh38/hg38` +and `80M InDels to initiate a local setup`. Each genome assembly will require the relevant files. The direct links from the US site are shown below and are correct at the time +of writing. + +.. parsed-literal:: + + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh38/whole_genome_SNVs.tsv.gz + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh38/whole_genome_SNVs.tsv.gz.tbi + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh38/InDels.tsv.gz + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh38/InDels.tsv.gz.tbi + + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/whole_genome_SNVs.tsv.gz + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/whole_genome_SNVs.tsv.gz.tbi + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/InDels.tsv.gz + wget https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/InDels.tsv.gz.tbi + +Enable Exomiser to use CADD by altering the ``application.properties`` file to enable these lines and ensure the +``cadd.version`` property matches the version you downloaded. + +.. parsed-literal:: + + cadd.version=1.4 + + exomiser.hg19.cadd-snv-path=${exomiser.data-directory}/cadd/${cadd.version}/hg19/whole_genome_SNVs.tsv.gz + exomiser.hg19.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/hg19/InDels.tsv.gz + + # and/or for hg38 + exomiser.hg38.cadd-snv-path=${exomiser.data-directory}/cadd/${cadd.version}/whole_genome_SNVs.tsv.gz + exomiser.hg38.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/InDels.tsv.gz + + +Exomiser will expect the tabix index ``.tbi`` file to be present in the same directory as the ``.tsv.gz`` files. To use +CADD scores in an analysis, the ``pathogenicitySources`` should contain the ``CADD`` property + +.. code-block:: yaml + + #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM + #REMM is trained on non-coding regulatory regions + #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + #and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT, CADD] + + +Configuring the application.properties +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Once you have downloaded and unzipped all the data, you will need to edit the exomiser-cli-\ |version|\/application.properties +file located in the main exomiser-cli directory. This file contains a lot of comments for optional data and assemblies. + +If you want to run Exomiser using data from a different release directory edit the line in ``application.properties``: + +.. parsed-literal:: + + exomiser.data-directory= + +with + +.. parsed-literal:: + + exomiser.data-directory=/full/path/to/alternative/data/directory + +For example, assuming you unzipped the contents of the `2202_hg38.zip` data file into `/data/exomiser-data`: + +.. parsed-literal:: + + exomiser.data-directory=/data/exomiser-data + +where the contents of `exomiser-data` looks something like this: + +.. code-block:: bash + + $ tree -L 1 /data/exomiser-data/ + /data/exomiser-data/ + ├── 2202_hg19 + ├── 2202_hg38 + ├── 2202_phenotype + ├── cadd + └── remm + + +By default Exomiser will look for data located in the exomiser-cli-\ |version|\/data directory. + +After defining the a `exomiser.data-directory`, a minimal setup for exome analysis using GRCh37/hg19 would only require +the ``application.properties`` to contain this: + +.. code-block:: yaml + + ### hg19 assembly ### + exomiser.hg19.data-version=2109 + exomiser.hg19.variant-white-list-path=2109_hg19_clinvar_whitelist.tsv.gz + + ### phenotypes ### + exomiser.phenotype.data-version=2109 + + +For a GRCh38/hg38 only setup: + +.. code-block:: yaml + + ### hg38 assembly ### + exomiser.hg38.data-version=2109 + exomiser.hg38.variant-white-list-path=2109_hg38_clinvar_whitelist.tsv.gz + + ### phenotypes ### + exomiser.phenotype.data-version=2109 + + +Or an install supporting both assemblies: + +.. code-block:: yaml + + ### hg19 assembly ### + exomiser.hg19.data-version=2109 + exomiser.hg19.variant-white-list-path=2109_hg19_clinvar_whitelist.tsv.gz + + ### hg38 assembly ### + exomiser.hg38.data-version=2109 + exomiser.hg38.variant-white-list-path=2109_hg38_clinvar_whitelist.tsv.gz + + ### phenotypes ### + exomiser.phenotype.data-version=2109 + + +*n.b.* each assembly will require approximately 1GB RAM to load. Attempting to analyse a VCF called using an +unsupported/unloaded assembly data will result in an unrecoverable error being thrown. + +Notice here that we are loading a whitelist created from ClinVar data. Exomiser will consider any variant on the whitelist +to be maximally pathogenic, regardless of the underlying data (*e.g.* variant effect, allele frequency, predicted pathogenicity) +and always included these in the results. + + +Troubleshooting +~~~~~~~~~~~~~~~ + + +Zip file reported as too big or corrupted +----------------------------------------- +If, when running 'unzip exomiser-cli-|version|-distribution.zip', you see the following: + +.. parsed-literal:: + + error: Zip file too big (greater than 4294959102 bytes) + Archive: exomiser-cli-|version|-distribution.zip + warning [exomiser-cli-|version|-distribution.zip]: 9940454202 extra bytes at beginning or within zipfile + (attempting to process anyway) + error [exomiser-cli-|version|-distribution.zip]: start of central directory not found; + zipfile corrupt. + (please check that you have transferred or created the zipfile in the + appropriate BINARY mode and that you have compiled UnZip properly) + + +Check that your unzip version was compiled with LARGE_FILE_SUPPORT and ZIP64_SUPPORT. This is standard with UnZip 6.00 and can be checked by typing: + +.. parsed-literal:: + + unzip -version +This shouldn't be an issue with more recent linux distributions. \ No newline at end of file diff --git a/docs/publications.rst b/docs/publications.rst index 1532187ae..d68759a7c 100644 --- a/docs/publications.rst +++ b/docs/publications.rst @@ -2,41 +2,60 @@ Publications ============ +| **100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report** +| 100,000 Genomes Project Pilot Investigators; Smedley D, ... Caulfield M. +| *N Engl J Med. 2021 Nov 11;385(20):1868-1880* +| PMID:34758253 DOI:`10.1056/NEJMoa2035790 `_ + + +| **An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data.** +| Cipriani V, Pontikos N, Arno G, Sergouniotis PI, Lenassi E, Thawong P, Danis D, Michaelides M, Webster AR, Moore AT, Robinson PN, Jacobsen JOB, Smedley D. +| *Genes (Basel). 2020 Apr 23;11(4):460* +| PMID:32340307 DOI:`10.3390/genes11040460 `_ + + | **A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.** | Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN. | *The American Journal of Human Genetics 2016;99;3;595-606* | PMID:27569544 DOI:`10.1016/j.ajhg.2016.07.005 `_ + | **Phenotype-driven strategies for exome prioritization of human Mendelian disease genes.** | Smedley D, Robinson PN. | *Genome Medicine 2015, 7(1):81* | PMID:26229552 DOI:`10.1186/s13073-015-0199-2 `_ + | **Next-generation diagnostics and disease-gene discovery with the Exomiser.** | Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M et al. | *Nature protocols 2015;10;12;2004-15* | PMID:26562621 DOI:`10.1038/nprot.2015.124 `_ + | **Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.** | Bone WP, Washington NL, Buske OJ, Adams DR, Davis J et al. | *Genetics in medicine : official journal of the American College of Medical Genetics 2015* | PMID:26562225 DOI:`10.1038/gim.2015.137 `_ + | **Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases.** | Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C et al. | *Bioinformatics (Oxford, England) 2014;30;22;3215-22* | PMID:25078397 DOI:`10.1093/bioinformatics/btu508 `_ + | **Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.** | Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J et al. | *Science translational medicine 2014;6;252;252ra123* | PMID:25186178 DOI:`10.1126/scitranslmed.3009262 `_ + | **Improved exome prioritization of disease genes through cross-species phenotype comparison.** | Robinson PN, Köhler S, Oellrich A, Sanger Mouse Genetics Project, Wang K et al. | *Genome research 2014;24;2;340-8* | PMID:24162188 DOI:`10.1101/gr.160325.113 `_ + Collaborations ============== @@ -47,11 +66,13 @@ Publications for other projects and resources in which the Exomiser is used as a | *Front Med (Lausanne). 2017;4 62* | PMID: 28603714 DOI:`10.3389/fmed.2017.00062 `_ + | **PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases.** | Orion J. Buske, Marta Girdea, Sergiu Dumitriu, Bailey Gallinger, Taila Hartley, Heather Trang, Andriy Misyura, Tal Friedman, Chandree Beaulieu, William P. Bone, Amanda E. Links, Nicole L. Washington, Melissa A. Haendel, Peter N. Robinson, Cornelius F. Boerkoel, David Adams, William A. Gahl, Kym M. Boycott, Michael Brudno. | *Human Mutation 2015, 36(10):931-940* | PMID: 26251998 DOI:`10.1002/humu.22851 `_ + | **Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data.** | Nikolas Pontikos, Jing Yu, Ismail Moghul, Lucy Withington, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun, Ernest Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene, Julius OB Jacobsen, Tristan Clark, David S. Gregory, Andrea M. Nemeth, Stephanie Halford, Chris F. Inglehearn, Susan Downes, Graeme C. Black, Andrew R. Webster, Alison J. Hardcastle, UKIRDC, Vincent Plagnol. | *Bioinformatics 2017,33(15):2421-2423* diff --git a/docs/result_interpretation.rst b/docs/result_interpretation.rst index b0f35b807..0843db304 100644 --- a/docs/result_interpretation.rst +++ b/docs/result_interpretation.rst @@ -1,3 +1,117 @@ +.. _result_interpretation: + ======================== Interpreting the Results ======================== + +Depending on the output options provided, Exomiser will write out at least an HTML results file in the `results` +sub-directory of the Exomiser installation. + +As a general rule all output files contain a ranked list of genes and/or variants with the top-ranked gene/variant +displayed first. The exception being the VCF output which, since version 13.1.0, is sorted according to VCF convention +and tabix indexed. + +Exomiser attempts to predict the variant or variants likely to be causative of a patient's phenotype and does so by +associating them with the gene (or genes in the case of large structural variations) they intersect with on the genomic +sequence. Variants occurring in intergenic regions are associated to the closest gene and those overlapping two genes +are associated with the gene in which they are predicted to have the largest consequence. + +Once associated with a gene, Exomiser uses the compatible modes of inheritance for a variant to assess it in the context +of any diseases associated with the gene or any mouse knockout models of that gene. These are all bundled together into +a `GeneScore` which features filtered variants located in that gene compatible with a given mode of inheritance. After +the filtering steps Exomiser ranks these GeneScores according to descending combined score. The results are then written +out to the files and formats specified in the output settings. + +Prior to 13.1.0 a TSV/VCF file for each mode of inheritance (MOI) was created, which led to misunderstandings and confusion +about how to deal with the data from them. The filenames were of the general pattern `output-prefix_MOI.genes.tsv` e.g. +`Pfeiffer-hiphive-exome-PASS_ONLY_AD.genes.tsv`, `Pfeiffer-hiphive-exome-PASS_ONLY_AR.genes.tsv`, `Pfeiffer-hiphive-exome-PASS_ONLY_AR.vcf`, +`Pfeiffer-hiphive-exome-PASS_ONLY_AR.variants.tsv`... **THESE FILES ARE NOW DEPRECATED AND WILL NOT APPEAR IN THE NEXT +VERSION**. Similarly the `variants.tsv` and `vcf` output formats have also been changed and will only feature a single, combined +output file of ranked genes/variants e.g. when supplying the `outputPrefix: Pfeiffer-hiphive-exome-PASS_ONLY` and +`outputFormats: [TSV_VARIANT, TSV_GENE, VCF]`, the following files will be written out: `Pfeiffer-hiphive-exome-PASS_ONLY.variants.tsv` +`Pfeiffer-hiphive-exome-PASS_ONLY.genes.tsv`, `Pfeiffer-hiphive-exome-PASS_ONLY.vcf` + +These formats are detailed below. + +HTML +==== + +.. figure:: images/exomiser-html-description-1.svg + +.. figure:: images/exomiser-html-description-2.svg + +JSON +==== + +The JSON file represents the most accurate representation of the data, as it is referenced internally by Exomiser. As +such, we don't provide a schema for this, but it has been pretty stable and breaking changes will only occur with major +version changes to the software. Minor additions are to be expected for minor releases, as per the `SemVer `_ +specification. + +We recommend using `Python `_ or +`JQ `_ to extract data from this file. + +TSV GENES +========= + +In the genes.tsv file it is possible for a gene to appear multiple times, depending on the MOI it is compatible with, +given the filtered variants. For example in the example below MUC6 is ranked 7th under the AD model and 8th under an AR +model. + +.. code-block:: tsv + + #RANK ID GENE_SYMBOL ENTREZ_GENE_ID MOI P-VALUE EXOMISER_GENE_COMBINED_SCORE EXOMISER_GENE_PHENO_SCORE EXOMISER_GENE_VARIANT_SCORE HUMAN_PHENO_SCORE MOUSE_PHENO_SCORE FISH_PHENO_SCORE WALKER_SCORE PHIVE_ALL_SPECIES_SCORE OMIM_SCORE MATCHES_CANDIDATE_GENE HUMAN_PHENO_EVIDENCE MOUSE_PHENO_EVIDENCE FISH_PHENO_EVIDENCE HUMAN_PPI_EVIDENCE MOUSE_PPI_EVIDENCE FISH_PPI_EVIDENCE + 1 FGFR2_AD FGFR2 2263 AD 0.0000 0.9981 1.0000 1.0000 0.8808 1.0000 0.0000 0.5095 1.0000 1.0000 0 Jackson-Weiss syndrome (OMIM:123150): Brachydactyly (HP:0001156)-Broad hallux (HP:0010055), Craniosynostosis (HP:0001363)-Craniosynostosis (HP:0001363), Broad thumb (HP:0011304)-Broad metatarsal (HP:0001783), Broad hallux (HP:0010055)-Broad hallux (HP:0010055), Brachydactyly (HP:0001156)-abnormal sternum morphology (MP:0000157), Craniosynostosis (HP:0001363)-premature cranial suture closure (MP:0000081), Broad thumb (HP:0011304)-abnormal sternum morphology (MP:0000157), Broad hallux (HP:0010055)-abnormal sternum morphology (MP:0000157), Proximity to FGF14 associated with Spinocerebellar ataxia 27 (OMIM:609307): Broad hallux (HP:0010055)-Pes cavus (HP:0001761), Proximity to FGF14 Brachydactyly (HP:0001156)-abnormal digit morphology (MP:0002110), Broad thumb (HP:0011304)-abnormal digit morphology (MP:0002110), Broad hallux (HP:0010055)-abnormal digit morphology (MP:0002110), + 2 ENPP1_AD ENPP1 5167 AD 0.0049 0.8690 0.5773 0.9996 0.6972 0.5773 0.5237 0.5066 0.6972 1.0000 0 Autosomal recessive hypophosphatemic rickets (ORPHA:289176): Brachydactyly (HP:0001156)-Genu varum (HP:0002970), Craniosynostosis (HP:0001363)-Craniosynostosis (HP:0001363), Broad thumb (HP:0011304)-Tibial bowing (HP:0002982), Broad hallux (HP:0010055)-Genu varum (HP:0002970), Brachydactyly (HP:0001156)-fused carpal bones (MP:0008915), Craniosynostosis (HP:0001363)-abnormal nucleus pulposus morphology (MP:0006392), Broad thumb (HP:0011304)-fused carpal bones (MP:0008915), Broad hallux (HP:0010055)-fused carpal bones (MP:0008915), Craniosynostosis (HP:0001363)-ceratohyal cartilage premature perichondral ossification, abnormal (ZP:0012007), Broad thumb (HP:0011304)-cleithrum nodular, abnormal (ZP:0006782), Proximity to PAPSS2 associated with Brachyolmia 4 with mild epiphyseal and metaphyseal changes (OMIM:612847): Brachydactyly (HP:0001156)-Brachydactyly (HP:0001156), Broad thumb (HP:0011304)-Brachydactyly (HP:0001156), Broad hallux (HP:0010055)-Brachydactyly (HP:0001156), Proximity to PAPSS2 Brachydactyly (HP:0001156)-abnormal long bone epiphyseal plate morphology (MP:0003055), Craniosynostosis (HP:0001363)-domed cranium (MP:0000440), Broad thumb (HP:0011304)-abnormal long bone epiphyseal plate morphology (MP:0003055), Broad hallux (HP:0010055)-abnormal long bone epiphyseal plate morphology (MP:0003055), + // + 7 MUC6_AD MUC6 4588 AD 0.0096 0.7532 0.5030 0.9990 0.0000 0.0000 0.0000 0.5030 0.5030 1.0000 0 Proximity to GKN2 Brachydactyly (HP:0001156)-brachydactyly (MP:0002544), Broad thumb (HP:0011304)-brachydactyly (MP:0002544), Broad hallux (HP:0010055)-brachydactyly (MP:0002544), + 8 MUC6_AR MUC6 4588 AR 0.0096 0.7531 0.5030 0.9990 0.0000 0.0000 0.0000 0.5030 0.5030 1.0000 0 Proximity to GKN2 Brachydactyly (HP:0001156)-brachydactyly (MP:0002544), Broad thumb (HP:0011304)-brachydactyly (MP:0002544), Broad hallux (HP:0010055)-brachydactyly (MP:0002544), + + +TSV VARIANTS +============ + +In the variants.tsv file it is possible for a variant, like a gene, to appear multiple times, depending on the MOI it is +compatible with. For example in the example below MUC6 has two variants ranked 7th under the AD model and two ranked 8th +under an AR (compound heterozygous) model. In the AD case the CONTRIBUTING_VARIANT column indicates whether the variant +was (1) or wasn't (0) used for calculating the EXOMISER_GENE_COMBINED_SCORE and EXOMISER_GENE_VARIANT_SCORE. + +.. code-block:: tsv + + #RANK ID GENE_SYMBOL ENTREZ_GENE_ID MOI P-VALUE EXOMISER_GENE_COMBINED_SCORE EXOMISER_GENE_PHENO_SCORE EXOMISER_GENE_VARIANT_SCORE EXOMISER_VARIANT_SCORE CONTRIBUTING_VARIANT WHITELIST_VARIANT VCF_ID RS_ID CONTIG START END REF ALT CHANGE_LENGTH QUAL FILTER GENOTYPE FUNCTIONAL_CLASS HGVS EXOMISER_ACMG_CLASSIFICATION EXOMISER_ACMG_EVIDENCE EXOMISER_ACMG_DISEASE_ID EXOMISER_ACMG_DISEASE_NAME CLINVAR_ALLELE_ID CLINVAR_PRIMARY_INTERPRETATION CLINVAR_STAR_RATING GENE_CONSTRAINT_LOEUF GENE_CONSTRAINT_LOEUF_LOWER GENE_CONSTRAINT_LOEUF_UPPER MAX_FREQ_SOURCE MAX_FREQ ALL_FREQ MAX_PATH_SOURCE MAX_PATH ALL_PATH + 1 10-123256215-T-G_AD FGFR2 2263 AD 0.0000 0.9981 1.0000 1.0000 1.0000 1 1 rs121918506 10 123256215 123256215 T G 0 100.0000 PASS 1|0 missense_variant FGFR2:ENST00000346997.2:c.1688A>C:p.(Glu563Ala) LIKELY_PATHOGENIC PM2,PP3_Strong,PP4,PP5 OMIM:123150 Jackson-Weiss syndrome 28333 LIKELY_PATHOGENIC 1 0.13692 0.074 0.27 REVEL 0.965 REVEL=0.965,MVP=0.9517972 + 2 6-132203615-G-A_AD ENPP1 5167 AD 0.0049 0.8690 0.5773 0.9996 0.9996 1 0 rs770775549 6 132203615 132203615 G A 0 922.9800 PASS 0/1 splice_donor_variant ENPP1:ENST00000360971.2:c.2230+1G>A:p.? UNCERTAIN_SIGNIFICANCE PVS1_Strong OMIM:615522 Cole disease NOT_PROVIDED 0 0.41042 0.292 0.586 GNOMAD_E_SAS 0.0032486517 TOPMED=7.556E-4,EXAC_NON_FINNISH_EUROPEAN=0.0014985314,GNOMAD_E_NFE=0.0017907989,GNOMAD_E_SAS=0.0032486517 + // + 7 11-1018088-TG-T_AD MUC6 4588 AD 0.0096 0.7532 0.5030 0.9990 0.9990 1 0 rs765231061 11 1018088 1018089 TG T -1 441.8100 PASS 0/1 frameshift_variant MUC6:ENST00000421673.2:c.4712del:p.(Pro1571Hisfs*21) UNCERTAIN_SIGNIFICANCE NOT_PROVIDED 0 0.79622 0.656 0.971 GNOMAD_G_NFE 0.0070363074 GNOMAD_E_AMR=0.0030803352,GNOMAD_G_NFE=0.0070363074 + 7 11-1018093-G-GT_AD MUC6 4588 AD 0.0096 0.7532 0.5030 0.9990 0.9989 0 0 rs376177791 11 1018093 1018093 G GT 1 592.4500 PASS 0/1 frameshift_elongation MUC6:ENST00000421673.2:c.4707dup:p.(Pro1570Thrfs*136) NOT_AVAILABLE NOT_PROVIDED 0 0.79622 0.656 0.971 GNOMAD_G_NFE 0.007835763 GNOMAD_G_NFE=0.007835763 + 8 11-1018088-TG-T_AR MUC6 4588 AR 0.0096 0.7531 0.5030 0.9990 0.9990 1 0 rs765231061 11 1018088 1018089 TG T -1 441.8100 PASS 0/1 frameshift_variant MUC6:ENST00000421673.2:c.4712del:p.(Pro1571Hisfs*21) UNCERTAIN_SIGNIFICANCE NOT_PROVIDED 0 0.79622 0.656 0.971 GNOMAD_G_NFE 0.0070363074 GNOMAD_E_AMR=0.0030803352,GNOMAD_G_NFE=0.0070363074 + 8 11-1018093-G-GT_AR MUC6 4588 AR 0.0096 0.7531 0.5030 0.9990 0.9989 1 0 rs376177791 11 1018093 1018093 G GT 1 592.4500 PASS 0/1 frameshift_elongation MUC6:ENST00000421673.2:c.4707dup:p.(Pro1570Thrfs*136) UNCERTAIN_SIGNIFICANCE NOT_PROVIDED 0 0.79622 0.656 0.971 GNOMAD_G_NFE 0.007835763 GNOMAD_G_NFE=0.007835763 + + +VCF +=== + +In the VCF file it is possible for a variant, like a gene, to appear multiple times, depending on the MOI it is +compatible with. For example in the example below MUC6 has two variants ranked 7th under the AD model and two ranked 8th +under an AR (compound heterozygous) model. In the AD case the CONTRIBUTING_VARIANT column indicates whether the variant +was (1) or wasn't (0) used for calculating the EXOMISER_GENE_COMBINED_SCORE and EXOMISER_GENE_VARIANT_SCORE. The ``INFO`` +field with the ``ID=Exomiser`` describes the internal format of this sub-field. Be aware that for multi-allelic sites, +Exomiser will decompose and trim them for the proband sample and this is what will be displayed in the Exomiser ``ID`` +sub-field e.g. ``11-1018088-TG-T_AD``. + +.. code-block:: vcf + + ##INFO= + #CHROM POS ID REF ALT QUAL FILTER INFO sample + 10 123256215 . T G 100 PASS Exomiser={1|10-123256215-T-G_AD|FGFR2|2263|AD|0.0000|0.9981|1.0000|1.0000|1.0000|1|1|missense_variant|FGFR2:ENST00000346997.2:c.1688A>C:p.(Glu563Ala)|LIKELY_PATHOGENIC|PM2,PP3_Strong,PP4,PP5|OMIM:123150|"Jackson-Weiss syndrome"};GENE=FGFR2;INHERITANCE=AD;MIM=101600 GT:DS:PL 1|0:2.000:50,11,0 + 11 1018088 . TG T 441.81 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=7.677;DP=162;DS;Exomiser={7|11-1018088-TG-T_AD|MUC6|4588|AD|0.0096|0.7532|0.5030|0.9990|0.9990|1|0|frameshift_variant|MUC6:ENST00000421673.2:c.4712del:p.(Pro1571Hisfs*21)|UNCERTAIN_SIGNIFICANCE|||""},{8|11-1018088-TG-T_AR|MUC6|4588|AR|0.0096|0.7531|0.5030|0.9990|0.9990|1|0|frameshift_variant|MUC6:ENST00000421673.2:c.4712del:p.(Pro1571Hisfs*21)|UNCERTAIN_SIGNIFICANCE|||""};FS=25.935;HRun=3;HaplotypeScore=1327.2952;MQ=43.58;MQ0=6;MQRankSum=-5.112;QD=2.31;ReadPosRankSum=2.472;set=variant GT:AD:DP:GQ:PL 0/1:146,45:162:99:481,0,5488 + 11 1018093 . G GT 592.45 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=8.019;DP=157;Exomiser={7|11-1018093-G-GT_AD|MUC6|4588|AD|0.0096|0.7532|0.5030|0.9990|0.9989|0|0|frameshift_elongation|MUC6:ENST00000421673.2:c.4707dup:p.(Pro1570Thrfs*136)|NOT_AVAILABLE|||""},{8|11-1018093-G-GT_AR|MUC6|4588|AR|0.0096|0.7531|0.5030|0.9990|0.9989|1|0|frameshift_elongation|MUC6:ENST00000421673.2:c.4707dup:p.(Pro1570Thrfs*136)|UNCERTAIN_SIGNIFICANCE|||""};FS=28.574;HRun=1;HaplotypeScore=1267.6968;MQ=44.06;MQ0=4;MQRankSum=-5.166;QD=3.26;ReadPosRankSum=1.328;set=variant GT:AD:DP:GQ:PL 0/1:140,42:157:99:631,0,4411 + 6 132203615 . G A 922.98 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-0.671;DP=94;Dels=0.00;Exomiser={2|6-132203615-G-A_AD|ENPP1|5167|AD|0.0049|0.8690|0.5773|0.9996|0.9996|1|0|splice_donor_variant|ENPP1:ENST00000360971.2:c.2230+1G>A:p.?|UNCERTAIN_SIGNIFICANCE|PVS1_Strong|OMIM:615522|"Cole disease"};FS=0.805;HRun=0;HaplotypeScore=3.5646;MQ=56.63;MQ0=0;MQRankSum=1.807;QD=9.82;ReadPosRankSum=-0.900;set=variant2 GT:AD:DP:GQ:PL 0/1:53,41:94:99:953,0,1075 + + +The VCF file is tabix-indexed and exomiser ranked alleles can be extracted using ``grep``. For example, to display the +top 5 ranked variants, you would issue the command: + +.. code-block:: shell + + zgrep -E '\{[1-5]{1}\|' Pfeiffer-hiphive-exome-PASS_ONLY.vcf.gz \ No newline at end of file diff --git a/docs/running.rst b/docs/running.rst new file mode 100644 index 000000000..67e4ac719 --- /dev/null +++ b/docs/running.rst @@ -0,0 +1,108 @@ +================ +Running Exomiser +================ + +Usage +===== + +In general we recommend running Exomiser from the install directory. A single sample exome analysis can be run using the +following command: + +.. parsed-literal:: + + # run a test exome analysis + cd exomiser-cli-|version| + java -jar exomiser-cli-|version|.jar --sample examples/pfeiffer-phenopacket.yml --vcf examples/Pfeiffer.vcf.gz --assembly hg19 + + +This command prioritises variants from the input `VCF `_ file, called +against the `GRCh37/hg19 reference assembly `_ in the context +of the sample phenotypes encoded using `Human Phenotype Ontology `_ terms contained in the +`Phenopacket `_ file. + +Running a multi-sample VCF for trios also requires a `PED `_ file. e.g. + +.. parsed-literal:: + + # run a test exome family analysis + cd exomiser-cli-|version| + java -jar exomiser-cli-|version|.jar --sample examples/pfeiffer-family.yml --vcf examples/Pfeiffer-quartet.vcf.gz --assembly hg19 --ped examples/Pfeiffer-quartet.ped + + +By default there will be two output files written to the ``results`` directory using the same filename as the input VCF file but +with ``_exomiser`` appended before a file extension of ``.json`` or ``.html`` e.g. + +.. parsed-literal:: + + ls results/Pfeiffer* + results/Pfeiffer_exomiser.html results/Pfeiffer_exomiser.json + +The HTML file is for human use, whilst the JSON file is better read by machines, for instance by using `jq `_. +Details on how to interpret the output can be found in the :ref:`result_interpretation` section. + +The ``examples`` directory contains a selection of single sample exome and genome analysis files, a multisample (family) +analysis with an associated pedigree in `PED `_ +format, and the respective `Phenopacket `_ representations of the proband or +family. + +Want help? +========== + +.. parsed-literal:: + + java -jar exomiser-cli-|version|.jar --help + + +Running from alternate directory +================================ + +If you're running the exomiser from a different directory to the one the exomiser-cli-|version|.jar file is located, +you will need to specify the path to the ``application.properties`` file in the start-up command. For example: + +.. parsed-literal:: + + java -Xmx4g -jar /full/path/to/your/exomiser-cli/directory/exomiser-cli-|version|.jar --analysis /full/path/to/your/exomiser-cli/directory/examples/test-analysis-exome.yml --spring.config.location=/full/path/to/your/exomiser-cli/directory/application.properties + + +*n.b.* the ``spring.config.location`` command **must be the last argument in the input commands!** + + +Troubleshooting +=============== + +java.lang.UnsupportedClassVersionError: +--------------------------------------- +If you get the following error message: + +.. code-block:: console + + Exception in thread "main" java.lang.UnsupportedClassVersionError: + org/monarchinitiative/exomiser/cli/Main : Unsupported major.minor version + + +or + +.. code-block:: console + + Error: A JNI error has occurred, please check your installation and try again + Exception in thread "main" java.lang.UnsupportedClassVersionError: org/monarchinitiative/exomiser/cli/Main has been + compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime + only recognizes class file versions up to 52.0 + + +You are running an older unsupported version of Java. Exomiser requires java version 11 or higher. This can be checked by running: + +.. code-block:: console + + $ java -version + +You should see something like this in response: + +.. code-block:: console + + openjdk version "11.0.11" 2021-04-20 + OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04) + OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing) + + +Versions lower than 11 (e.g. 1.5, 1.6, 1.7, 1.8, 9, 10) will not run exomiser, so you will need to install the latest java version. diff --git a/docs/sv_prioritisation.rst b/docs/sv_prioritisation.rst new file mode 100644 index 000000000..b8e91610b --- /dev/null +++ b/docs/sv_prioritisation.rst @@ -0,0 +1,57 @@ +.. _sv_prioritisation: + +================================= +Structural Variant Prioritisation +================================= + +Exomiser v13.0.0 is capable of jointly prioritising structural and sequence variants from a combined VCF file. For the +purposes of the analysis a structural variant is defined as a variant >= 50 nucleotides in length or a symbolic variant +(e.g. a variant with a VCF ALT allele of the form ```` instead of an actual sequence). There are many, many callers +to choose from so performance will depend heavily on these as well as the underlying sequencing technology (e.g. Illumina +short-read vs PacBio or Oxford Nanopore long-read sequencing). Exomiser has been tested on `Manta +`_ and `Canvas `_ calls from Illumina short-reads +produced for the 100K genomes project, with some compatibility testing against `PacBio pbsv `_. + +Prioritisation Overview +======================= + +Assuming the recommended analysis steps are being used, Exomiser will broadly consider structural variants in a similar +manner to sequence variants, with the major difference being that the precise size, position and sequence change is not +known, especially for symbolic variants. Briefly, Exomiser performs these steps on each SV: + +- Predict variant effects based on overlapping transcripts +- Assign variant to all genes for which it overlaps a transcript +- Assign variant pathogenicity score according to variant effect and known similar ClinVar variants +- Assign variant frequency score according to similar alleles in gnomAD-SV, DECIPHER, dbVar, DGV, GoNL + +Following these SV-specific steps, the variant is considered in the same way as a sequence variant and is filtered and +prioritised accordingly. This allows compound heterozygous genotypes of structural and sequence variants to be considered +during an analysis. + +Multiple Gene Overlaps +====================== + +If a variant overlaps more than one gene, the variant will be associated with all of these genes and reported with the +most severe variant effect it is predicted to have on each gene in the results. + +For example, if a variant 1-23456-78910-N- completely deletes GENE:1 and deletes the first exon of GENE:2, the +variant will be reported twice, once for each associated gene. The following pseudo-code tries to illustrate this. + +.. code-block:: yaml + + GENE1: + variants: + - 1-23456-78910-N- + variantEffect: TRANSCRIPT_ABLATION + GENE2: + variants: + - 1-23456-78910-N- + variantEffect: EXON_LOSS_VARIANT + + +SV Similarity +============= + +Given their imprecise nature, SVs are not looked-up in the database using precise coordinates, instead they are +considered 'equal' if their genomic coordinates have a jaccard similarity of 0.8 and they constitute an equivalent broad +type - gain, loss, me_gain, me_loss, inversion or complex. diff --git a/exomiser-cli/CHANGELOG.md b/exomiser-cli/CHANGELOG.md index 2b45aa76c..087782ed6 100644 --- a/exomiser-cli/CHANGELOG.md +++ b/exomiser-cli/CHANGELOG.md @@ -1,5 +1,18 @@ # The Exomiser Command Line Executable - Changelog +## 13.1.0 2022-07-29 + +- Added new automated ACMG annotations for top-scoring variants in known disease-causing genes. +- Added new combined score p-value +- Added new TSV_GENE, TSV_VARIANT and VCF output files containing ranked genes/variants for all the assessed modes of + inheritance. Note that __these new file formats will supersede the existing individual MOI-specific TSV/VCF files which + will be removed in the next major release__. See the [online documentation](https://exomiser.readthedocs.io/en/latest/result_interpretation.html) for details. +- New update online documentation! See https://exomiser.readthedocs.io/en/latest/ +- New Docker hub images for CLI and web on https://hub.docker.com/u/exomiser +- Added checks to ensure user specifies genome assembly if user specifies vcf path outside of phenopacket/analysis +- Added `--output-prefix` option to enable output prefix directly on the command line +- Updated examples to use the latest recommended settings as per preset derived from 100,000 genomes project + ## 13.0.1 2021-11-23 - Bug fix for issue where application fails to start when only specifying hg38 data in `application.properties` diff --git a/exomiser-cli/README.md b/exomiser-cli/README.md index df69b46ee..7f3566daf 100644 --- a/exomiser-cli/README.md +++ b/exomiser-cli/README.md @@ -2,10 +2,11 @@ The Exomiser is a tool to perform genome-wide prioritisation of genomic variants including non-coding and regulatory variants using patient phenotypes as a means of differentiating candidate genes. -To perform an analysis, Exomiser requires the patient's genome/exome in VCF format and their phenotype encoded in HPO terms. The exomiser is also capable of analysing trios/small family genomes, so long as a pedigree in PED format is also provided. -See [Usage](#usage) section for info on running an analysis. +To perform an analysis, Exomiser requires the patient's genome/exome in VCF format and their phenotype encoded in HPO +terms. The exomiser is also capable of analysing trios/small family genomes, so long as a pedigree in PED format is also +provided. See [Usage](#usage) section for info on running an analysis. -Further information can be found in the [online documentation](http://exomiser.github.io/Exomiser/). +Further information can be found in the [online documentation](https://exomiser.readthedocs.io/en/latest/). ## Software and Hardware requirements - For exome analysis of a 30,000 variant sample 4GB RAM should suffice. @@ -19,38 +20,42 @@ Further information can be found in the [online documentation](http://exomiser.g ## Installation -Windows: - - 1. Install 7-Zip (http://www.7-zip.org) for unzipping the archive files. The built-in archiving software has issues extracting the zip files. - 2. Download the data and distribution files from ```https://data.monarchinitiative.org/exomiser/latest``` - 3. Extract the distribution files by right-clicking exomiser-cli-${project.version}-distribution.zip and selecting 7-Zip > Extract Here - 4. Extract the data files (e.g. 1711_phenotype.zip, 1711_hg19.zip) by right-clicking the archive and selecting 7-Zip > Extract files... - 4.1 Extract the files to the exomiser data directory. By default exomiser expects this to be ```exomiser-cli-${project.version}/data```, but this can be changed in the ```application.properties``` - 5. cd exomiser-cli-${project.version} - 6. java -Xms2g -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml - -Linux: +### Windows + +1. Install 7-Zip (http://www.7-zip.org) for unzipping the archive files. The built-in archiving software has issues + extracting the zip files. +2. Download the data and distribution files from ```https://data.monarchinitiative.org/exomiser/latest``` +3. Extract the distribution files by right-clicking exomiser-cli-${project.version}-distribution.zip and selecting + 7-Zip > Extract Here +4. Extract the data files (e.g. 1711_phenotype.zip, 1711_hg19.zip) by right-clicking the archive and selecting 7-Zip > + Extract files... 4.1 Extract the files to the exomiser data directory. By default exomiser expects this to + be ```exomiser-cli-${project.version}/data```, but this can be changed in the ```application.properties``` +5. cd exomiser-cli-${project.version} +6. java -Xms2g -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml + +### Linux + The following shell script should work- - #download the distribution (won't take long) + # download the distribution (won't take long) wget https://data.monarchinitiative.org/exomiser/latest/exomiser-cli-${project.version}-distribution.zip - #download the data (this is ~20GB and will take a while) + # download the data (this is ~20GB and will take a while) wget https://data.monarchinitiative.org/exomiser/latest/2109_hg19.zip wget https://data.monarchinitiative.org/exomiser/latest/2109_hg38.zip wget https://data.monarchinitiative.org/exomiser/latest/2109_phenotype.zip - #unzip the distribution and data files - this will create a directory called 'exomiser-cli-${project.version}' in the current working directory + # unzip the distribution and data files - this will create a directory called 'exomiser-cli-${project.version}' in the current working directory unzip exomiser-cli-${project.version}-distribution.zip unzip 2109_*.zip -d exomiser-cli-${project.version}/data - #Check the application.properties are pointing to the correct versions - #exomiser.hg19.data-version=2109 - #exomiser.hg38.data-version=2109 - #exomiser.phenotype.data-version=2109 + # Check the application.properties are pointing to the correct versions: + # exomiser.hg19.data-version=2109 + # exomiser.hg38.data-version=2109 + # exomiser.phenotype.data-version=2109 - #run a test genomiser analysis + # run a test exome analysis cd exomiser-cli-${project.version} - java -Xms2g -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml + java -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml This script will download, verify and extract the exomiser files and then run the analysis contained in the file 'test-analysis-exome.yml' from the examples sub-directory. This contains a known pathogenic missense variant in the FGFR2 gene. @@ -66,8 +71,8 @@ could add the entry like this: If this step is omitted, the application will throw and error and stop any analysis which defines ```REMM``` in the ```pathogenicitySources``` section of an analysis yml file. Having done this, run the analysis like this: - - java -Xms4g -Xmx6g -jar exomiser-cli-${project.version}.jar --analysis examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml + + java -Xmx6g -jar exomiser-cli-${project.version}.jar --analysis examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml This is an analysis for an autosomal recessive 5'UTR variant located in POMP gene on chromosome 13. The phenotype HPO terms are taken from the clinical synopsis of OMIM #601952 (http://www.omim.org/clinicalSynopsis/601952) @@ -101,7 +106,7 @@ and pathogenicity data sources and the ability to tweak the order that analysis See the test-analysis-exome.yml and test-analysis-genome.yml files located in the base install directory for details. - java -Xms2g -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml + java -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml These files an also be used to run full-genomes, however they will require substantially more RAM to do so. For example a 4.4 million variant analysis requires approximately 12GB RAM. However, RAM requirements can be greatly reduced by @@ -109,11 +114,11 @@ setting the analysisMode option to PASS_ONLY. This will also aid your ability to Analyses can be run in batch mode. Simply put the path to each analysis file in the batch file - one file path per line. - java -Xms2g -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis-batch examples/test-analysis-batch.txt + java -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis-batch examples/test-analysis-batch.txt If you're running the exomiser from a different directory to the one the jar file is located in, you will need to specify the path to the ```application.properties``` file in the start-up command. For example: - java -Xms2g -Xmx4g -jar $path_to_exomiser/exomiser-cli-${project.version}.jar --analysis $path_to_exomiser/examples/test-analysis-exome.yml --spring.config.location=$path_to_exomiser/application.properties + java -Xmx4g -jar $path_to_exomiser/exomiser-cli-${project.version}.jar --analysis $path_to_exomiser/examples/test-analysis-exome.yml --spring.config.location=$path_to_exomiser/application.properties ### Want help? @@ -123,24 +128,30 @@ If you're running the exomiser from a different directory to the one the jar fil ## Troubleshooting ### java.lang.UnsupportedClassVersionError: - If you get the following error message: - + +If you get the following error message: + Exception in thread "main" java.lang.UnsupportedClassVersionError: org/monarchinitiative/exomiser/cli/Main : Unsupported major.minor version - You are running an older unsupported version of Java. Exomiser requires java version 8 or higher. This can be checked by running: - +You are running an older unsupported version of Java. Exomiser requires java version 11 or higher. This can be checked +by running: + java -version - - You should see something like this in response: - - java version "1.8.0_65" - - versions lower than 1.8 (e.g. 1.5, 1.6 or 1.7) will not run exomiser so you will need to install the latest java version. - + +You should see something like this in response: + + openjdk version "11.0.11" 2021-04-20 + OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04) + OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing) + +versions lower than 11 (e.g. 1.5, 1.6, 1.7, 1.8, 9, 10) will not run exomiser, so you will need to install the latest +java version. + ### Zip file reported as too big or corrupted - If, when running unzip 'exomiser-cli-${project.version}-distribution.zip', you see the following: - + +If, when running 'unzip exomiser-cli-${project.version}-distribution.zip', you see the following: + error: Zip file too big (greater than 4294959102 bytes) Archive: exomiser-cli-${project.version}-distribution.zip warning [exomiser-cli-${project.version}-distribution.zip]: 9940454202 extra bytes at beginning or within zipfile @@ -150,8 +161,65 @@ If you're running the exomiser from a different directory to the one the jar fil (please check that you have transferred or created the zipfile in the appropriate BINARY mode and that you have compiled UnZip properly) - Check that your unzip version was compiled with LARGE_FILE_SUPPORT and ZIP64_SUPPORT. This is standard with UnZip 6.00 and can be checked by typing: - +Check that your unzip version was compiled with LARGE_FILE_SUPPORT and ZIP64_SUPPORT. This is standard with UnZip 6.00 +and can be checked by typing: + unzip -version - - This shouldn't be an issue with more recent linux distributions. \ No newline at end of file + +This shouldn't be an issue with more recent linux distributions. + +## Docker images with jib + +Docker images are build using [jib](https://github.com/GoogleContainerTools/jib/tree/master/jib-maven-plugin#quickstart) +which does not require a Docker daemon to be running/installed in order to build an image. Tar images are built by +default and are found in the `target` directory. + +Tar images can be installed locally like so and will create a Docker image: + +```shell +$ docker load --input Exomiser/exomiser-cli/target/jib-image.tar +$ docker image list +REPOSITORY TAG IMAGE ID CREATED SIZE +localhost/exomiser-cli latest c12b1878a8f3 52 years ago 273 MB +localhost/exomiser-cli ${project.version} c12b1878a8f3 52 years ago 273 MB +``` + +To run the image you will need the standard exomiser directory layout to mount as separate volumes as in the cli and +supply an `application.properties` file or environmental variables to point to the data required _e.g._ + +```shell +docker run -v "/data/exomiser-data:/exomiser-data" \ + -v "/opt/exomiser/exomiser-config/:/exomiser" \ + -v "/opt/exomiser/exomiser-cli-${project.version}/results:/results" \ + localhost/exomiser-cli:${project.version} \ + --analysis /exomiser/test-analysis-exome.yml \ + --vcf /exomiser/Pfeiffer.vcf.gz \ + --spring.config.location=/exomiser/application.properties +``` + +or using Spring configuration arguments instead of the `application.properties`: + +```shell +docker run -v "/data/exomiser-data:/exomiser-data" \ + -v "/opt/exomiser/exomiser-config/:/exomiser" \ + -v "/opt/exomiser/exomiser-cli-${project.version}/results:/results" \ + localhost/exomiser-cli:${project.version} \ + --analysis /exomiser/test-analysis-exome.yml \ + --vcf /exomiser/Pfeiffer.vcf.gz \ + # minimal requirements for an hg19 exome sample + --exomiser.data-directory=/exomiser-data \ + --exomiser.hg19.data-version=2109 \ + --exomiser.phenotype.data-version=2109 +``` + +Here the contents of `/opt/exomiser/exomiser-config` is simply the `application.properties` file and the example files +to test all is working correctly. + +```shell +$ tree /opt/exomiser/exomiser-config/ +exomiser-config/ +├── application.properties +├── Pfeiffer.vcf.gz +├── Pfeiffer.vcf.gz.tbi +└── test-analysis-exome.yml +``` \ No newline at end of file diff --git a/exomiser-cli/pom.xml b/exomiser-cli/pom.xml index c2e9f1bb3..2f3d0d1f8 100644 --- a/exomiser-cli/pom.xml +++ b/exomiser-cli/pom.xml @@ -1,7 +1,7 @@ @@ -195,6 +195,39 @@ + + com.google.cloud.tools + jib-maven-plugin + 3.2.0 + + + install + + buildTar + + + + + + + ${docker.base.image} + + + ${project.artifactId}:${project.parent.version} + + latest + + + + + + /exomiser-data + /exomiser + /results + + + + diff --git a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineJobReader.java b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineJobReader.java index 93099c338..f2eb3b292 100644 --- a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineJobReader.java +++ b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineJobReader.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -29,6 +29,7 @@ import org.monarchinitiative.exomiser.api.v1.SampleProto; import org.monarchinitiative.exomiser.core.analysis.JobReader; import org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketPedigreeReader; +import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; import org.monarchinitiative.exomiser.core.proto.ProtoParser; import org.monarchinitiative.exomiser.core.writers.OutputFormat; import org.phenopackets.schema.v1.Family; @@ -38,7 +39,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.annotation.Nullable; import java.nio.file.Path; import java.util.Arrays; import java.util.List; @@ -99,6 +99,7 @@ public List readJobs(CommandLine commandLine) { // "sample", "output" // "sample", "vcf", "output" // "sample", "vcf", "ped", "output" + // "sample", "vcf", "ped", "output", "output-prefix" if (userOptions.contains("sample") || userOptions.contains("analysis")) { return handleMultipleUserOptions(commandLine, userOptions); } @@ -132,9 +133,16 @@ private List handleMultipleUserOptions(CommandLine commandLine, Se if (userOptions.contains("ped")) { handlePedOption(commandLine.getOptionValue("ped"), jobBuilder); } + if (userOptions.contains("output-prefix")) { + handleOutputPrefixOption(commandLine.getOptionValue("output-prefix"), jobBuilder); + } if (!jobBuilder.hasSample() && !jobBuilder.hasPhenopacket() && !jobBuilder.hasFamily()) { throw new CommandLineParseError("No sample specified!"); } + // Make sure Exomiser will return some results! Adding defaults to the initial builder will result in potential + // duplicates of the default output file types. + ensureOutputSettingsSpecifyOutputFormat(jobBuilder); + logger.debug("Submitting Exomiser job: {}", jobBuilder); return List.of(jobBuilder.build()); } @@ -148,13 +156,19 @@ private JobProto.Job.Builder newDefaultJobBuilder() { private OutputProto.OutputOptions createDefaultOutputOptions() { return OutputProto.OutputOptions.newBuilder() .setOutputPrefix("") - .addOutputFormats(OutputFormat.HTML.toString()) - .addOutputFormats(OutputFormat.JSON.toString()) .setNumGenes(0) .setOutputContributingVariantsOnly(false) .build(); } + private void ensureOutputSettingsSpecifyOutputFormat(JobProto.Job.Builder jobBuilder) { + if (jobBuilder.getOutputOptions().getOutputFormatsList().isEmpty()) { + jobBuilder.getOutputOptionsBuilder() + .addOutputFormats(OutputFormat.HTML.toString()) + .addOutputFormats(OutputFormat.JSON.toString()); + } + } + private void handleSampleOption(String sampleOptionValue, JobProto.Job.Builder jobBuilder) { Path samplePath = Path.of(sampleOptionValue); // This could be a Sample a Phenopacket or a Family @@ -178,10 +192,14 @@ private void handleAnalysisOption(String analysisOptionValue, JobProto.Job.Build } } - private void handleVcfAndAssemblyOptions(String vcfOptionValue, @Nullable String assemblyOptionValue, JobProto.Job.Builder jobBuilder) { + private void handleVcfAndAssemblyOptions(String vcfOptionValue, String assemblyOptionValue, JobProto.Job.Builder jobBuilder) { logger.debug("Handling VCF/assembly option {} {}", vcfOptionValue, assemblyOptionValue); Path vcfPath = Path.of(vcfOptionValue); - String assembly = assemblyOptionValue == null ? "GRCh37" : assemblyOptionValue; + if (assemblyOptionValue == null || assemblyOptionValue.isEmpty()) { + // Using the incorrect assembly would lead to *very* incorrect results. + throw new CommandLineParseError("assembly must be included when specifying vcf!"); + } + String assembly = GenomeAssembly.parseAssembly(assemblyOptionValue).toGrcString(); if (jobBuilder.hasPhenopacket()) { Phenopacket.Builder phenopacketBuilder = jobBuilder.getPhenopacketBuilder(); if (phenopacketBuilder.getHtsFilesCount() != 0) { @@ -242,6 +260,15 @@ private void handleOutputOption(String outputOptionValue, JobProto.Job.Builder j jobBuilder.setOutputOptions(readOutputOptions(outputOptionPath)); } + private void handleOutputPrefixOption(String outputPrefixOptionValue, JobProto.Job.Builder jobBuilder) { + Path outputPrefixOptionPath = Path.of(outputPrefixOptionValue); + logger.debug("Setting output-prefix to {}", outputPrefixOptionPath); + OutputProto.OutputOptions.Builder builder = jobBuilder + .getOutputOptions().toBuilder() + .setOutputPrefix(outputPrefixOptionPath.toString()); + jobBuilder.setOutputOptions(builder); + } + private AnalysisProto.Analysis readAnalysis(Path analysisPath) { AnalysisProto.Analysis analysis = ProtoParser.parseFromJsonOrYaml(AnalysisProto.Analysis.newBuilder(), analysisPath) .build(); diff --git a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParser.java b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParser.java index 135f8a162..606d15192 100644 --- a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParser.java +++ b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParser.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,6 +21,7 @@ package org.monarchinitiative.exomiser.cli; import org.apache.commons.cli.*; +import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; import java.nio.file.Files; import java.nio.file.Path; @@ -70,7 +71,7 @@ public class CommandLineOptionsParser { options.addOption(Option.builder() .longOpt("vcf") - .desc("Path to sample VCF file.") + .desc("Path to sample VCF file. Also requires 'assembly' option to be defined.") .hasArg() .argName("file") .build()); @@ -109,6 +110,13 @@ public class CommandLineOptionsParser { .hasArg() .argName("string") .build()); + + options.addOption(Option.builder() + .longOpt("output-prefix") + .desc("Path/filename without an extension to be prepended to the output file format options.") + .hasArg() + .argName("string") + .build()); } private CommandLineOptionsParser() { @@ -143,6 +151,17 @@ private static CommandLine validate(CommandLine commandLine) { throw new CommandLineParseError("assembly present without vcf option"); } + if (commandLine.hasOption("vcf") && !commandLine.hasOption("assembly")) { + throw new CommandLineParseError("--assembly option required when specifying vcf!"); + } + if (commandLine.hasOption("assembly")) { + try { + GenomeAssembly.parseAssembly(commandLine.getOptionValue("assembly")); + } catch (Exception e) { + throw new CommandLineParseError(e.getMessage()); + } + } + if (!hasInputFileOption(commandLine)) { throw new CommandLineParseError("Missing an input file option!"); } diff --git a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/config/MainConfig.java b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/config/MainConfig.java index 3ffd2cf29..32b748eee 100644 --- a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/config/MainConfig.java +++ b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/config/MainConfig.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -77,8 +77,9 @@ public Path exomiserDataDirectory(Path exomiserHome, Environment env) { String dataDirValue = env.getProperty("exomiser.data-directory"); if (dataDirValue == null || dataDirValue.isEmpty()) { return findDefaultDataDir(exomiserHome); + } else { + logger.debug("Data source directory defined in properties as: {}", dataDirValue); } - logger.info("Data source directory defined in properties as: {}", dataDirValue); Path dataPath = exomiserHome.resolve(dataDirValue).toAbsolutePath(); logger.info("Root data source directory set to: {}", dataPath); return dataPath; diff --git a/exomiser-cli/src/main/resources/application.properties b/exomiser-cli/src/main/resources/application.properties index 28aa83826..5e29c73bf 100644 --- a/exomiser-cli/src/main/resources/application.properties +++ b/exomiser-cli/src/main/resources/application.properties @@ -19,8 +19,10 @@ # ## exomiser root data directory ## -# root path where data is to be downloaded and worked on it is assumed that all the files required by exomiser listed -# in this properties file will be found in the data directory, unless specifically overridden here. +# root path where data is to be downloaded and worked on. It is assumed that all the files required by exomiser listed +# in this properties file will be found in the data directory, unless specifically overridden here. Exomiser will default +# to using a directory named 'data' in the installation directory, however it is often a good idea to specify the full +# system path as this will allow the data to be installed in a different directory to the application. #exomiser.data-directory=/data/exomiser-data ## optional data sources ## diff --git a/exomiser-cli/src/main/resources/examples/NA19722_252900_AR_SGSH_1_NONSYNONYMOUS.yml b/exomiser-cli/src/main/resources/examples/NA19722_252900_AR_SGSH_1_NONSYNONYMOUS.yml index 9aa520c7f..c4f921c7f 100644 --- a/exomiser-cli/src/main/resources/examples/NA19722_252900_AR_SGSH_1_NONSYNONYMOUS.yml +++ b/exomiser-cli/src/main/resources/examples/NA19722_252900_AR_SGSH_1_NONSYNONYMOUS.yml @@ -32,7 +32,7 @@ sample: 'HP:0002240', 'HP:0002360', 'HP:0002788', - 'HP:0003309'] + 'HP:0003309' ] analysis: # These are the default settings, with values representing the maximum minor allele frequency in percent (%) permitted for an # allele to be considered as a causative candidate under that mode of inheritance. @@ -76,7 +76,7 @@ analysis: GNOMAD_E_AFR, GNOMAD_E_AMR, -# GNOMAD_E_ASJ, + # GNOMAD_E_ASJ, GNOMAD_E_EAS, GNOMAD_E_FIN, GNOMAD_E_NFE, @@ -85,45 +85,45 @@ analysis: GNOMAD_G_AFR, GNOMAD_G_AMR, -# GNOMAD_G_ASJ, + # GNOMAD_G_ASJ, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT, REMM] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP, REMM ] #this is the recommended order for a genome-sized analysis. #all steps are optional steps: [ + hiPhivePrioritiser: { }, + #running the prioritiser followed by a priorityScoreFilter will remove genes + #which are least likely to contribute to the phenotype defined in hpoIds, this will + #dramatically reduce the time and memory required to analyse a genome. + # 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive + priorityScoreFilter: { priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501 }, #intervalFilter: {interval: 'chr10:123256200-123256300'}, # or for multiple intervals: #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF #intervalFilter: {bed: /full/path/to/bed_file.bed}, - #failedVariantFilter: {}, + failedVariantFilter: { }, #genePanelFilter: {geneSymbols: ['POMP','SUMF1','JUP']}, - hiPhivePrioritiser: {}, - #running the prioritiser followed by a priorityScoreFilter will remove genes - #which are least likely to contribute to the phenotype defined in hpoIds, this will - #dramatically reduce the time and memory required to analyse a genome. - # 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive - priorityScoreFilter: {priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501}, #variantEffectFilter: {remove: [SYNONYMOUS_VARIANT]}, #regulatoryFeatureFilter removes all non-regulatory non-coding variants over 20Kb from a known gene. - regulatoryFeatureFilter: {}, + regulatoryFeatureFilter: { }, #knownVariantFilter: {}, #removes variants represented in the database - frequencyFilter: {maxFrequency: 2.0}, - pathogenicityFilter: {keepNonPathogenic: true}, + frequencyFilter: { maxFrequency: 2.0 }, + pathogenicityFilter: { keepNonPathogenic: true }, #inheritanceFilter and omimPrioritiser should always run AFTER all other filters have completed #they will analyse genes according to the specified modeOfInheritance above- UNDEFINED will not be analysed. - inheritanceFilter: {}, + inheritanceFilter: { }, #omimPrioritiser isn't mandatory. - omimPrioritiser: {} + omimPrioritiser: { } #Other prioritisers: Only combine omimPrioritiser with one of these. #Don't include any if you only want to filter the variants. #hiPhivePrioritiser: {}, @@ -133,14 +133,14 @@ analysis: #exomeWalkerPrioritiser: {seedGeneIds: [11111, 22222, 33333]} ] outputOptions: - outputContributingVariantsOnly: false - #numGenes options: 0 = all or specify a limit e.g. 500 for the first 500 results - numGenes: 0 - #outputPrefix options: specify the path/filename without an extension and this will be added - # according to the outputFormats option. If unspecified this will default to the following: - # {exomiserDir}/results/input-vcf-name-exomiser-results.html - # alternatively, specify a fully qualifed path only. e.g. /users/jules/exomes/analysis - outputPrefix: results/NA19722_252900_AR_SGSH_1_NONSYNONYMOUS - #out-format options: HTML, JSON, TSV_GENE, TSV_VARIANT, VCF (default: HTML) - outputFormats: [HTML, JSON, TSV_GENE, TSV_VARIANT, VCF] + outputContributingVariantsOnly: false + #numGenes options: 0 = all or specify a limit e.g. 500 for the first 500 results + numGenes: 0 + #outputPrefix options: specify the path/filename without an extension and this will be added + # according to the outputFormats option. If unspecified this will default to the following: + # {exomiserDir}/results/input-vcf-name-exomiser-results.html + # alternatively, specify a fully qualifed path only. e.g. /users/jules/exomes/analysis + outputPrefix: results/NA19722_252900_AR_SGSH_1_NONSYNONYMOUS + #out-format options: HTML, JSON, TSV_GENE, TSV_VARIANT, VCF (default: HTML) + outputFormats: [ HTML, JSON, TSV_GENE, TSV_VARIANT, VCF ] \ No newline at end of file diff --git a/exomiser-cli/src/main/resources/examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml b/exomiser-cli/src/main/resources/examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml index 96f2ad646..7bb5e025e 100644 --- a/exomiser-cli/src/main/resources/examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml +++ b/exomiser-cli/src/main/resources/examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml @@ -3,12 +3,12 @@ # your own set-up. --- analysis: - # hg19 or hg38 - ensure that the application has been configured to run the specified assembly otherwise it will halt. - genomeAssembly: hg19 - vcf: examples/NA19722_CHR13_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.vcf.gz - ped: - proband: - hpoIds: ['HP:0000982', + # hg19 or hg38 - ensure that the application has been configured to run the specified assembly otherwise it will halt. + genomeAssembly: hg19 + vcf: examples/NA19722_CHR13_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.vcf.gz + ped: + proband: + hpoIds: [ 'HP:0000982', 'HP:0001036', 'HP:0001367', 'HP:0001795', @@ -17,97 +17,97 @@ analysis: 'HP:0007490', 'HP:0008064', 'HP:0008404', - 'HP:0009775'] - # These are the default settings, with values representing the maximum minor allele frequency in percent (%) permitted for an - # allele to be considered as a causative candidate under that mode of inheritance. - # If you just want to analyse a sample under a single inheritance mode, delete/comment-out the others. For AUTOSOMAL_RECESSIVE - # or X_RECESSIVE ensure *both* relevant HOM_ALT and COMP_HET modes are present. - # In cases where you do not want any cut-offs applied an empty map should be used e.g. inheritanceModes: {} - inheritanceModes: { - AUTOSOMAL_DOMINANT: 0.1, - AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, - AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, - X_DOMINANT: 0.1, - X_RECESSIVE_HOM_ALT: 0.1, - X_RECESSIVE_COMP_HET: 2.0, - MITOCHONDRIAL: 0.2 - } - #FULL or PASS_ONLY - analysisMode: PASS_ONLY - #Possible frequencySources: - #Thousand Genomes project - http://www.1000genomes.org/ (THOUSAND_GENOMES) - #TOPMed - https://www.nhlbi.nih.gov/science/precision-medicine-activities (TOPMED) - #UK10K - http://www.uk10k.org/ (UK10K) - #ESP project - http://evs.gs.washington.edu/EVS/ (ESP_) - # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, - #ExAC project http://exac.broadinstitute.org/about (EXAC_) - # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, - # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, - # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, - # EXAC_OTHER - #gnomAD - http://gnomad.broadinstitute.org/ (GNOMAD_E, GNOMAD_G) - frequencySources: [ - THOUSAND_GENOMES, - TOPMED, - UK10K, + 'HP:0009775' ] + # These are the default settings, with values representing the maximum minor allele frequency in percent (%) permitted for an + # allele to be considered as a causative candidate under that mode of inheritance. + # If you just want to analyse a sample under a single inheritance mode, delete/comment-out the others. For AUTOSOMAL_RECESSIVE + # or X_RECESSIVE ensure *both* relevant HOM_ALT and COMP_HET modes are present. + # In cases where you do not want any cut-offs applied an empty map should be used e.g. inheritanceModes: {} + inheritanceModes: { + AUTOSOMAL_DOMINANT: 0.1, + AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, + AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, + X_DOMINANT: 0.1, + X_RECESSIVE_HOM_ALT: 0.1, + X_RECESSIVE_COMP_HET: 2.0, + MITOCHONDRIAL: 0.2 + } + #FULL or PASS_ONLY + analysisMode: PASS_ONLY + #Possible frequencySources: + #Thousand Genomes project - http://www.1000genomes.org/ (THOUSAND_GENOMES) + #TOPMed - https://www.nhlbi.nih.gov/science/precision-medicine-activities (TOPMED) + #UK10K - http://www.uk10k.org/ (UK10K) + #ESP project - http://evs.gs.washington.edu/EVS/ (ESP_) + # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + #ExAC project http://exac.broadinstitute.org/about (EXAC_) + # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + # EXAC_OTHER + #gnomAD - http://gnomad.broadinstitute.org/ (GNOMAD_E, GNOMAD_G) + frequencySources: [ + THOUSAND_GENOMES, + TOPMED, + UK10K, - ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, - EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, - EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, - EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, - EXAC_OTHER, + EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + EXAC_OTHER, - GNOMAD_E_AFR, - GNOMAD_E_AMR, -# GNOMAD_E_ASJ, - GNOMAD_E_EAS, - GNOMAD_E_FIN, - GNOMAD_E_NFE, - GNOMAD_E_OTH, - GNOMAD_E_SAS, + GNOMAD_E_AFR, + GNOMAD_E_AMR, + # GNOMAD_E_ASJ, + GNOMAD_E_EAS, + GNOMAD_E_FIN, + GNOMAD_E_NFE, + GNOMAD_E_OTH, + GNOMAD_E_SAS, - GNOMAD_G_AFR, - GNOMAD_G_AMR, -# GNOMAD_G_ASJ, - GNOMAD_G_EAS, - GNOMAD_G_FIN, - GNOMAD_G_NFE, - GNOMAD_G_OTH, - GNOMAD_G_SAS - ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT, REMM] - #this is the recommended order for a genome-sized analysis. - #all steps are optional - steps: [ - #intervalFilter: {interval: 'chr10:123256200-123256300'}, - # or for multiple intervals: - #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, - # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF - #intervalFilter: {bed: /full/path/to/bed_file.bed}, - #failedVariantFilter: {}, - #genePanelFilter: {geneSymbols: ['POMP','SUMF1','JUP']}, - hiPhivePrioritiser: {}, - #running the prioritiser followed by a priorityScoreFilter will remove genes - #which are least likely to contribute to the phenotype defined in hpoIds, this will - #dramatically reduce the time and memory required to analyse a genome. - # 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive - priorityScoreFilter: {priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501}, - #variantEffectFilter: {remove: [SYNONYMOUS_VARIANT]}, - #regulatoryFeatureFilter removes all non-regulatory non-coding variants over 20Kb from a known gene. - regulatoryFeatureFilter: {}, - #knownVariantFilter: {}, #removes variants represented in the database - frequencyFilter: {maxFrequency: 2.0}, - pathogenicityFilter: {keepNonPathogenic: true}, - #inheritanceFilter and omimPrioritiser should always run AFTER all other filters have completed - #they will analyse genes according to the specified modeOfInheritance above- UNDEFINED will not be analysed. - inheritanceFilter: {}, - #omimPrioritiser isn't mandatory. - omimPrioritiser: {} + GNOMAD_G_AFR, + GNOMAD_G_AMR, + # GNOMAD_G_ASJ, + GNOMAD_G_EAS, + GNOMAD_G_FIN, + GNOMAD_G_NFE, + GNOMAD_G_OTH, + GNOMAD_G_SAS + ] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP, REMM ] + #this is the recommended order for a genome-sized analysis. + #all steps are optional + steps: [ + hiPhivePrioritiser: { }, + #running the prioritiser followed by a priorityScoreFilter will remove genes + #which are least likely to contribute to the phenotype defined in hpoIds, this will + #dramatically reduce the time and memory required to analyse a genome. + # 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive + priorityScoreFilter: { priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501 }, + #intervalFilter: {interval: 'chr10:123256200-123256300'}, + # or for multiple intervals: + #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, + # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF + #intervalFilter: {bed: /full/path/to/bed_file.bed}, + failedVariantFilter: { }, + #genePanelFilter: {geneSymbols: ['POMP','SUMF1','JUP']}, + #variantEffectFilter: {remove: [SYNONYMOUS_VARIANT]}, + #regulatoryFeatureFilter removes all non-regulatory non-coding variants over 20Kb from a known gene. + regulatoryFeatureFilter: { }, + #knownVariantFilter: {}, #removes variants represented in the database + frequencyFilter: { maxFrequency: 2.0 }, + pathogenicityFilter: { keepNonPathogenic: true }, + #inheritanceFilter and omimPrioritiser should always run AFTER all other filters have completed + #they will analyse genes according to the specified modeOfInheritance above- UNDEFINED will not be analysed. + inheritanceFilter: { }, + #omimPrioritiser isn't mandatory. + omimPrioritiser: { } #Other prioritisers: Only combine omimPrioritiser with one of these. #Don't include any if you only want to filter the variants. #hiPhivePrioritiser: {}, @@ -115,16 +115,16 @@ analysis: #hiPhivePrioritiser: {diseaseId: 'OMIM:101600', candidateGeneSymbol: FGFR2, runParams: 'human,mouse,fish,ppi'}, #phenixPrioritiser: {} #exomeWalkerPrioritiser: {seedGeneIds: [11111, 22222, 33333]} - ] + ] outputOptions: - outputContributingVariantsOnly: false - #numGenes options: 0 = all or specify a limit e.g. 500 for the first 500 results - numGenes: 0 - #outputPrefix options: specify the path/filename without an extension and this will be added - # according to the outputFormats option. If unspecified this will default to the following: - # {exomiserDir}/results/input-vcf-name-exomiser-results.html - # alternatively, specify a fully qualifed path only. e.g. /users/jules/exomes/analysis - outputPrefix: results/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38 - #out-format options: HTML, JSON, TSV_GENE, TSV_VARIANT, VCF (default: HTML) - outputFormats: [HTML, JSON, TSV_GENE, TSV_VARIANT, VCF] + outputContributingVariantsOnly: false + #numGenes options: 0 = all or specify a limit e.g. 500 for the first 500 results + numGenes: 0 + #outputPrefix options: specify the path/filename without an extension and this will be added + # according to the outputFormats option. If unspecified this will default to the following: + # {exomiserDir}/results/input-vcf-name-exomiser-results.html + # alternatively, specify a fully qualifed path only. e.g. /users/jules/exomes/analysis + outputPrefix: results/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38 + #out-format options: HTML, JSON, TSV_GENE, TSV_VARIANT, VCF (default: HTML) + outputFormats: [ HTML, JSON, TSV_GENE, TSV_VARIANT, VCF ] diff --git a/exomiser-cli/src/main/resources/examples/test-analysis-exome.yml b/exomiser-cli/src/main/resources/examples/test-analysis-exome.yml index 62d814752..9f887cbe5 100644 --- a/exomiser-cli/src/main/resources/examples/test-analysis-exome.yml +++ b/exomiser-cli/src/main/resources/examples/test-analysis-exome.yml @@ -15,38 +15,38 @@ analysis: # or X_RECESSIVE ensure *both* relevant HOM_ALT and COMP_HET modes are present. # In cases where you do not want any cut-offs applied an empty map should be used e.g. inheritanceModes: {} inheritanceModes: { - AUTOSOMAL_DOMINANT: 0.1, - AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, - AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, - X_DOMINANT: 0.1, - X_RECESSIVE_HOM_ALT: 0.1, - X_RECESSIVE_COMP_HET: 2.0, - MITOCHONDRIAL: 0.2 + AUTOSOMAL_DOMINANT: 0.1, + AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, + AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, + X_DOMINANT: 0.1, + X_RECESSIVE_HOM_ALT: 0.1, + X_RECESSIVE_COMP_HET: 2.0, + MITOCHONDRIAL: 0.2 } - #FULL or PASS_ONLY + #FULL or PASS_ONLY analysisMode: PASS_ONLY - #Possible frequencySources: - #Thousand Genomes project http://www.1000genomes.org/ - # THOUSAND_GENOMES, - #ESP project http://evs.gs.washington.edu/EVS/ - # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, - #ExAC project http://exac.broadinstitute.org/about - # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, - # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, - # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, - # EXAC_OTHER - #Possible frequencySources: - #Thousand Genomes project - http://www.1000genomes.org/ (THOUSAND_GENOMES) - #TOPMed - https://www.nhlbi.nih.gov/science/precision-medicine-activities (TOPMED) - #UK10K - http://www.uk10k.org/ (UK10K) - #ESP project - http://evs.gs.washington.edu/EVS/ (ESP_) - # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, - #ExAC project http://exac.broadinstitute.org/about (EXAC_) - # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, - # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, - # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, - # EXAC_OTHER - #gnomAD - http://gnomad.broadinstitute.org/ (GNOMAD_E, GNOMAD_G) + # Possible frequencySources: + # Thousand Genomes project http://www.1000genomes.org/ + # THOUSAND_GENOMES, + # ESP project http://evs.gs.washington.edu/EVS/ + # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + # ExAC project http://exac.broadinstitute.org/about + # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + # EXAC_OTHER + # Possible frequencySources: + # Thousand Genomes project - http://www.1000genomes.org/ (THOUSAND_GENOMES) + # TOPMed - https://www.nhlbi.nih.gov/science/precision-medicine-activities (TOPMED) + # UK10K - http://www.uk10k.org/ (UK10K) + # ESP project - http://evs.gs.washington.edu/EVS/ (ESP_) + # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + # ExAC project http://exac.broadinstitute.org/about (EXAC_) + # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + # EXAC_OTHER + # gnomAD - http://gnomad.broadinstitute.org/ (GNOMAD_E, GNOMAD_G) frequencySources: [ THOUSAND_GENOMES, TOPMED, @@ -70,38 +70,38 @@ analysis: GNOMAD_G_AFR, GNOMAD_G_AMR, -# GNOMAD_G_ASJ, + # GNOMAD_G_ASJ, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT] - #this is the standard exomiser order. - #all steps are optional - steps: [ - #intervalFilter: {interval: 'chr10:123256200-123256300'}, - # or for multiple intervals: - #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, - # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF - #intervalFilter: {bed: /full/path/to/bed_file.bed}, - #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - #failedVariantFilter: {}, - #qualityFilter: {minQuality: 50.0}, + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP ] + # this is the standard exomiser order. + # all steps are optional + steps: [ + #intervalFilter: {interval: 'chr10:123256200-123256300'}, + # or for multiple intervals: + #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, + # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF + #intervalFilter: {bed: /full/path/to/bed_file.bed}, + #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, + failedVariantFilter: { }, + #qualityFilter: {minQuality: 50.0}, variantEffectFilter: { - remove: [ - FIVE_PRIME_UTR_EXON_VARIANT, - FIVE_PRIME_UTR_INTRON_VARIANT, - THREE_PRIME_UTR_EXON_VARIANT, - THREE_PRIME_UTR_INTRON_VARIANT, - NON_CODING_TRANSCRIPT_EXON_VARIANT, - NON_CODING_TRANSCRIPT_INTRON_VARIANT, - CODING_TRANSCRIPT_INTRON_VARIANT, + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + NON_CODING_TRANSCRIPT_INTRON_VARIANT, + CODING_TRANSCRIPT_INTRON_VARIANT, UPSTREAM_GENE_VARIANT, DOWNSTREAM_GENE_VARIANT, INTERGENIC_VARIANT, diff --git a/exomiser-cli/src/main/resources/examples/test-analysis-genome.yml b/exomiser-cli/src/main/resources/examples/test-analysis-genome.yml index c80dcbf4a..afe9f9272 100644 --- a/exomiser-cli/src/main/resources/examples/test-analysis-genome.yml +++ b/exomiser-cli/src/main/resources/examples/test-analysis-genome.yml @@ -15,28 +15,28 @@ analysis: # or X_RECESSIVE ensure *both* relevant HOM_ALT and COMP_HET modes are present. # In cases where you do not want any cut-offs applied an empty map should be used e.g. inheritanceModes: {} inheritanceModes: { - AUTOSOMAL_DOMINANT: 0.1, - AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, - AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, - X_DOMINANT: 0.1, - X_RECESSIVE_HOM_ALT: 0.1, - X_RECESSIVE_COMP_HET: 2.0, - MITOCHONDRIAL: 0.2 + AUTOSOMAL_DOMINANT: 0.1, + AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, + AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, + X_DOMINANT: 0.1, + X_RECESSIVE_HOM_ALT: 0.1, + X_RECESSIVE_COMP_HET: 2.0, + MITOCHONDRIAL: 0.2 } - #FULL or PASS_ONLY + #FULL or PASS_ONLY analysisMode: PASS_ONLY - #Possible frequencySources: - #Thousand Genomes project - http://www.1000genomes.org/ (THOUSAND_GENOMES) - #TOPMed - https://www.nhlbi.nih.gov/science/precision-medicine-activities (TOPMED) - #UK10K - http://www.uk10k.org/ (UK10K) - #ESP project - http://evs.gs.washington.edu/EVS/ (ESP_) - # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, - #ExAC project http://exac.broadinstitute.org/about (EXAC_) - # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, - # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, - # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, - # EXAC_OTHER - #gnomAD - http://gnomad.broadinstitute.org/ (GNOMAD_E, GNOMAD_G) + # Possible frequencySources: + # Thousand Genomes project - http://www.1000genomes.org/ (THOUSAND_GENOMES) + # TOPMed - https://www.nhlbi.nih.gov/science/precision-medicine-activities (TOPMED) + # UK10K - http://www.uk10k.org/ (UK10K) + # ESP project - http://evs.gs.washington.edu/EVS/ (ESP_) + # ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, + # ExAC project http://exac.broadinstitute.org/about (EXAC_) + # EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, + # EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, + # EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, + # EXAC_OTHER + # gnomAD - http://gnomad.broadinstitute.org/ (GNOMAD_E, GNOMAD_G) frequencySources: [ THOUSAND_GENOMES, TOPMED, @@ -60,44 +60,45 @@ analysis: GNOMAD_G_AFR, GNOMAD_G_AMR, -# GNOMAD_G_ASJ, + # GNOMAD_G_ASJ, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT, REMM] - #this is the recommended order for a genome-sized analysis. - #all steps are optional - steps: [ - #intervalFilter: {interval: 'chr10:123256200-123256300'}, - # or for multiple intervals: - #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, - # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF - #intervalFilter: {bed: /full/path/to/bed_file.bed}, - #failedVariantFilter: {}, - #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - hiPhivePrioritiser: {}, - #running the prioritiser followed by a priorityScoreFilter will remove genes - #which are least likely to contribute to the phenotype defined in hpoIds, this will - #dramatically reduce the time and memory required to analyse a genome. - # 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive - priorityScoreFilter: {priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501}, - #variantEffectFilter: {remove: [SYNONYMOUS_VARIANT]}, - #regulatoryFeatureFilter removes all non-regulatory non-coding variants over 20Kb from a known gene. - regulatoryFeatureFilter: {}, - #knownVariantFilter: {}, #removes variants represented in the database - frequencyFilter: {maxFrequency: 2.0}, - pathogenicityFilter: {keepNonPathogenic: true}, - #inheritanceFilter and omimPrioritiser should always run AFTER all other filters have completed - #they will analyse genes according to the specified modeOfInheritance above- UNDEFINED will not be analysed. - inheritanceFilter: {}, - #omimPrioritiser isn't mandatory. + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP, REMM ] + # this is the recommended order for a genome-sized analysis. + # all steps are optional + steps: [ + hiPhivePrioritiser: { }, + #running the prioritiser followed by a priorityScoreFilter will remove genes + #which are least likely to contribute to the phenotype defined in hpoIds, this will + #dramatically reduce the time and memory required to analyse a genome. + # 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive + priorityScoreFilter: { priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501 }, + failedVariantFilter: { }, + #intervalFilter: {interval: 'chr10:123256200-123256300'}, + # or for multiple intervals: + #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, + # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF + #intervalFilter: {bed: /full/path/to/bed_file.bed}, + #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, + #qualityFilter: {minQuality: 50.0}, + #variantEffectFilter: {remove: [SYNONYMOUS_VARIANT]}, + #regulatoryFeatureFilter removes all non-regulatory non-coding variants over 20Kb from a known gene. + regulatoryFeatureFilter: { }, + #knownVariantFilter: {}, #removes variants represented in the database + frequencyFilter: { maxFrequency: 2.0 }, + pathogenicityFilter: { keepNonPathogenic: true }, + #inheritanceFilter and omimPrioritiser should always run AFTER all other filters have completed + #they will analyse genes according to the specified modeOfInheritance above- UNDEFINED will not be analysed. + inheritanceFilter: { }, + #omimPrioritiser isn't mandatory. omimPrioritiser: {} #Other prioritisers: Only combine omimPrioritiser with one of these. #Don't include any if you only want to filter the variants. diff --git a/exomiser-cli/src/main/resources/examples/test-analysis-multisample.yml b/exomiser-cli/src/main/resources/examples/test-analysis-multisample.yml index c7b3104fa..23d7876d1 100644 --- a/exomiser-cli/src/main/resources/examples/test-analysis-multisample.yml +++ b/exomiser-cli/src/main/resources/examples/test-analysis-multisample.yml @@ -59,38 +59,38 @@ analysis: GNOMAD_G_AFR, GNOMAD_G_AMR, -# GNOMAD_G_ASJ, + # GNOMAD_G_ASJ, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS - ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT] - #this is the standard exomiser order. - #all steps are optional + ] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP ] + # this is the standard exomiser order. + # all steps are optional steps: [ - #intervalFilter: {interval: 'chr10:123256200-123256300'}, - # or for multiple intervals: - #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, - # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF - #intervalFilter: {bed: /full/path/to/bed_file.bed}, - #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - #failedVariantFilter: {}, - #qualityFilter: {minQuality: 50.0}, + #intervalFilter: {interval: 'chr10:123256200-123256300'}, + # or for multiple intervals: + #intervalFilter: {intervals: ['chr10:123256200-123256300', 'chr10:123256290-123256350']}, + # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF + #intervalFilter: {bed: /full/path/to/bed_file.bed}, + #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, + failedVariantFilter: { }, + #qualityFilter: {minQuality: 50.0}, variantEffectFilter: { - remove: [ - FIVE_PRIME_UTR_EXON_VARIANT, - FIVE_PRIME_UTR_INTRON_VARIANT, - THREE_PRIME_UTR_EXON_VARIANT, - THREE_PRIME_UTR_INTRON_VARIANT, - NON_CODING_TRANSCRIPT_EXON_VARIANT, - UPSTREAM_GENE_VARIANT, - INTERGENIC_VARIANT, + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + UPSTREAM_GENE_VARIANT, + INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT, CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, diff --git a/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineJobReaderTest.java b/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineJobReaderTest.java index 7922d6545..23f63156e 100644 --- a/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineJobReaderTest.java +++ b/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineJobReaderTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -49,7 +49,8 @@ import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.Matchers.equalTo; import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource.*; +import static org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource.MVP; +import static org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource.REVEL; /** * @author Jules Jacobsen @@ -260,7 +261,8 @@ class CommandLineJobReaderTest { FrequencySource.GNOMAD_G_OTH, FrequencySource.GNOMAD_G_SAS )) - .pathogenicitySources(ImmutableSet.of(POLYPHEN, MUTATION_TASTER, SIFT)) + .pathogenicitySources(ImmutableSet.of(REVEL, MVP)) + .addFailedVariantFilter() .addVariantEffectFilter(ImmutableSet.of( FIVE_PRIME_UTR_EXON_VARIANT, FIVE_PRIME_UTR_INTRON_VARIANT, @@ -414,6 +416,28 @@ void readCliSampleOnlyWithSample() { assertThat(jobs, equalTo(List.of(expected))); } + @Test + void readCliSampleWithOutputPrefix() { + String outputPrefixOption = "wibble"; + CommandLine commandLine = CommandLineOptionsParser.parse( + "--sample", "src/test/resources/pfeiffer-sample.yml", + "--output-prefix", outputPrefixOption + ); + List jobs = instance.readJobs(commandLine); + + OutputProto.OutputOptions outputOptions = DEFAULT_OUTPUT_OPTIONS.toBuilder() + .setOutputPrefix(outputPrefixOption) + .build(); + + JobProto.Job expected = JobProto.Job.newBuilder() + .setSample(SAMPLE) + .setPreset(AnalysisProto.Preset.EXOME) + .setOutputOptions(outputOptions) + .build(); + + assertThat(jobs, equalTo(List.of(expected))); + } + @Test void readCliSampleOnlyWithPhenopacket() { CommandLine commandLine = CommandLineOptionsParser.parse( @@ -511,7 +535,7 @@ void readCliBatch() { // --sample src/test/resources/pfeiffer-phenopacket.json --vcf src/test/resources/Pfeiffer.vcf --assembly hg19 Path vcfPath = Path.of("src/test/resources/Pfeiffer.vcf").toAbsolutePath(); - HtsFile htsFile = HtsFile.newBuilder().setUri(vcfPath.toUri().toString()).setHtsFormat(HtsFile.HtsFormat.VCF).setGenomeAssembly("hg19").build(); + HtsFile htsFile = HtsFile.newBuilder().setUri(vcfPath.toUri().toString()).setHtsFormat(HtsFile.HtsFormat.VCF).setGenomeAssembly("GRCh37").build(); JobProto.Job expected = JobProto.Job.newBuilder() .setPhenopacket(PHENOPACKET.toBuilder().setHtsFiles(0, htsFile).build()) .setPreset(AnalysisProto.Preset.EXOME) @@ -520,7 +544,7 @@ void readCliBatch() { // --sample src/test/resources/pfeiffer-sample.json --vcf src/test/resources/Pfeiffer.vcf --assembly hg19 JobProto.Job updateSampleJsonHg19AssemblyNoAnalysisOption = JobProto.Job.newBuilder() - .setSample(SAMPLE.toBuilder().setVcf(vcfPath.toString()).setGenomeAssembly("hg19").build()) + .setSample(SAMPLE.toBuilder().setVcf(vcfPath.toString()).setGenomeAssembly("GRCh37").build()) .setPreset(AnalysisProto.Preset.EXOME) .setOutputOptions(DEFAULT_OUTPUT_OPTIONS) .build(); @@ -580,7 +604,8 @@ void readCliFamilyExome() { void readCliFamilyExomeWithVcfOption() { CommandLine commandLine = CommandLineOptionsParser.parse( "--sample", "src/test/resources/pfeiffer-family.yml", - "--vcf", "src/test/resources/Pfeiffer.vcf" + "--vcf", "src/test/resources/Pfeiffer.vcf", + "--assembly", "GRCh37" ); List jobs = instance.readJobs(commandLine); @@ -606,8 +631,9 @@ void readCliFamilyExomeWithVcfAndPedigreeOption() { CommandLine commandLine = CommandLineOptionsParser.parse( "--sample", "src/test/resources/pfeiffer-family.yml", "--vcf", "src/test/resources/Pfeiffer.vcf", + "--assembly", "GRCh37", "--ped", "src/test/resources/pfeiffer-singleton.ped" - ); + ); List jobs = instance.readJobs(commandLine); Path vcfPath = Path.of("src/test/resources/Pfeiffer.vcf").toAbsolutePath(); @@ -635,6 +661,7 @@ void readCliPhenopacketWithVcfAndPedigreeOption() { CommandLine commandLine = CommandLineOptionsParser.parse( "--sample", "src/test/resources/pfeiffer-phenopacket.yml", "--vcf", "src/test/resources/Pfeiffer.vcf", + "--assembly", "hg19", "--ped", "src/test/resources/pfeiffer-singleton.ped" ); List jobs = instance.readJobs(commandLine); @@ -762,6 +789,33 @@ void readCliSampleAnalysisWithPhenopacket() { assertThat(jobs, equalTo(List.of(expected))); } + @Test + void readCliLegacyAnalysisWithVcfOverrideRequiresAssembly() { + assertThrows(CommandLineParseError.class, ()-> CommandLineOptionsParser.parse( + "--analysis", "src/test/resources/pfeiffer-analysis-v8-12.yml", + "--vcf", "src/test/resources/Pfeiffer.vcf" + ), "-assembly option required when specifying vcf!"); + } + + @Test + void readCliLegacyAnalysisWithVcfOverrideSetsNewAssembly() { + CommandLine commandLine = CommandLineOptionsParser.parse( + "--analysis", "src/test/resources/pfeiffer-analysis-v8-12.yml", + "--vcf", "src/test/resources/Pfeiffer.vcf", + "--assembly", "hg38" + ); + List jobs = instance.readJobs(commandLine); + + SampleProto.Sample updated = SampleProto.Sample.newBuilder() + .setVcf(Path.of("src/test/resources/Pfeiffer.vcf").toAbsolutePath().toString()) + .setGenomeAssembly("GRCh38") + .build(); + + JobProto.Job expected = PFEIFFER_SAMPLE_JOB.toBuilder().mergeSample(updated).build(); + + assertThat(jobs, equalTo(List.of(expected))); + } + @Disabled("Potentially confusing, but still legal input") @Test void readCliSampleWithLegacyAnalysisThrowsException() { diff --git a/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParserTest.java b/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParserTest.java index 13e660172..77ef811a0 100644 --- a/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParserTest.java +++ b/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineOptionsParserTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -89,13 +89,22 @@ void parseIllegalSampleAssemblyCombination() { )); } -// @Test -// void parseIllegalAnalysisVcfCombination() { -// assertThrows(CommandLineParseError.class, () -> CommandLineOptionsParser.parse( -// "--analysis", resource("pfeiffer-analysis-v8-12.yml"), -// "--vcf", resource("Pfeiffer.vcf") -// )); -// } + @Test + void parseIllegalMissingAssemblyAnalysisVcfCombination() { + assertThrows(CommandLineParseError.class, () -> CommandLineOptionsParser.parse( + "--analysis", resource("pfeiffer-analysis-v8-12.yml"), + "--vcf", resource("Pfeiffer.vcf")), + "--assembly option required when specifying vcf!"); + } + + @Test + void parseIllegalAssemblyValue() { + assertThrows(CommandLineParseError.class, () -> CommandLineOptionsParser.parse( + "--sample", resource("pfeiffer-job-sample.yml"), + "--assembly", "wibble"), + "'wibble' is not a valid/supported genome assembly." + ); + } @Test void parseWillStopAtUnknownArgumentBefore() { @@ -142,11 +151,32 @@ void parseSample() { void parseSampleAndVcf() { CommandLine commandLine = CommandLineOptionsParser.parse( "--sample", resource("exome-analysis.yml"), - "--vcf", resource("Pfeiffer.vcf")); + "--vcf", resource("Pfeiffer.vcf"), + "--assembly", "hg19"); + assertTrue(commandLine.hasOption("sample")); + assertThat(commandLine.getOptionValue("sample"), equalTo(resource("exome-analysis.yml"))); + assertTrue(commandLine.hasOption("vcf")); + assertThat(commandLine.getOptionValue("vcf"), equalTo(resource("Pfeiffer.vcf"))); + assertTrue(commandLine.hasOption("assembly")); + assertThat(commandLine.getOptionValue("assembly"), equalTo("hg19")); + } + + @Test + void parseSampleVcfAndOutputPrefix() { + CommandLine commandLine = CommandLineOptionsParser.parse( + "--sample", resource("exome-analysis.yml"), + "--vcf", resource("Pfeiffer.vcf"), + "--assembly", "hg19", + "--output-prefix", "results/pfeiffer-exome-analysis-results" + ); assertTrue(commandLine.hasOption("sample")); assertThat(commandLine.getOptionValue("sample"), equalTo(resource("exome-analysis.yml"))); assertTrue(commandLine.hasOption("vcf")); assertThat(commandLine.getOptionValue("vcf"), equalTo(resource("Pfeiffer.vcf"))); + assertTrue(commandLine.hasOption("assembly")); + assertThat(commandLine.getOptionValue("assembly"), equalTo("hg19")); + assertTrue(commandLine.hasOption("output-prefix")); + assertThat(commandLine.getOptionValue("output-prefix"), equalTo("results/pfeiffer-exome-analysis-results")); } @Test diff --git a/exomiser-cli/src/test/resources/exome-analysis.yml b/exomiser-cli/src/test/resources/exome-analysis.yml index 6263f05e9..85217d133 100644 --- a/exomiser-cli/src/test/resources/exome-analysis.yml +++ b/exomiser-cli/src/test/resources/exome-analysis.yml @@ -64,11 +64,11 @@ frequencySources: [ GNOMAD_G_OTH, GNOMAD_G_SAS ] -#Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM -#REMM is trained on non-coding regulatory regions -#*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files -#and updated their location in the application.properties. Exomiser will not run without this. -pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT] +# Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM +# REMM is trained on non-coding regulatory regions +# *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files +# and updated their location in the application.properties. Exomiser will not run without this. +pathogenicitySources: [ REVEL, MVP ] #this is the standard exomiser order. #all steps are optional steps: [ @@ -80,17 +80,17 @@ steps: [ # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF #intervalFilter: {bed: /full/path/to/bed_file.bed}, #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - #failedVariantFilter: {}, + failedVariantFilter: { }, #qualityFilter: {minQuality: 50.0}, - variantEffectFilter: { - remove: [ - FIVE_PRIME_UTR_EXON_VARIANT, - FIVE_PRIME_UTR_INTRON_VARIANT, - THREE_PRIME_UTR_EXON_VARIANT, - THREE_PRIME_UTR_INTRON_VARIANT, - NON_CODING_TRANSCRIPT_EXON_VARIANT, - UPSTREAM_GENE_VARIANT, - INTERGENIC_VARIANT, + variantEffectFilter: { + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + UPSTREAM_GENE_VARIANT, + INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT, CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, diff --git a/exomiser-cli/src/test/resources/pfeiffer-analysis-v8-12.yml b/exomiser-cli/src/test/resources/pfeiffer-analysis-v8-12.yml index c96d3ed07..9bd7ba1ab 100644 --- a/exomiser-cli/src/test/resources/pfeiffer-analysis-v8-12.yml +++ b/exomiser-cli/src/test/resources/pfeiffer-analysis-v8-12.yml @@ -76,11 +76,11 @@ analysis: GNOMAD_G_OTH, GNOMAD_G_SAS ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP ] #this is the standard exomiser order. #all steps are optional steps: [ @@ -92,17 +92,17 @@ analysis: # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF #intervalFilter: {bed: /full/path/to/bed_file.bed}, #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - #failedVariantFilter: {}, + failedVariantFilter: { }, #qualityFilter: {minQuality: 50.0}, - variantEffectFilter: { - remove: [ - FIVE_PRIME_UTR_EXON_VARIANT, - FIVE_PRIME_UTR_INTRON_VARIANT, - THREE_PRIME_UTR_EXON_VARIANT, - THREE_PRIME_UTR_INTRON_VARIANT, - NON_CODING_TRANSCRIPT_EXON_VARIANT, - UPSTREAM_GENE_VARIANT, - INTERGENIC_VARIANT, + variantEffectFilter: { + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + UPSTREAM_GENE_VARIANT, + INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT, CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, diff --git a/exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml b/exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml index fd3ff0a2d..a46bf2d56 100644 --- a/exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml +++ b/exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml @@ -115,11 +115,11 @@ analysis: GNOMAD_G_OTH, GNOMAD_G_SAS ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP ] #this is the standard exomiser order. #all steps are optional steps: [ @@ -131,17 +131,17 @@ analysis: # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF #intervalFilter: {bed: /full/path/to/bed_file.bed}, #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - #failedVariantFilter: {}, + failedVariantFilter: { }, #qualityFilter: {minQuality: 50.0}, - variantEffectFilter: { - remove: [ - FIVE_PRIME_UTR_EXON_VARIANT, - FIVE_PRIME_UTR_INTRON_VARIANT, - THREE_PRIME_UTR_EXON_VARIANT, - THREE_PRIME_UTR_INTRON_VARIANT, - NON_CODING_TRANSCRIPT_EXON_VARIANT, - UPSTREAM_GENE_VARIANT, - INTERGENIC_VARIANT, + variantEffectFilter: { + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + UPSTREAM_GENE_VARIANT, + INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT, CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, diff --git a/exomiser-cli/src/test/resources/pfeiffer-job-sample.yml b/exomiser-cli/src/test/resources/pfeiffer-job-sample.yml index bad03eeb7..5c9b1a412 100644 --- a/exomiser-cli/src/test/resources/pfeiffer-job-sample.yml +++ b/exomiser-cli/src/test/resources/pfeiffer-job-sample.yml @@ -83,11 +83,11 @@ analysis: GNOMAD_G_OTH, GNOMAD_G_SAS ] - #Possible pathogenicitySources: POLYPHEN, MUTATION_TASTER, SIFT, CADD, REMM - #REMM is trained on non-coding regulatory regions - #*WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files - #and updated their location in the application.properties. Exomiser will not run without this. - pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT] + # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM + # REMM is trained on non-coding regulatory regions + # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files + # and updated their location in the application.properties. Exomiser will not run without this. + pathogenicitySources: [ REVEL, MVP ] #this is the standard exomiser order. #all steps are optional steps: [ @@ -99,17 +99,17 @@ analysis: # or using a BED file - NOTE this should be 0-based, Exomiser otherwise uses 1-based coordinates in line with VCF #intervalFilter: {bed: /full/path/to/bed_file.bed}, #genePanelFilter: {geneSymbols: ['FGFR1','FGFR2']}, - #failedVariantFilter: {}, + failedVariantFilter: { }, #qualityFilter: {minQuality: 50.0}, - variantEffectFilter: { - remove: [ - FIVE_PRIME_UTR_EXON_VARIANT, - FIVE_PRIME_UTR_INTRON_VARIANT, - THREE_PRIME_UTR_EXON_VARIANT, - THREE_PRIME_UTR_INTRON_VARIANT, - NON_CODING_TRANSCRIPT_EXON_VARIANT, - UPSTREAM_GENE_VARIANT, - INTERGENIC_VARIANT, + variantEffectFilter: { + remove: [ + FIVE_PRIME_UTR_EXON_VARIANT, + FIVE_PRIME_UTR_INTRON_VARIANT, + THREE_PRIME_UTR_EXON_VARIANT, + THREE_PRIME_UTR_INTRON_VARIANT, + NON_CODING_TRANSCRIPT_EXON_VARIANT, + UPSTREAM_GENE_VARIANT, + INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT, CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, diff --git a/exomiser-core/CHANGELOG.md b/exomiser-core/CHANGELOG.md index 5a1b8b63c..92462de53 100644 --- a/exomiser-core/CHANGELOG.md +++ b/exomiser-core/CHANGELOG.md @@ -1,5 +1,48 @@ # The Exomiser - Core Library Changelog +## 13.1.0 2022-07-29 + +The three new features for this release is the autoated ACMG classification of small sequence variants, calculating +p-values for the combined scores and providing new and more interpretable TSV and VCF output files. + +- Added new automated ACMG annotations for top-scoring variants in known disease-causing genes. +- Added new combined score p-value +- Added new TSV_GENE, TSV_VARIANT and VCF output files containing ranked genes/variants for all the assessed modes of + inheritance. Note that __these new file formats will supersede the existing individual MOI-specific TSV/VCF files which + will be removed in the next major release__. See the [online documentation](https://exomiser.readthedocs.io/en/latest/result_interpretation.html) for details. +- New update online documentation! See https://exomiser.readthedocs.io/en/latest/ + +API breaking changes: + +- None + +New APIs: + +- New `Analysis.getMainPrioritiser()` +- New `AnalysisStep.isGenePrioritiser()` +- New `Gene.getAssociatedDiseases()` method +- New `Gene.getCompatibleGeneScores()` +- New `Gene.pValue()` and `GeneScore.pValue()` methods +- New `CombinedScorePvalueCalculator` class +- New `acmg` package +- New `GeneScore.getAcmgAssignments()` +- New `GeneScore.Builder.acmgAssignments()` and `pValue()` setters +- New `TranscriptAnnotation.rank()`, `getRankTotal()` and `getRankType()` for intron/exon numbering of variant position. +- New `ExomiserConfigReporter` class for logging startup configuration +- New `OutputSettings.applyOutputSettings()` +- New `GeneScoreRanker` to help with new output writers +- New `TsvGeneAllMoiResultsWriter` +- New `TsvVariantAllMoiResultsWriter` +- New `VcfAllMoiResultsWriter` + + +Other changes: +- Updated Spring Boot to version 2.6.9 +- Added automated docker build for CLI and web +- Update HtmlResultsWriter to detect transcript data source +- Fix broken StringDB links in HTML output + + ## 13.0.0 2021-09-21 This release is primarily focussed on enabling simultaneous prioritisation of structural and non-structural variation diff --git a/exomiser-core/pom.xml b/exomiser-core/pom.xml index 2bc6b9006..a103a1a81 100644 --- a/exomiser-core/pom.xml +++ b/exomiser-core/pom.xml @@ -30,7 +30,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java index 2cfc69bfb..0f3ecc475 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java @@ -34,15 +34,13 @@ import java.nio.file.Path; import java.time.Duration; import java.time.Instant; -import java.util.ArrayList; -import java.util.Collections; -import java.util.List; -import java.util.Map; +import java.util.*; import java.util.concurrent.atomic.AtomicInteger; import java.util.function.Consumer; import java.util.function.Function; import java.util.function.Predicate; import java.util.function.UnaryOperator; +import java.util.stream.Collectors; import java.util.stream.Stream; import static java.util.stream.Collectors.toConcurrentMap; @@ -60,7 +58,7 @@ abstract class AbstractAnalysisRunner implements AnalysisRunner { protected final VariantFilterRunner variantFilterRunner; private final GeneFilterRunner geneFilterRunner; - public AbstractAnalysisRunner(GenomeAnalysisService genomeAnalysisService, VariantFilterRunner variantFilterRunner, GeneFilterRunner geneFilterRunner) { + protected AbstractAnalysisRunner(GenomeAnalysisService genomeAnalysisService, VariantFilterRunner variantFilterRunner, GeneFilterRunner geneFilterRunner) { this.genomeAnalysisService = genomeAnalysisService; this.variantFilterRunner = variantFilterRunner; @@ -141,16 +139,13 @@ public AnalysisResults run(Sample sample, Analysis analysis) { } logger.info("Scoring genes"); - List genes; - List variants; - GeneScorer geneScorer = new RawScoreGeneScorer(probandIdentifier, sample.getSex(), inheritanceModeAnnotator); - if (variantsLoaded) { - genes = geneScorer.scoreGenes(getGenesWithVariants(allGenes)); - variants = getFinalVariantList(variantEvaluations); - } else { - genes = geneScorer.scoreGenes(new ArrayList<>(allGenes.values())); - variants = Collections.emptyList(); - } + List genesToScore = variantsLoaded ? getGenesWithVariants(allGenes) : List.copyOf(allGenes.values()); + // Temporarily add a new PValueGeneScorer so as not to break semver will revert to RawScoreGeneScorer in 14.0.0 + CombinedScorePvalueCalculator combinedScorePvalueCalculator = buildCombinedScorePvalueCalculator(sample, analysis, genesToScore.size()); + GeneScorer geneScorer = new PvalueGeneScorer(probandIdentifier, sample.getSex(), inheritanceModeAnnotator, combinedScorePvalueCalculator); + + List genes = geneScorer.scoreGenes(genesToScore); + List variants = variantsLoaded ? getFinalVariantList(variantEvaluations) : List.of(); logger.info("Analysed {} genes containing {} filtered variants", genes.size(), variants.size()); @@ -170,6 +165,13 @@ public AnalysisResults run(Sample sample, Analysis analysis) { return analysisResults; } + private CombinedScorePvalueCalculator buildCombinedScorePvalueCalculator(Sample sample, Analysis analysis, int numFilteredGenes) { + var prioritiser = analysis.getMainPrioritiser(); + List knownGenes = genomeAnalysisService.getKnownGenes(); + int bootStrapValue = 2_000; + return prioritiser == null ? CombinedScorePvalueCalculator.withRandomScores(bootStrapValue, knownGenes.size(), numFilteredGenes) : CombinedScorePvalueCalculator.of(bootStrapValue, prioritiser, sample.getHpoIds(), knownGenes, numFilteredGenes); + } + /** * @return a map of genes indexed by gene symbol. */ @@ -185,16 +187,20 @@ private List loadAndFilterVariants(VariantFactory variantFact List filteredVariants; VariantLogger variantLogger = new VariantLogger(); + + // this can be done using parallel which dramatically reduces runtime at the expense of RAM and + // inability to scale past one job running on one machine try (Stream variantStream = variantFactory.createVariantEvaluations()) { - filteredVariants = variantStream - .peek(variantLogger.logLoadedAndPassedVariants()) - .filter(isObservedInProband(probandIdentifier)) - .map(geneReassigner::reassignRegulatoryAndNonCodingVariantAnnotations) - .map(flagWhiteListedVariants()) - .filter(isAssociatedWithKnownGene(allGenes)) - .filter(runVariantFilters(variantFilters, filterStats)) - .peek(variantLogger.countPassedVariant()) - .collect(toList()); + filteredVariants = variantStream +// .parallel() + .peek(variantLogger.logLoadedAndPassedVariants()) + .filter(isObservedInProband(probandIdentifier)) + .map(geneReassigner::reassignRegulatoryAndNonCodingVariantAnnotations) + .map(flagWhiteListedVariants()) + .filter(isAssociatedWithKnownGene(allGenes)) + .filter(runVariantFilters(variantFilters, filterStats)) + .peek(variantLogger.countPassedVariant()) + .collect(toList()); } variantLogger.logResults(); return filteredVariants; @@ -287,7 +293,7 @@ private void assignVariantsToGenes(List variantEvaluations, M * @return */ protected List getGenesWithVariants(Map allGenes) { - return allGenes.values().stream().filter(Gene::hasVariants).collect(toList()); + return allGenes.values().stream().filter(Gene::hasVariants).collect(Collectors.toUnmodifiableList()); } abstract List getFinalVariantList(List variants); diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/Analysis.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/Analysis.java index 25e96bc71..b1b852710 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/Analysis.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/Analysis.java @@ -36,12 +36,14 @@ import org.monarchinitiative.exomiser.core.analysis.util.InheritanceModeOptions; import org.monarchinitiative.exomiser.core.model.frequency.FrequencySource; import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource; +import org.monarchinitiative.exomiser.core.prioritisers.OmimPriority; import org.monarchinitiative.exomiser.core.prioritisers.Prioritiser; import org.monarchinitiative.exomiser.core.prioritisers.PriorityResult; import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import javax.annotation.Nullable; import java.util.*; /** @@ -110,6 +112,17 @@ public PriorityType getMainPrioritiserType() { return PriorityType.NONE; } + @JsonIgnore + @Nullable + public Prioritiser getMainPrioritiser() { + for (AnalysisStep analysisStep : analysisSteps) { + if (analysisStep instanceof Prioritiser && !(analysisStep instanceof OmimPriority)) { + return (Prioritiser) analysisStep; + } + } + return null; + } + /** * Returns a new builder instance for creating Analysis objects. *CAUTION* It is strongly advisable to create Analysis * objects using the {@link AnalysisBuilder} objects created with the {@link AnalysisFactory}. This will ensure the diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStep.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStep.java index 29cec9b6c..1f2106e77 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStep.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStep.java @@ -47,6 +47,11 @@ default boolean isVariantFilter() { return this instanceof VariantFilter; } + @JsonIgnore + default boolean isGenePrioritiser() { + return this instanceof Prioritiser; + } + @JsonIgnore default boolean isOnlyGeneDependent() { if (isInheritanceModeDependent()) { diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/PassOnlyAnalysisRunner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/PassOnlyAnalysisRunner.java index 8d3378b62..152d65821 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/PassOnlyAnalysisRunner.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/PassOnlyAnalysisRunner.java @@ -32,8 +32,7 @@ import java.util.Map; import java.util.function.Predicate; import java.util.function.UnaryOperator; - -import static java.util.stream.Collectors.toList; +import java.util.stream.Collectors; /** * @since 7.0.0 @@ -73,10 +72,10 @@ protected Predicate runVariantFilters(List var protected List getGenesWithVariants(Map allGenes) { return allGenes.values() .stream() + .map(removeFailedVariants()) .filter(Gene::hasVariants) .filter(Gene::passedFilters) - .map(removeFailedVariants()) - .collect(toList()); + .collect(Collectors.toUnmodifiableList()); } private UnaryOperator removeFailedVariants() { @@ -94,6 +93,6 @@ private Predicate variantFailedFilters() { protected List getFinalVariantList(List variants) { return variants.stream() .filter(VariantEvaluation::passedFilters) - .collect(toList()); + .collect(Collectors.toUnmodifiableList()); } } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/SimpleAnalysisRunner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/SimpleAnalysisRunner.java index 684fe0d7b..9b9b7fe76 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/SimpleAnalysisRunner.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/SimpleAnalysisRunner.java @@ -62,6 +62,6 @@ protected Predicate runVariantFilters(List var @Override protected List getFinalVariantList(List variants) { - return variants; + return List.copyOf(variants); } } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/sample/AgeRange.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/sample/AgeRange.java new file mode 100644 index 000000000..33e23b1b0 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/sample/AgeRange.java @@ -0,0 +1,74 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.sample; + +import java.util.Objects; + +/** + * @author Jules Jacobsen + */ +public class AgeRange { + + private final Age lower; + private final Age upper; + + private AgeRange(Age lower, Age upper) { + this.lower = lower; + this.upper = upper; + } + + public static AgeRange between(Age lower, Age upper) { + if (lower.toPeriod().toTotalMonths() > upper.toPeriod().toTotalMonths()) { + throw new IllegalArgumentException("Upper age limit must be greater than lower"); + } + return new AgeRange(lower, upper); + } + + public static AgeRange over(Age limit) { + return new AgeRange(limit, Age.unknown()); + } + + public static AgeRange under(Age limit) { + return new AgeRange(Age.unknown(), limit); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (!(o instanceof AgeRange)) return false; + AgeRange ageRange = (AgeRange) o; + return lower.equals(ageRange.lower) && + upper.equals(ageRange.upper); + } + + @Override + public int hashCode() { + return Objects.hash(lower, upper); + } + + @Override + public String toString() { + return "AgeRange{" + + "lower=" + lower + + ", upper=" + upper + + '}'; + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/sample/Onset.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/sample/Onset.java new file mode 100644 index 000000000..8b2815c4b --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/sample/Onset.java @@ -0,0 +1,87 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.sample; + +import java.util.Objects; + +/** + * Class representing the HPO term HP:0003674 (Onset) and its child terms. + * + * @author Jules Jacobsen + */ +public enum Onset { + + // Root term of Onset branch + // The age group in which disease manifestations appear. + ONSET("HP:0003674", "Onset", AgeRange.under(Age.of(0, 0, 0))), + + // Onset prior to birth. + ANTENATAL("HP:0030674", "Antenatal onset", AgeRange.under(Age.of(0, 0, 0))), + // Onset of disease at up to 8 weeks of gestation. + EMBRYONAL("HP:0011460", "Embryonal onset", AgeRange.under(Age.gestational(8, 0))), + // Onset prior to birth but after 8 weeks of gestation. + FETAL("HP:0011461", "Fetal onset", AgeRange.over(Age.gestational(8, 0))), + + // A phenotypic abnormality that is present at birth. + CONGENITAL("HP:0003577", "Congenital onset", AgeRange.under(Age.of(0, 0, 0))), + // Onset of signs or symptoms of disease within the first 28 days of life. + NEONATAL("HP:0003623", "Neonatal onset", AgeRange.under(Age.of(0, 0, 28))), + // TODO Check what is 1M ? 31D or 28D? there could be a bug here - check other offsets too and consider using + // overlapping terms if within a period +/- x of a boundary e.g. Neonatal and Infantile for 26D or 1M3D + // Onset of disease manifestations before adulthood, defined here as before the age of 16 years, but excluding neonatal or congenital onset. + PEDIATRIC("HP:0410280", "Pediatric onset", AgeRange.between(Age.of(0, 1, 0), Age.of(16, 0, 0))), + // Onset of signs or symptoms of disease between 28 days to one year of life. + INFANTILE("HP:0003593", "Infantile onset", AgeRange.between(Age.of(0, 1, 0), Age.of(1, 0, 0))), + // Onset of disease at the age of between 1 and 5 years. + CHILDHOOD("HP:0011463", "Childhood onset", AgeRange.between(Age.of(1, 1, 0), Age.of(5, 0, 0))), + // Onset of signs or symptoms of disease between the age of 5 and 15 years. + JUVENILE("HP:0003621", "Juvenile onset", AgeRange.between(Age.of(5, 1, 0), Age.of(15, 11, 0))), + + //Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later. + ADULT("HP:0003581", "Adult onset", AgeRange.over(Age.of(16, 0, 0))), + // Onset of disease at the age of between 16 and 40 years. + YOUNG_ADULT("HP:0011462", "Young adult onset", AgeRange.between(Age.of(16, 0, 0), Age.of(40, 0, 0))), + // A type of adult onset with onset of symptoms at the age of 40 to 60 years. + MIDDLE_AGE("HP:0003596", "Middle age onset", AgeRange.between(Age.of(40, 1, 0), Age.of(59, 11, 0))), + // A type of adult onset with onset of symptoms after the age of 60 years., + LATE("HP:0003584", "Late onset", AgeRange.over(Age.of(60, 0, 0))); + + private final String id; + private final String label; + private final AgeRange ageRange; + + Onset(String id, String label, AgeRange ageRange) { + this.id = id; + this.label = label; + this.ageRange = ageRange; + } + + public Onset parseHpoId(String hpoId) { + Objects.requireNonNull(hpoId); + for (Onset onset : Onset.values()) { + if (onset.id.equalsIgnoreCase(hpoId)) { + return onset; + } + } + return Onset.ONSET; + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/CombinedScorePvalueCalculator.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/CombinedScorePvalueCalculator.java new file mode 100644 index 000000000..8f17c4425 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/CombinedScorePvalueCalculator.java @@ -0,0 +1,93 @@ +package org.monarchinitiative.exomiser.core.analysis.util; + +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.prioritisers.Prioritiser; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; +import java.util.concurrent.ThreadLocalRandom; + +/** + * @since 13.1.0 + */ +public class CombinedScorePvalueCalculator { + + private static final Logger logger = LoggerFactory.getLogger(CombinedScorePvalueCalculator.class); + + private final int bootStrapValue; + private final int numFilteredGenes; + + private final double[] phenoScoreCache; + private final int phenoScoreCacheSize; + private final Set priorityTypes; + + CombinedScorePvalueCalculator(int bootStrapValue, PriorityType prioritiserType, double[] phenoScoreCache, int numFilteredGenes) { + this.bootStrapValue = bootStrapValue; + this.phenoScoreCache = phenoScoreCache; + this.phenoScoreCacheSize = phenoScoreCache.length; + this.priorityTypes = Set.of(prioritiserType); + this.numFilteredGenes = numFilteredGenes; + } + + /** + * Creates a {@link CombinedScorePvalueCalculator} with a randomly generated set of phenotype scores - the size of + * which is specified by the user. + * @param bootStrapValue number of iterations of the bootstrap process. + * @param numScores number of scores to randomly generate + * @return a {@link CombinedScorePvalueCalculator} instance + * @since 13.1.0 + */ + public static CombinedScorePvalueCalculator withRandomScores(int bootStrapValue, long numScores, int numFilteredGenes) { + logger.info("Setting up phenotype score cache on {} random scores", numScores); + var phenoScoreCache = ThreadLocalRandom.current().doubles(numScores).toArray(); + return new CombinedScorePvalueCalculator(bootStrapValue, PriorityType.NONE, phenoScoreCache, numFilteredGenes); + } + + public static CombinedScorePvalueCalculator of(int bootStrapValue, Prioritiser prioritiser, List sampleHpoIds, List unscoredGenes, int numFilteredGenes) { + Objects.requireNonNull(prioritiser); + Objects.requireNonNull(sampleHpoIds); + Objects.requireNonNull(unscoredGenes); + logger.info("Setting up phenotype score cache on {} genes", unscoredGenes.size()); + var phenoScoreCache = generatePhenoScoreCache(prioritiser, sampleHpoIds, unscoredGenes); + logger.info("Bootstrapping combined scores for {} filtered genes (bootstrap value = {})", numFilteredGenes, bootStrapValue); + return new CombinedScorePvalueCalculator(bootStrapValue, prioritiser.getPriorityType(), phenoScoreCache, numFilteredGenes); + } + + private static double[] generatePhenoScoreCache(Prioritiser prioritiser, List hpoIds, List genes) { + prioritiser.prioritizeGenes(hpoIds, genes); + PriorityType priorityType = prioritiser.getPriorityType(); + return genes.stream() + .mapToDouble(gene -> { + PriorityResult priorityResult = gene.getPriorityResult(priorityType); + if (priorityResult != null) { + return priorityResult.getScore(); + } + return 0.0; + }) + .toArray(); + } + + double calculatePvalueFromCombinedScore(double combinedScore) { + if (combinedScore == 0 || phenoScoreCacheSize == 0) { + return 1d; + } + int numHigherScores = 1; + for (int i = 0; i < bootStrapValue; ++i) { + for (int j = 0; j < numFilteredGenes; j++) { + int index = ThreadLocalRandom.current().nextInt(phenoScoreCacheSize); + double randomPhenoScore = phenoScoreCache[index]; + double randomVariantScore = ThreadLocalRandom.current().nextDouble(); + double randomCombined = GeneScorer.calculateCombinedScore(randomVariantScore, randomPhenoScore, priorityTypes); + if (randomCombined >= combinedScore) { + ++numHigherScores; + } + } + } + + return (double) numHigherScores / (bootStrapValue * numFilteredGenes); + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraint.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraint.java new file mode 100644 index 000000000..7e4ad7adc --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraint.java @@ -0,0 +1,122 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util; + +import java.util.Objects; + +// pLI (probability of being loss-of-function intolerant) +// pLI scores closer to one indicate more intolerance to protein-truncating variation. For a set of transcripts +// intolerant of protein-truncating variation, we suggest pLI ≥ 0.9. + +// Observed / expected (oe) +// The constraint score shown in gnomAD is the ratio of the observed / expected (oe) number of loss-of-function variants in that gene. +// The expected counts are based on a mutational model that takes sequence context, coverage and methylation into account. +// Interpretation +// Observed/expected (oe) is a continuous measure of how tolerant a gene is to a certain class of variation (e.g. loss-of-function). +// When a gene has a low oe value, it is under stronger selection for that class of variation than a gene with a higher value. +// Because counts depend on gene size and sample size, the precision of the oe values varies a lot from one gene to the next. +// Therefore in addition to the oe value, we also display the 90% confidence interval (CI) for each of the oe values. +// When evaluating how constrained a gene is, it is essential to take the 90% CI into consideration. +// Although oe is a continuous value, we understand that it can be useful to use a threshold for certain applications. +// In particular, for the interpretation of Mendelian diseases cases, we suggest using the upper bound of the oe CI < 0.35 as a threshold if needed. +// Again, ideally oe should be used as a continuous value rather than a cutoff and evaluating the oe 90% CI is a must. +/** + * @since 13.1.0 + */ +public class GeneConstraint { + + private final String geneSymbol; + private final String transcriptId; + private final double pLI; + private final double loeuf; + private final double loeufLower; + private final double loeufUpper; + + public GeneConstraint(String geneSymbol, String transcriptId, double pLI, double loeuf, double loeufLower, double loeufUpper) { + this.geneSymbol = geneSymbol; + this.transcriptId = transcriptId; + this.pLI = pLI; + this.loeuf = loeuf; + this.loeufLower = loeufLower; + this.loeufUpper = loeufUpper; + } + + public String geneSymbol() { + return geneSymbol; + } + + public String transcriptId() { + return transcriptId; + } + + public double pLI() { + return pLI; + } + + public double loeuf() { + return loeuf; + } + + public double loeufLower() { + return loeufLower; + } + + public double loeufUpper() { + return loeufUpper; + } + + /** + * For the interpretation of Mendelian diseases cases, we suggest using the upper bound of the oe CI < 0.35 as a threshold if needed. + * + * @return true if the loeufUpper is less than 0.35 + */ + public boolean isLossOfFunctionIntolerant() { + //gnomAD suggest using a loeufUpper < 0.35; + // However varsome suggests a relaxed metric has better recall due to lower FP. + // https://varsome.com/about/resources/acmg-implementation/#pvs1 + return loeuf < 0.7635; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + GeneConstraint that = (GeneConstraint) o; + return Double.compare(that.pLI, pLI) == 0 && Double.compare(that.loeuf, loeuf) == 0 && Double.compare(that.loeufLower, loeufLower) == 0 && Double.compare(that.loeufUpper, loeufUpper) == 0 && geneSymbol.equals(that.geneSymbol) && transcriptId.equals(that.transcriptId); + } + + @Override + public int hashCode() { + return Objects.hash(geneSymbol, transcriptId, pLI, loeuf, loeufLower, loeufUpper); + } + + @Override + public String toString() { + return "GeneContraint{" + + "geneSymbol='" + geneSymbol + '\'' + + ", transcriptId='" + transcriptId + '\'' + + ", pLI=" + pLI + + ", loeuf=" + loeuf + + ", loeufLower=" + loeufLower + + ", loeufUpper=" + loeufUpper + + '}'; + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraints.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraints.java new file mode 100644 index 000000000..eb6a45068 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraints.java @@ -0,0 +1,110 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util; + +import javax.annotation.Nullable; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Optional; + +/** + * @since 13.1.0 + */ +public class GeneConstraints { + + private static final Map geneConstraints = GnomadGeneConstraintParser.readGeneConstraints("gnomad.v2.1.1.gene-constraints.tsv"); + + private GeneConstraints() { + } + + @Nullable + public static GeneConstraint geneContraint(String geneSymbol) { + return geneConstraints.get(geneSymbol); + } + + private static class GnomadGeneConstraintParser { + + private static Map readGeneConstraints(String constraintsFile) { + Map geneConstraints = new LinkedHashMap<>(); + // #gene transcript pLI oe_lof oe_lof_lower oe_lof_upper + try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(getResourceAsStream(constraintsFile)))) { + for (String line; (line = bufferedReader.readLine()) != null; ) { + if (!line.startsWith("#")) { + GeneConstraint geneContraint = parseGeneConstraint(line); + if (!Double.isNaN(geneContraint.loeufUpper())) { + geneConstraints.put(geneContraint.geneSymbol(), geneContraint); + } + } + } + } catch (IOException e) { + e.printStackTrace(); + } + return Collections.unmodifiableMap(geneConstraints); + } + + private static GeneConstraint parseGeneConstraint(String line) { + String[] fields = line.split("\t"); + String geneSymbol = fields[0]; + String transcriptId = fields[1]; + double pLI = parseDouble(fields[2]); + double loeuf = parseDouble(fields[3]); + double loeufLower = parseDouble(fields[4]); + double loeufUpper = parseDouble(fields[5]); + return new GeneConstraint(geneSymbol, transcriptId, pLI, loeuf, loeufLower, loeufUpper); + } + + private static double parseDouble(String field) { + try { + return Double.parseDouble(field); + } catch (NumberFormatException e) { + // swallow + } + return Double.NaN; + } + + private static InputStream getResourceAsStream(String path) { + InputStream localResourceStream = GnomadGeneConstraintParser.class.getClassLoader().getResourceAsStream(path); + if (localResourceStream != null) { + return localResourceStream; + } + localResourceStream = ClassLoader.getSystemClassLoader().getResourceAsStream(path); + if (localResourceStream != null) { + return localResourceStream; + } + // load from the module path + Optional moduleOptional = ModuleLayer.boot().findModule("org.monarchitiative.exomiser"); + if (moduleOptional.isPresent()) { + Module module = moduleOptional.get(); + try { + return module.getResourceAsStream(path); + } catch (IOException e) { + // swallow and fall through + } + } + throw new IllegalStateException("Unable to load resource " + path); + } + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneScorer.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneScorer.java index 9a53d34f4..e6d2ebf9f 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneScorer.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/GeneScorer.java @@ -27,9 +27,11 @@ import org.monarchinitiative.exomiser.core.model.Gene; import org.monarchinitiative.exomiser.core.model.GeneScore; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; import java.util.Collections; import java.util.List; +import java.util.Set; import java.util.function.Function; /** @@ -51,4 +53,29 @@ default List scoreGenes(List genes) { Collections.sort(genes); return genes; } + + static double calculateCombinedScore(double variantScore, double priorityScore, Set prioritiesRun) { + if (variantScore == 0.0 && priorityScore == 0.0) { + return 0.0; + } else if (prioritiesRun.contains(PriorityType.HIPHIVE_PRIORITY)) { + return hiPhiveLogitScore(variantScore, priorityScore); + } else if (prioritiesRun.contains(PriorityType.EXOMEWALKER_PRIORITY)) { + return walkerLogitScore(variantScore, priorityScore); + } else if (prioritiesRun.contains(PriorityType.PHENIX_PRIORITY)) { + return phenixLogitScore(variantScore, priorityScore); + } + return (priorityScore + variantScore) / 2.0; + } + + private static double hiPhiveLogitScore(double variantScore, double priorityScore) { + return 1.0 / (1.0 + Math.exp(-(-13.28813 + 10.39451 * priorityScore + 9.18381 * variantScore))); + } + + private static double walkerLogitScore(double variantScore, double priorityScore) { + return 1.0 / (1.0 + Math.exp(-(-8.67972 + 219.40082 * priorityScore + 8.54374 * variantScore))); + } + + private static double phenixLogitScore(double variantScore, double priorityScore) { + return 1.0 / (1.0 + Math.exp(-(-11.15659 + 13.21835 * priorityScore + 4.08667 * variantScore))); + } } \ No newline at end of file diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/InheritanceModeAnnotator.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/InheritanceModeAnnotator.java index 8e5088bc7..da9c862d0 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/InheritanceModeAnnotator.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/InheritanceModeAnnotator.java @@ -152,6 +152,8 @@ private List getCompatibleVariantsUnderFrequencyThreshold(Lis FrequencyData frequencyData = variantEvaluation.getFrequencyData(); if (frequencyData.getMaxFreq() <= maxFreqForMode || variantEvaluation.isWhiteListed()) { compatibleVariants.add(variantEvaluation); + } else { + logger.debug("FAIL variant freq {} >= {} (maxFreq for MOI) {}", frequencyData.getMaxFreq(), maxFreqForMode, variantEvaluation); } } return compatibleVariants; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/PvalueGeneScorer.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/PvalueGeneScorer.java new file mode 100644 index 000000000..e0e1866ca --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/PvalueGeneScorer.java @@ -0,0 +1,133 @@ +package org.monarchinitiative.exomiser.core.analysis.util; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.*; +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.model.GeneScore; +import org.monarchinitiative.exomiser.core.model.Pedigree; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; + +/** + * @since 13.1.0 + */ +public class PvalueGeneScorer implements GeneScorer { + + private static final Logger logger = LoggerFactory.getLogger(PvalueGeneScorer.class); + private static final EnumSet JUST_ANY = EnumSet.of(ModeOfInheritance.ANY); + + private final Set inheritanceModes; + + private final ContributingAlleleCalculator contributingAlleleCalculator; + private final GenePriorityScoreCalculator genePriorityScoreCalculator; + private final CombinedScorePvalueCalculator pValueCalculator; + private final AcmgAssignmentCalculator acmgAssignmentCalculator; + + /** + * @param probandId Sample id of the proband in the VCF. + * @param inheritanceModeAnnotator An {@code InheritanceModeAnnotator} for the pedigree related to the proband. + * @throws NullPointerException if any input arguments are null. + * @since 10.0.0 + */ + public PvalueGeneScorer(String probandId, Pedigree.Individual.Sex probandSex, InheritanceModeAnnotator inheritanceModeAnnotator, CombinedScorePvalueCalculator pValueCalculator) { + Objects.requireNonNull(probandId); + Objects.requireNonNull(inheritanceModeAnnotator); + this.inheritanceModes = inheritanceModeAnnotator.getDefinedModes(); + this.contributingAlleleCalculator = new ContributingAlleleCalculator(probandId, probandSex, inheritanceModeAnnotator); + this.genePriorityScoreCalculator = new GenePriorityScoreCalculator(); + this.pValueCalculator = Objects.requireNonNull(pValueCalculator); + AcmgEvidenceAssigner acmgEvidenceAssigner = new Acmg2015EvidenceAssigner(probandId, inheritanceModeAnnotator.getPedigree()); + AcmgEvidenceClassifier acmgEvidenceClassifier = new Acgs2020Classifier(); + this.acmgAssignmentCalculator = new AcmgAssignmentCalculator(acmgEvidenceAssigner, acmgEvidenceClassifier); + } + + @Override + public List scoreGenes(List genes) { + // TODO: v14.0.0 - return stream().toList() can't do this here as it breaks the sorting for the + // MOI-dependent writers. These will be removed in v14.0.0. + return genes.stream() + .parallel() + .map(gene -> { + List geneScores = scoreGene().apply(gene); + gene.addGeneScores(geneScores); + return gene; + }) + .sorted() + .collect(Collectors.toList()); + } + + /** + * Calculates the final ranks of all genes that have survived the filtering + * and prioritising steps. The strategy is that for autosomal dominant + * diseases, we take the single most pathogenic score of any variant + * affecting the gene; for autosomal recessive diseases, we take the mean of + * the two most pathogenic variants. X-linked diseases are filtered such + * that only X-chromosomal genes are left over, and the single worst variant + * is taken. + */ + @Override + public Function> scoreGene() { + return gene -> { + //Handle the scenario where no inheritance mode-dependent step was run + if (inheritanceModes.isEmpty() || inheritanceModes.equals(JUST_ANY)) { + GeneScore geneScore = calculateGeneScore(gene, ModeOfInheritance.ANY); + logger.debug("{}", geneScore); + return Collections.singletonList(geneScore); + } + + List geneScores = new ArrayList<>(inheritanceModes.size()); + for (ModeOfInheritance modeOfInheritance : inheritanceModes) { + GeneScore geneScore = calculateGeneScore(gene, modeOfInheritance); + logger.debug("{}", geneScore); + // IMPORTANT: Do not skip score without variants! + // A gene needs to have a score for each MOI as this will effect the overall ranks depending on the inheritance mode + // the phenotype score and how omim dealt with the inheritance mode compatibility for known diseases affecting that gene. + geneScores.add(geneScore); + } + return geneScores; + }; + } + + private GeneScore calculateGeneScore(Gene gene, ModeOfInheritance modeOfInheritance) { + //It is critical only the PASS variants are used in the scoring + List contributingVariants = contributingAlleleCalculator.findContributingVariantsForInheritanceMode(modeOfInheritance, gene.getPassedVariantEvaluations()); + + GenePriorityScoreCalculator.GenePriorityScore priorityScore = genePriorityScoreCalculator.calculateGenePriorityScore(gene, modeOfInheritance); + + double variantScore = contributingVariants.stream() + .mapToDouble(VariantEvaluation::getVariantScore) + .average() + .orElse(0); + + double combinedScore = GeneScorer.calculateCombinedScore(variantScore, priorityScore.getScore(), gene.getPriorityResults().keySet()); + + double pValue = pValueCalculator.calculatePvalueFromCombinedScore(combinedScore); + + List> compatibleDiseaseMatches = priorityScore.getCompatibleDiseaseMatches(); + + List acmgAssignments = acmgAssignmentCalculator.calculateAcmgAssignments(modeOfInheritance, gene, contributingVariants, compatibleDiseaseMatches); + + return GeneScore.builder() + .geneIdentifier(gene.getGeneIdentifier()) + .modeOfInheritance(modeOfInheritance) + .variantScore(variantScore) + .phenotypeScore(priorityScore.getScore()) + .combinedScore(combinedScore) + .pValue(pValue) + .contributingVariants(contributingVariants) + // TODO this would be a good place to put a contributingModel + // i.e. from HiPhivePrioritiserResult see issue #363 +// .contributingModel() + .compatibleDiseaseMatches(compatibleDiseaseMatches) + .acmgAssignments(acmgAssignments) + .build(); + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/RawScoreGeneScorer.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/RawScoreGeneScorer.java index 1077d2269..e4f1e8abe 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/RawScoreGeneScorer.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/RawScoreGeneScorer.java @@ -26,11 +26,13 @@ package org.monarchinitiative.exomiser.core.analysis.util; import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.*; import org.monarchinitiative.exomiser.core.model.Gene; import org.monarchinitiative.exomiser.core.model.GeneScore; import org.monarchinitiative.exomiser.core.model.Pedigree.Individual.Sex; import org.monarchinitiative.exomiser.core.model.VariantEvaluation; -import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -53,6 +55,8 @@ public class RawScoreGeneScorer implements GeneScorer { private final ContributingAlleleCalculator contributingAlleleCalculator; private final GenePriorityScoreCalculator genePriorityScoreCalculator; + private final AcmgAssignmentCalculator acmgAssignmentCalculator; + /** * @param probandId Sample id of the proband in the VCF. * @param inheritanceModeAnnotator An {@code InheritanceModeAnnotator} for the pedigree related to the proband. @@ -65,6 +69,19 @@ public RawScoreGeneScorer(String probandId, Sex probandSex, InheritanceModeAnnot this.inheritanceModes = inheritanceModeAnnotator.getDefinedModes(); this.contributingAlleleCalculator = new ContributingAlleleCalculator(probandId, probandSex, inheritanceModeAnnotator); this.genePriorityScoreCalculator = new GenePriorityScoreCalculator(); + AcmgEvidenceAssigner acmgEvidenceAssigner = new Acmg2015EvidenceAssigner(probandId, inheritanceModeAnnotator.getPedigree()); + AcmgEvidenceClassifier acmgEvidenceClassifier = new Acgs2020Classifier(); + this.acmgAssignmentCalculator = new AcmgAssignmentCalculator(acmgEvidenceAssigner, acmgEvidenceClassifier); + } + + @Override + public List scoreGenes(List genes) { + for (Gene gene : genes) { + List geneScores = scoreGene().apply(gene); + gene.addGeneScores(geneScores); + } + Collections.sort(genes); + return genes; } /** @@ -110,8 +127,11 @@ private GeneScore calculateGeneScore(Gene gene, ModeOfInheritance modeOfInherita .average() .orElse(0); - double combinedScore = calculateCombinedScore(variantScore, priorityScore.getScore(), gene.getPriorityResults() - .keySet()); + double combinedScore = GeneScorer.calculateCombinedScore(variantScore, priorityScore.getScore(), gene.getPriorityResults().keySet()); + + List> compatibleDiseaseMatches = priorityScore.getCompatibleDiseaseMatches(); + + List acmgAssignments = acmgAssignmentCalculator.calculateAcmgAssignments(modeOfInheritance, gene, contributingVariants, compatibleDiseaseMatches); return GeneScore.builder() .geneIdentifier(gene.getGeneIdentifier()) @@ -122,45 +142,10 @@ private GeneScore calculateGeneScore(Gene gene, ModeOfInheritance modeOfInherita .contributingVariants(contributingVariants) // TODO this would be a good place to put a contributingModel // i.e. from HiPhivePrioritiserResult see issue #363 - // TODO add in/ use pLOF Haploinsufficieny/Triplosensitivity scores here too? // .contributingModel() - .compatibleDiseaseMatches(priorityScore.getCompatibleDiseaseMatches()) + .compatibleDiseaseMatches(compatibleDiseaseMatches) + .acmgAssignments(acmgAssignments) .build(); } - /** - * Calculate the combined score of this gene based on the relevance of the - * gene (priorityScore) and the predicted effects of the variants - * (variantScore). - *

- * Note that this method assumes we have already calculated the filter and variant scores. - */ - private double calculateCombinedScore(double variantScore, double priorityScore, Set prioritiesRun) { - if (variantScore == 0 && priorityScore == 0) { - return 0; - } - // its possible that all of these could have been run, but we'll just take the first. Ideally there should be a - // check somewhere else in the system to prevent more than one prioritiser being run. - if (prioritiesRun.contains(PriorityType.HIPHIVE_PRIORITY)) { - return hiPhiveLogitScore(variantScore, priorityScore); - } else if (prioritiesRun.contains(PriorityType.EXOMEWALKER_PRIORITY)) { - return walkerLogitScore(variantScore, priorityScore); - } else if (prioritiesRun.contains(PriorityType.PHENIX_PRIORITY)) { - return phenixLogitScore(variantScore, priorityScore); - } - return (priorityScore + variantScore) / 2d; - } - - private double hiPhiveLogitScore(double variantScore, double priorityScore) { - return 1 / (1 + Math.exp(-(-13.28813 + 10.39451 * priorityScore + 9.18381 * variantScore))); - } - - private double walkerLogitScore(double variantScore, double priorityScore) { - //NB this is based on raw walker score - return 1 / (1 + Math.exp(-(-8.67972 + 219.40082 * priorityScore + 8.54374 * variantScore))); - } - - private double phenixLogitScore(double variantScore, double priorityScore) { - return 1 / (1 + Math.exp(-(-11.15659 + 13.21835 * priorityScore + 4.08667 * variantScore))); - } } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020Classifier.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020Classifier.java new file mode 100644 index 000000000..7c7746632 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020Classifier.java @@ -0,0 +1,104 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import java.util.ArrayList; +import java.util.List; + +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgClassification.*; + +/** + * Implementation of the ACGS v4 guidelines, Table 3 from + * https://www.acgs.uk.com/media/11631/uk-practice-guidelines-for-variant-classification-v4-01-2020.pdf + * + * @since 13.1.0 + */ +public final class Acgs2020Classifier implements AcmgEvidenceClassifier { + + public AcmgClassification classify(AcmgEvidence acmgEvidence) { + if (acmgEvidence == null || acmgEvidence.isEmpty()) { + return AcmgClassification.UNCERTAIN_SIGNIFICANCE; + } + + int pvs = acmgEvidence.pvs(); + int ps = acmgEvidence.ps(); + int pm = acmgEvidence.pm(); + int pp = acmgEvidence.pp(); + + int ba = acmgEvidence.ba(); + int bs = acmgEvidence.bs(); + int bp = acmgEvidence.bp(); + + return classifyCriteriaCounts(pvs, ps, pm, pp, ba, bs, bp); + } + + private static AcmgClassification classifyCriteriaCounts(int pvs, int ps, int pm, int pp, int ba, int bs, int bp) { + List classifications = new ArrayList<>(2); + // Table 3 of https://www.acgs.uk.com/media/11631/uk-practice-guidelines-for-variant-classification-v4-01-2020.pdf + if (isPathogenic(pvs, ps, pm, pp)) { + classifications.add(PATHOGENIC); + } else if (isLikelyPathogenic(pvs, ps, pm, pp)) { + classifications.add(LIKELY_PATHOGENIC); + } + + if (isBenign(ba, bs)) { + classifications.add(BENIGN); + } else if (isLikelyBenign(bs, bp)) { + classifications.add(LIKELY_BENIGN); + } + // Uncertain significance: + // (i) Other criteria shown above are not met OR + // (ii) the criteria for benign and pathogenic are contradictory + return classifications.size() != 1 ? UNCERTAIN_SIGNIFICANCE : classifications.get(0); + } + + private static boolean isPathogenic(int pvs, int ps, int pm, int pp) { + if (pvs >= 2 || pvs == 1 && (ps >= 1 || pm >= 1 || pp >= 2)) { + return true; + } + return ps >= 3 || ps == 2 && (pm >= 1 || pp >= 2) || ps == 1 && (pm >= 3 || (pm >= 2 && pp >= 2) || (pm >= 1 && pp >= 4)); + } + + private static boolean isLikelyPathogenic(int pvs, int ps, int pm, int pp) { + if (ps >= 2) { + return true; + } + if ((ps == 1 && (pm == 1 || pm == 2)) || (ps == 1 && pp >= 2)) { + return true; + } + // https://varsome.com/about/resources/acmg-implementation/#acmgverdict + // "Since we can only automate 3 of the 5 pathogenic supporting rules, we have also adjusted the verdict so that + // 1 Moderate + 3 Supporting Pathogenic rules is sufficient to trigger 'Likely Pathogenic' (the standard + // requires 1 Moderate + 4 Supporting)." + // standard ACMG guidelines require pm = 1 && pp >= 4 +// return pm >= 3 || pm == 2 && pp >= 2 || pm == 1 && pp >= 4; + return pm >= 3 || pm == 2 && pp >= 2 || pm == 1 && pp >= 3; + } + + private static boolean isBenign(int ba, int bs) { + return ba == 1 || bs >= 2; + } + + private static boolean isLikelyBenign(int bs, int bp) { + return bs == 1 && bp == 1 || bp >= 2; + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015Classifier.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015Classifier.java new file mode 100644 index 000000000..29671b8ea --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015Classifier.java @@ -0,0 +1,104 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import java.util.ArrayList; +import java.util.List; + +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgClassification.*; + +/** + * Implementation of the 2015 ACMG Standards guidelines for interpretation of sequence variants (Richards et al. doi:10.1038/gim.2015.30). + * Table 5 'Rules for combining criteria to classify sequence variants' + * + * @since 13.1.0 + */ +public final class Acmg2015Classifier implements AcmgEvidenceClassifier { + + public AcmgClassification classify(AcmgEvidence acmgEvidence) { + if (acmgEvidence == null || acmgEvidence.isEmpty()) { + return AcmgClassification.UNCERTAIN_SIGNIFICANCE; + } + + int pvs = acmgEvidence.pvs(); + int ps = acmgEvidence.ps(); + int pm = acmgEvidence.pm(); + int pp = acmgEvidence.pp(); + + int ba = acmgEvidence.ba(); + int bs = acmgEvidence.bs(); + int bp = acmgEvidence.bp(); + + return classifyCriteriaCounts(pvs, ps, pm, pp, ba, bs, bp); + } + + private static AcmgClassification classifyCriteriaCounts(int pvs, int ps, int pm, int pp, int ba, int bs, int bp) { + List classifications = new ArrayList<>(2); + // Table 5 of https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf + if (isPathogenic(pvs, ps, pm, pp)) { + classifications.add(PATHOGENIC); + } else if (isLikelyPathogenic(pvs, ps, pm, pp)) { + classifications.add(LIKELY_PATHOGENIC); + } + + if (isBenign(ba, bs)) { + classifications.add(BENIGN); + } else if (isLikelyBenign(bs, bp)) { + classifications.add(LIKELY_BENIGN); + } + // Uncertain significance: + // (i) Other criteria shown above are not met OR + // (ii) the criteria for benign and pathogenic are contradictory + return classifications.size() != 1 ? UNCERTAIN_SIGNIFICANCE : classifications.get(0); + } + + private static boolean isPathogenic(int pvs, int ps, int pm, int pp) { + if (pvs == 1 && (ps >= 1 || pm >= 2 || (pm == 1 && pp == 1) || pp >= 2)) { + return true; + } + return ps >= 2 || ps == 1 && (pm >= 3 || pm == 2 && pp >= 2 || pm == 1 && pp >= 4); + } + + private static boolean isLikelyPathogenic(int pvs, int ps, int pm, int pp) { + if (pvs == 1 && pm == 1) { + return true; + } + if (ps == 1 && (pm == 1 || pm == 2) || ps == 1 && pp >= 2) { + return true; + } + // https://varsome.com/about/resources/acmg-implementation/#acmgverdict + // "Since we can only automate 3 of the 5 pathogenic supporting rules, we have also adjusted the verdict so that + // 1 Moderate + 3 Supporting Pathogenic rules is sufficient to trigger 'Likely Pathogenic' (the standard + // requires 1 Moderate + 4 Supporting)." + // standard ACMG guidelines require pm = 1 && pp >= 4 +// return pm >= 3 || pm == 2 && pp >= 2 || pm == 1 && pp >= 4; + return pm >= 3 || pm == 2 && pp >= 2 || pm == 1 && pp >= 3; + } + + private static boolean isBenign(int ba, int bs) { + return ba == 1 || bs >= 2; + } + + private static boolean isLikelyBenign(int bs, int bp) { + return bs == 1 && bp == 1 || bp >= 2; + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java new file mode 100644 index 000000000..15f32e46e --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java @@ -0,0 +1,562 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import de.charite.compbio.jannovar.annotation.VariantEffect; +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.analysis.util.GeneConstraint; +import org.monarchinitiative.exomiser.core.analysis.util.GeneConstraints; +import org.monarchinitiative.exomiser.core.analysis.util.InheritanceModeAnalyser; +import org.monarchinitiative.exomiser.core.model.Pedigree; +import org.monarchinitiative.exomiser.core.model.Pedigree.Individual; +import org.monarchinitiative.exomiser.core.model.SampleGenotype; +import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.model.frequency.FrequencyData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.*; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; + +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.stream.Collectors; + +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.*; + +/** + * @since 13.1.0 + */ +public class Acmg2015EvidenceAssigner implements AcmgEvidenceAssigner { + + private final String probandId; + private final Individual.Sex probandSex; + private final Pedigree pedigree; + + public Acmg2015EvidenceAssigner(String probandId, Pedigree pedigree) { + this.probandId = Objects.requireNonNull(probandId); + this.pedigree = pedigree == null || pedigree.isEmpty() ? Pedigree.justProband(probandId) : pedigree; + Individual proband = this.pedigree.getIndividualById(probandId); + if (proband == null) { + throw new IllegalArgumentException("Proband '" + probandId + "' not found in pedigree " + pedigree); + } + this.probandSex = proband.getSex(); + } + + /** + * Assesses the provided {@link VariantEvaluation} against the ACMG criteria (Richards et al. 2015 doi:10.1038/gim.2015.30). + * This class will assign the criteria codes and evidence strength based on the current {@link ModeOfInheritance} + * being tested, the known diseases for this MOI, other contributing variants, the patients pedigree, and the phenotypic + * similarity of the patient to the compatible diseases. + * + * CAUTION! This method expects the variant evaluation to be compatible with the given mode of inheritance. This + * class is expected to be run downstream of an {@link InheritanceModeAnalyser} and accessed via the {@link AcmgAssignmentCalculator}. Failure to do this will result in + * incorrect assignments. + * + * @param variantEvaluation + * @param modeOfInheritance + * @param contributingVariants + * @param knownDiseases + * @param compatibleDiseaseMatches + * @return + */ + // https://www.ncbi.nlm.nih.gov/clinvar/variation/464/ - check in ClinVar VCF if there is MOI information for a classification + public AcmgEvidence assignVariantAcmgEvidence(VariantEvaluation variantEvaluation, ModeOfInheritance modeOfInheritance, List contributingVariants, List knownDiseases, List> compatibleDiseaseMatches) { + // try strict ACMG assignments only if there are known disease-gene associations + if (knownDiseases.isEmpty()) { + return AcmgEvidence.empty(); + } + + AcmgEvidence.Builder acmgEvidenceBuilder = AcmgEvidence.builder(); + + boolean hasCompatibleDiseaseMatches = !compatibleDiseaseMatches.isEmpty(); + + // PVS1 "null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease" + assignPVS1(acmgEvidenceBuilder, variantEvaluation, modeOfInheritance, knownDiseases); + + // PS1 "Same amino acid change as a previously established pathogenic variant regardless of nucleotide change" + // Should NOT assign for PS1 for same base change. Unable to assign PS1 due to lack of AA change info in database +// assignPS1(acmgEvidenceBuilder, variantEvaluation.getVariantEffect(), variantEvaluation.getPathogenicityData().getClinVarData()); + + if (pedigree.containsId(probandId)) { + Individual proband = pedigree.getIndividualById(probandId); + // PS2 "De novo (both maternity and paternity confirmed) in a patient with the disease and no family history" + assignPS2(acmgEvidenceBuilder, variantEvaluation, modeOfInheritance, contributingVariants, hasCompatibleDiseaseMatches, proband); + // PM6 "Assumed de novo, but without confirmation of paternity and maternity" +// assignPM6(acmgEvidenceBuilder, variantEvaluation, modeOfInheritance, contributingVariants, hasCompatibleDiseaseMatches); + // BS4 "Lack of segregation in affected members of a family" + assignBS4(acmgEvidenceBuilder, variantEvaluation, proband); + } + + FrequencyData frequencyData = variantEvaluation.getFrequencyData(); + // PM2 "Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium" + assignPM2(acmgEvidenceBuilder, frequencyData); + // BA1 "Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium" + assignBA1(acmgEvidenceBuilder, frequencyData); + + // PM3 "For recessive disorders, detected in trans with a pathogenic variant" + assignPM3orBP2(acmgEvidenceBuilder, variantEvaluation, modeOfInheritance, contributingVariants, hasCompatibleDiseaseMatches); + // PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants + assignPM4(acmgEvidenceBuilder, variantEvaluation); + // TODO: PM5 "Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before + + // PP4 "Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology" + assignPP4(acmgEvidenceBuilder, compatibleDiseaseMatches); + + PathogenicityData pathogenicityData = variantEvaluation.getPathogenicityData(); + ClinVarData clinVarData = variantEvaluation.getPathogenicityData().getClinVarData(); + if (!clinVarData.isEmpty()) { + // PP5 "Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation" + assignPP5(acmgEvidenceBuilder, clinVarData); + // BP6 "Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation" + assignBP6(acmgEvidenceBuilder, clinVarData); + } + // PP3 "Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)" + // BP4 "Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)" + // TODO: internalise in PathogenicityData and create proper cutoff values adding isPath/isbenign to PathogenicityScore + assignPP3orBP4(acmgEvidenceBuilder, pathogenicityData); + + return acmgEvidenceBuilder.build(); + } + + /** + * PVS1 "null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease" + */ + private void assignPVS1(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluation variantEvaluation, ModeOfInheritance modeOfInheritance, List knownDiseases) { + // TODO: add new method - gene.getAssociatedDiseases() + // also need ClinvarCache.getClinvarDataForGene(GeneIdentifier geneIdentifier) + + // Certain types of variants (e.g., nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single exon or multiexon + // deletion) can often be assumed to disrupt gene function by leading to a complete absence of the gene product by lack of tran- + // scription or nonsense-mediated decay of an altered transcript. One must, however, exercise caution when classifying these + // variants as pathogenic by considering the following principles: + // (i) When classifying such variants as pathogenic, one must ensure that null variants are a known mechanism of + // pathogenicity consistent with the established inheritance pattern for the disease. For example, there are genes for + // which only heterozygous missense variants cause disease and null variants are benign in a heterozygous state (e.g., + // many hypertrophic cardiomyopathy genes). A novel heterozygous nonsense variant in the MYH7 gene would + // not be considered pathogenic for dominant hypertrophic cardiomyopathy based solely on this evidence, whereas a + // novel heterozygous nonsense variant in the CFTR gene would likely be considered a recessive pathogenic variant. + // Caveats: + // • Beware of genes where LOF is not a known disease mechanism (e.g., GFAP, MYH7) + // • Use caution interpreting LOF variants at the extreme 3′ end of a gene + // • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact + // • Use caution in the presence of multiple transcripts + + GeneConstraint geneContraint = GeneConstraints.geneContraint(variantEvaluation.getGeneSymbol()); + // Should this be using the hasCompatibleDiseaseMatches variable? + boolean inGeneWithKnownDiseaseAssociations = !knownDiseases.isEmpty(); + if (inGeneWithKnownDiseaseAssociations && isLossOfFunctionEffect(variantEvaluation.getVariantEffect()) + && (modeOfInheritance == ModeOfInheritance.ANY + || compatibleWithRecessive(modeOfInheritance) + || compatibleWithDominant(modeOfInheritance) && (geneContraint != null && geneContraint.isLossOfFunctionIntolerant()) + ) + ) { + if (variantEvaluation.hasTranscriptAnnotations()) { + TranscriptAnnotation transcriptAnnotation = variantEvaluation.getTranscriptAnnotations().get(0); + if (predictedToLeadToNmd(transcriptAnnotation)) { + acmgEvidenceBuilder.add(PVS1); + } else { + // Not predicted to lead to NMD? Downgrade to STRONG + acmgEvidenceBuilder.add(PVS1, Evidence.STRONG); + } + } else { + // shouldn't happen that there are no transcript annotations, but just in case... + acmgEvidenceBuilder.add(PVS1, Evidence.STRONG); + } + } + } + + private boolean predictedToLeadToNmd(TranscriptAnnotation transcriptAnnotation) { + // predicted to lead to NMD if in last exon or last 50bp of penultimate exon, or in single exon transcript + boolean notInLastExon = transcriptAnnotation.getRank() < transcriptAnnotation.getRankTotal(); + boolean isSingleExonTranscript = transcriptAnnotation.getRankTotal() == 1; + return transcriptAnnotation.getRankType() == TranscriptAnnotation.RankType.EXON && (notInLastExon || isSingleExonTranscript); + } + + private boolean compatibleWithRecessive(ModeOfInheritance modeOfInheritance) { + if (modeOfInheritance == ModeOfInheritance.AUTOSOMAL_RECESSIVE) { + return true; + } + return probandSex == Individual.Sex.FEMALE && modeOfInheritance == ModeOfInheritance.X_RECESSIVE; + } + + private boolean compatibleWithDominant(ModeOfInheritance modeOfInheritance) { + if (modeOfInheritance == ModeOfInheritance.AUTOSOMAL_DOMINANT) { + return true; + } + if (probandSex == Individual.Sex.MALE && (modeOfInheritance == ModeOfInheritance.X_RECESSIVE || modeOfInheritance == ModeOfInheritance.X_DOMINANT)) { + return true; + } + return (probandSex == Individual.Sex.FEMALE || probandSex == Individual.Sex.UNKNOWN) && modeOfInheritance == ModeOfInheritance.X_DOMINANT; + } + + private boolean isLossOfFunctionEffect(VariantEffect variantEffect) { + return variantEffect == VariantEffect.INITIATOR_CODON_VARIANT + || variantEffect == VariantEffect.START_LOST + || variantEffect == VariantEffect.STOP_LOST + || variantEffect == VariantEffect.STOP_GAINED + || variantEffect == VariantEffect.FRAMESHIFT_ELONGATION + || variantEffect == VariantEffect.FRAMESHIFT_TRUNCATION + || variantEffect == VariantEffect.FRAMESHIFT_VARIANT + || variantEffect == VariantEffect.SPLICE_ACCEPTOR_VARIANT + || variantEffect == VariantEffect.SPLICE_DONOR_VARIANT + || variantEffect == VariantEffect.EXON_LOSS_VARIANT; + } + + /** + * PM3 "For recessive disorders, detected in trans with a pathogenic variant" + * Note: This requires testing of parents (or offspring) to determine phase + */ + private void assignPM3orBP2(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluation variantEvaluation, ModeOfInheritance modeOfInheritance, List contributingVariants, boolean hasCompatibleDiseaseMatches) { + if (hasCompatibleDiseaseMatches) { + SampleGenotype thisVariantGenotype = variantEvaluation.getSampleGenotype(probandId); + if (contributingVariants.size() >= 2 && contributingVariants.contains(variantEvaluation)) { + for (VariantEvaluation otherVariant : contributingVariants) { + SampleGenotype otherVariantGenotype = otherVariant.getSampleGenotype(probandId); + ClinVarData otherClinVarData = otherVariant.getPathogenicityData().getClinVarData(); + if (otherClinVarData.getPrimaryInterpretation() == ClinVarData.ClinSig.PATHOGENIC && !otherVariant.equals(variantEvaluation)) { + // X = this variant, P = other pathogenic variant + boolean inTrans = inTrans(thisVariantGenotype, otherVariantGenotype); + boolean inCis = inCis(thisVariantGenotype, otherVariantGenotype); + if (inTrans && modeOfInheritance == ModeOfInheritance.AUTOSOMAL_RECESSIVE) { + // -------P- (AR) + // ---X------ + acmgEvidenceBuilder.add(PM3); + } else if (inCis && modeOfInheritance == ModeOfInheritance.AUTOSOMAL_RECESSIVE) { + // ---X---P- (AR) + // --------- + acmgEvidenceBuilder.add(BP2); + } else if (inTrans && modeOfInheritance == ModeOfInheritance.AUTOSOMAL_DOMINANT) { + // -------P- (AD) + // ---X------ + acmgEvidenceBuilder.add(BP2); + } + } + } + } + } + } + + private boolean inTrans(SampleGenotype thisVariantGenotype, SampleGenotype otherVariantGenotype) { + // GT in trans = (1|0 && 0|1) (variant in both copies of gene) + // GT in cis = (1|0 && 1|0) or (0|1 && 0|1) (variant in same copy of gene) + return thisVariantGenotype.isPhased() && thisVariantGenotype.isHet() + && otherVariantGenotype.isPhased() && otherVariantGenotype.isHet() + && !thisVariantGenotype.equals(otherVariantGenotype); + } + + private boolean inCis(SampleGenotype thisVariantGenotype, SampleGenotype otherVariantGenotype) { + // GT in trans = (1|0 && 0|1) (variant in both copies of gene) + // GT in cis = (1|0 && 1|0) or (0|1 && 0|1) (variant in same copy of gene) + return thisVariantGenotype.isPhased() && thisVariantGenotype.isHet() + && otherVariantGenotype.isPhased() && otherVariantGenotype.isHet() + && thisVariantGenotype.equals(otherVariantGenotype); + } + + /** + * PS1 "Same amino acid change as a previously established pathogenic variant regardless of nucleotide change" + */ + private void assignPS1(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEffect variantEffect, ClinVarData clinVarData) { + ClinVarData.ClinSig primaryInterpretation = clinVarData.getPrimaryInterpretation(); + if (isMissense(variantEffect) && isPathOrLikelyPath(primaryInterpretation) && clinVarData.starRating() >= 2) { + // PS1 "Same amino acid change as a previously established pathogenic variant regardless of nucleotide change" + // TODO: can't quite do this fully as also need to know others with same AA change, if not identical + acmgEvidenceBuilder.add(PS1); + } + } + + private boolean isMissense(VariantEffect variantEffect) { + return variantEffect == VariantEffect.MISSENSE_VARIANT; + } + + /** + * PP5 "Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation" + */ + private void assignPP5(AcmgEvidence.Builder acmgEvidenceBuilder, ClinVarData clinVarData) { + ClinVarData.ClinSig primaryInterpretation = clinVarData.getPrimaryInterpretation(); + boolean pathOrLikelyPath = isPathOrLikelyPath(primaryInterpretation); + if (pathOrLikelyPath && clinVarData.starRating() == 1) { + acmgEvidenceBuilder.add(PP5); + } else if (pathOrLikelyPath && clinVarData.starRating() >= 2) { + acmgEvidenceBuilder.add(PP5, Evidence.STRONG); + } + } + + private boolean isPathOrLikelyPath(ClinVarData.ClinSig clinSig) { + return clinSig == ClinVarData.ClinSig.PATHOGENIC || clinSig == ClinVarData.ClinSig.LIKELY_PATHOGENIC || clinSig == ClinVarData.ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC; + } + + /** + * BP6 "Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation" + */ + private void assignBP6(AcmgEvidence.Builder acmgEvidenceBuilder, ClinVarData clinVarData) { + // these are likely never to be triggered as the variants will have been filtered out already + ClinVarData.ClinSig primaryInterpretation = clinVarData.getPrimaryInterpretation(); + boolean benignOrLikelyBenign = isBenignOrLikelyBenign(primaryInterpretation); + if (benignOrLikelyBenign && clinVarData.starRating() == 1) { + acmgEvidenceBuilder.add(BP6); + } else if (benignOrLikelyBenign && clinVarData.starRating() >= 2) { + acmgEvidenceBuilder.add(BP6, Evidence.STRONG); + } + } + + private boolean isBenignOrLikelyBenign(ClinVarData.ClinSig clinSig) { + return clinSig == ClinVarData.ClinSig.BENIGN || clinSig == ClinVarData.ClinSig.LIKELY_BENIGN || clinSig == ClinVarData.ClinSig.BENIGN_OR_LIKELY_BENIGN; + } + + /** + * PS2 "De novo (both maternity and paternity confirmed) in a patient with the disease and no family history" + * see also PM6. + */ + private void assignPS2(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluation variantEvaluation, ModeOfInheritance modeOfInheritance, List contributingVariants, boolean hasCompatibleDiseaseMatches, Individual proband) { + if (modeOfInheritance.isDominant() && hasCompatibleDiseaseMatches && contributingVariants.contains(variantEvaluation)) { + List ancestors = pedigree.anscestorsOf(proband); + boolean noFamilyHistoryOfDisease = true; + boolean noFamilyHistoryOfAllele = true; + if (ancestors.size() >= 2) { + SampleGenotype probandGenotype = variantEvaluation.getSampleGenotype(probandId); + for (Individual ancestor : ancestors) { + SampleGenotype ancestorGenotype = variantEvaluation.getSampleGenotype(ancestor.getId()); + // It may be the case that the pedigree contains a relative but the relative was not sequenced, + // so these are considered independently + if (ancestor.isAffected()) { + noFamilyHistoryOfDisease = false; + } + if ((ancestorGenotype.isHet() || ancestorGenotype.isHomAlt()) && (probandGenotype.isHet() || probandGenotype.isHomAlt())) { + // See comment below about possible de novo + noFamilyHistoryOfAllele = false; + } + } + if (noFamilyHistoryOfDisease && noFamilyHistoryOfAllele) { + acmgEvidenceBuilder.add(PS2); + } + } + } + } + + // n.b. this method is a little more obvious about what it expects compared to the test for noFamilyHistoryOfAllele in the PS2 method + // plus it doesn't assign a 0/1 or ./. genotypes in a parent as being a possible de novo in a 0/0 proband. This case shouldn't occur + // however, as Exomiser removes 0/0 proband variants. + private boolean possibleDeNovo(SampleGenotype ancestorGenotype, SampleGenotype probandGenotype) { + return (ancestorGenotype.isNoCall() || ancestorGenotype.isHomRef()) && (probandGenotype.isHet() || probandGenotype.isHomAlt()); + } + + /** + * PM1 "Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation" + */ + private void assignPM1(Map acmgEvidenceBuilder) { + // TODO - need UniProt domain / site info and clinvar counts + // can upgrade to STRONG + } + + /** + * PM2 "Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium" + */ + private void assignPM2(AcmgEvidence.Builder acmgEvidenceBuilder, FrequencyData frequencyData) { + if (!frequencyData.hasEspData() && !frequencyData.hasExacData() && !frequencyData.hasDbSnpData()) { + acmgEvidenceBuilder.add(PM2); + } + // TODO: require disease incidence in carriers and penetrance to be able to calculate expected frequencies for AR + } + + /** + * PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants + */ + private void assignPM4(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluation variantEvaluation) { + boolean isInFrameInDel = variantEvaluation.getVariantEffect() == VariantEffect.INFRAME_INSERTION || variantEvaluation.getVariantEffect() == VariantEffect.INFRAME_DELETION; + // avoid double-counting same affects if PVS1 already applied + if (!acmgEvidenceBuilder.contains(PVS1) && variantEvaluation.getVariantEffect() == VariantEffect.STOP_LOST || isInFrameInDel) { + acmgEvidenceBuilder.add(PM4); + } + // TODO if can assess whether the variant is an inframe indel in an unconserved or repetitive region then can assign BP3 + } + + /** + * PM6 "Assumed de novo, but without confirmation of paternity and maternity" + * See also PS2. + */ + private void assignPM6(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluation variantEvaluation, ModeOfInheritance modeOfInheritance, List contributingVariants, boolean hasCompatibleDiseaseMatches) { +// (iii) The phenotype in the patient matches the gene’s disease +// association with reasonable specificity. For example, this +// argument is strong for a patient with a de novo variant +// in the NIPBL gene who has distinctive facial features, +// hirsutism, and upper-limb defects (i.e., Cornelia de Lange syndrome), +// whereas it would be weaker for a de +// novo variant found by exome sequencing in a child with +// nonspecific features such as developmental delay. + if (hasCompatibleDiseaseMatches && modeOfInheritance.isDominant() + && contributingVariants.contains(variantEvaluation) + && variantEvaluation.getSampleGenotypes().size() == 1 && variantEvaluation.getSampleGenotype(probandId).isHet()) { + // making an assumption that this could be a de novo + acmgEvidenceBuilder.add(PM6); + } + } + + /** + * PP3 "Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)" + * BP4 "Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)" + */ + private void assignPP3orBP4(AcmgEvidence.Builder acmgEvidenceBuilder, PathogenicityData pathogenicityData) { + // These approaches are broadly similar in recommending just using one predictor and REVEL is consistently + // seen to out-perform other predictors. In our testing we also found that the REVEL-only approach worked best. + + // updated from "Evidence-based calibration of computational tools for missense variant pathogenicity + // classification and ClinGen recommendations for clinical use of PP3/BP4 criteria" + // https://www.biorxiv.org/content/10.1101/2022.03.17.484479v1 + // + var revelScore = pathogenicityData.getPredictedScore(PathogenicitySource.REVEL); + if (revelScore != null) { + assignRevelBasedPP3BP4Classification(acmgEvidenceBuilder, revelScore); + } else { + // See "Assessing performance of pathogenicity predictors using clinically relevant variant datasets" + // http://dx.doi.org/10.1136/jmedgenet-2020-107003 + assignEnsembleBasedPP3BP4Classification(acmgEvidenceBuilder, pathogenicityData); + } + } + + /* + * Updated classification from "Evidence-based calibration of computational tools for missense variant pathogenicity + * classification and ClinGen recommendations for clinical use of PP3/BP4 criteria" + * https://www.biorxiv.org/content/10.1101/2022.03.17.484479v1 + * + * This method provided much better + */ + private void assignRevelBasedPP3BP4Classification(AcmgEvidence.Builder acmgEvidenceBuilder, PathogenicityScore revelScore) { + var revel = revelScore.getRawScore(); + // Taken from table 2 of https://www.biorxiv.org/content/10.1101/2022.03.17.484479v1 + // P_Strong P_Moderate P_Supporting B_Supporting B_Moderate B_Strong B_Very Strong + // ≥ 0.932 [0.773, 0.932) [0.644, 0.773) (0.183, 0.290] (0.016, 0.183] (0.003, 0.016] ≤ 0.003 + // PATHOGENIC categories + + if (revel >= 0.932f) { + acmgEvidenceBuilder.add(PP3, Evidence.STRONG); + } else if (revel < 0.932f && revel >= 0.773f) { + acmgEvidenceBuilder.add(PP3, Evidence.MODERATE); + } else if (revel < 0.773f && revel >= 0.644f) { + acmgEvidenceBuilder.add(PP3, Evidence.SUPPORTING); + } + // BENIGN categories + else if (revel > 0.183f && revel <= 0.290f) { + acmgEvidenceBuilder.add(BP4, Evidence.SUPPORTING); + } else if (revel > 0.016f && revel <= 0.183f) { + acmgEvidenceBuilder.add(BP4, Evidence.MODERATE); + } else if (revel > 0.003f && revel <= 0.016f) { + acmgEvidenceBuilder.add(BP4, Evidence.STRONG); + } else if (revel <= 0.003f) { + acmgEvidenceBuilder.add(BP4, Evidence.VERY_STRONG); + } + } + + /* + * Ensemble-based approach suggested in + * See "Assessing performance of pathogenicity predictors using clinically relevant variant datasets" + * http://dx.doi.org/10.1136/jmedgenet-2020-107003 + */ + private void assignEnsembleBasedPP3BP4Classification(AcmgEvidence.Builder acmgEvidenceBuilder, PathogenicityData pathogenicityData) { + int numBenign = 0; + int numPathogenic = 0; + List predictedPathogenicityScores = pathogenicityData.getPredictedPathogenicityScores(); + for (PathogenicityScore pathogenicityScore : predictedPathogenicityScores) { + if (isPathogenic(pathogenicityScore)) { + numPathogenic++; + } else { + numBenign++; + } + } + if (predictedPathogenicityScores.size() > 1 && numPathogenic > numBenign) { + acmgEvidenceBuilder.add(PP3); + } + if (predictedPathogenicityScores.size() > 1 && numBenign > numPathogenic) { + acmgEvidenceBuilder.add(BP4); + } + } + + private boolean isPathogenic(PathogenicityScore pathogenicityScore) { + if (pathogenicityScore instanceof SiftScore) { + SiftScore score = (SiftScore) pathogenicityScore; + return score.getRawScore() < SiftScore.SIFT_THRESHOLD; + } + if (pathogenicityScore instanceof MutationTasterScore) { + MutationTasterScore score = (MutationTasterScore) pathogenicityScore; + return score.getScore() > MutationTasterScore.MTASTER_THRESHOLD; + } + if (pathogenicityScore instanceof PolyPhenScore) { + PolyPhenScore score = (PolyPhenScore) pathogenicityScore; + return score.getScore() > PolyPhenScore.POLYPHEN_PROB_DAMAGING_THRESHOLD; + } + if (pathogenicityScore instanceof CaddScore) { + CaddScore score = (CaddScore) pathogenicityScore; + // 95-99% most deleterious. + return score.getRawScore() >= 13.0f; + } + return pathogenicityScore.getScore() > 0.5f; + } + + /** + * PP4 "Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology" + */ + private void assignPP4(AcmgEvidence.Builder acmgEvidenceBuilder, List> compatibleDiseaseMatches) { + double humanGenePhenotypeScoreForMoi = 0; + for (ModelPhenotypeMatch diseaseModelPhenotypeMatch : compatibleDiseaseMatches) { + humanGenePhenotypeScoreForMoi = Math.max(humanGenePhenotypeScoreForMoi, diseaseModelPhenotypeMatch.getScore()); + } + if (humanGenePhenotypeScoreForMoi >= 0.6) { + acmgEvidenceBuilder.add(PP4); + } + } + + /** + * BA1 "Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium" + */ + private void assignBA1(AcmgEvidence.Builder acmgEvidenceBuilder, FrequencyData frequencyData) { + if (frequencyData.getMaxFreq() >= 5.0) { + acmgEvidenceBuilder.add(BA1); + } + } + + /** + * BS4 "Lack of segregation in affected members of a family" + */ + //TODO: implement PP1 - Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease + private void assignBS4(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluation variantEvaluation, Individual proband) { + if (pedigree.size() >= 2) { + List affectedFamilyMembers = pedigree.getIndividuals().stream() + .filter(Individual::isAffected) + .filter(individual -> !individual.getId().equals(probandId)) + .filter(individual -> individual.getFamilyId().equals(proband.getFamilyId())) + .collect(Collectors.toList()); + boolean segregatesWithAffectedInFamily = true; + SampleGenotype probandGenotype = variantEvaluation.getSampleGenotype(probandId); + if (!affectedFamilyMembers.isEmpty()) { + for (Individual affected : affectedFamilyMembers) { + SampleGenotype affectedGenotype = variantEvaluation.getSampleGenotype(affected.getId()); + if ((affectedGenotype.isHomRef() || affectedGenotype.isNoCall() || affectedGenotype.isEmpty()) && (probandGenotype.isHet() || probandGenotype.isHomAlt())) { + segregatesWithAffectedInFamily = false; + } + } + } + if (!segregatesWithAffectedInFamily) { + acmgEvidenceBuilder.add(BS4); + } + } + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignment.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignment.java new file mode 100644 index 000000000..812ff8075 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignment.java @@ -0,0 +1,151 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.genome.HgvsUtil; +import org.monarchinitiative.exomiser.core.model.GeneIdentifier; +import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; + +import java.util.Objects; + +/** + * @since 13.1.0 + */ +public class AcmgAssignment { + + // MOI, Disease, Variant(s), transcript, AA change, AcmgCriteria... + @JsonProperty + private final VariantEvaluation variantEvaluation; + @JsonProperty + private final GeneIdentifier geneIdentifier; + @JsonProperty + private final ModeOfInheritance modeOfInheritance; + @JsonProperty + private final Disease disease; + @JsonProperty + private final AcmgEvidence acmgEvidence; + @JsonProperty + private final AcmgClassification acmgClassification; + + private AcmgAssignment(VariantEvaluation variantEvaluation, GeneIdentifier geneIdentifier, ModeOfInheritance modeOfInheritance, Disease disease, AcmgEvidence acmgEvidence, AcmgClassification acmgClassification) { + this.variantEvaluation = variantEvaluation; + this.geneIdentifier = geneIdentifier; + this.modeOfInheritance = modeOfInheritance; + this.disease = disease; + this.acmgEvidence = acmgEvidence; + this.acmgClassification = acmgClassification; + } + + @JsonCreator + public static AcmgAssignment of(VariantEvaluation variant, GeneIdentifier geneIdentifier, ModeOfInheritance modeOfInheritance, Disease disease, AcmgEvidence acmgEvidence, AcmgClassification acmgClassification) { + Objects.requireNonNull(variant); + Objects.requireNonNull(geneIdentifier); + Objects.requireNonNull(disease); + Objects.requireNonNull(modeOfInheritance); + Objects.requireNonNull(acmgEvidence); + Objects.requireNonNull(acmgClassification); + return new AcmgAssignment(variant, geneIdentifier, modeOfInheritance, disease, acmgEvidence, acmgClassification); + } + + public VariantEvaluation variantEvaluation() { + return variantEvaluation; + } + + public GeneIdentifier geneIdentifier() { + return geneIdentifier; + } + + public Disease disease() { + return disease; + } + + public ModeOfInheritance modeOfInheritance() { + return modeOfInheritance; + } + + public AcmgEvidence acmgEvidence() { + return acmgEvidence; + } + + public AcmgClassification acmgClassification() { + return acmgClassification; + } + + public String toDisplayString() { + // report as HGVS, ACMG, Disease, MOI + // e.g. FGFR2(NM_014008.5):c.2T>G (p.M1T), likely pathogenic, Apert syndrome, autosomal dominant + String transcriptinfo = transcriptDisplayString(); + + String diseaseInfo = ""; + if (!disease.getDiseaseId().isEmpty()) { + diseaseInfo = disease.getDiseaseName() + " (" + disease.getDiseaseId() + "), "; + } + + return variantEvaluation.toGnomad() + + ", " + HgvsUtil.toHgvsGenomic(variantEvaluation) + + ", " + transcriptinfo + + ", " + acmgClassification + + ", " + acmgEvidence + + ", " + diseaseInfo + + modeOfInheritance; + } + + private String transcriptDisplayString() { + if (variantEvaluation.hasTranscriptAnnotations()) { + TranscriptAnnotation transcriptAnnotation = variantEvaluation.getTranscriptAnnotations().get(0); + return transcriptAnnotation.getGeneSymbol() + + "(" + transcriptAnnotation.getAccession() + ")" + + ":" + transcriptAnnotation.getHgvsCdna() + + ":" + transcriptAnnotation.getHgvsProtein(); + } + return ""; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + AcmgAssignment that = (AcmgAssignment) o; + return variantEvaluation.equals(that.variantEvaluation) && geneIdentifier.equals(that.geneIdentifier) && disease.equals(that.disease) && modeOfInheritance == that.modeOfInheritance && acmgEvidence.equals(that.acmgEvidence) && acmgClassification == that.acmgClassification; + } + + @Override + public int hashCode() { + return Objects.hash(variantEvaluation, geneIdentifier, disease, modeOfInheritance, acmgEvidence, acmgClassification); + } + + @Override + public String toString() { + return "AcmgAssignment{" + + "variant=" + variantEvaluation + + ", geneIdentifier=" + geneIdentifier + + ", disease=" + disease + + ", modeOfInheritance=" + modeOfInheritance + + ", acmgEvidence=" + acmgEvidence + + ", acmgClassification=" + acmgClassification + + '}'; + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentCalculator.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentCalculator.java new file mode 100644 index 000000000..33a1a0199 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentCalculator.java @@ -0,0 +1,88 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2022 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; + +import java.util.List; +import java.util.function.Function; +import java.util.stream.Collectors; + +/** + * @since 13.1.0 + */ +public class AcmgAssignmentCalculator { + + private static final Disease EMPTY_DISEASE = Disease.builder().build(); + + private final AcmgEvidenceAssigner acmgEvidenceAssigner; + private final AcmgEvidenceClassifier acmgEvidenceClassifier; + + public AcmgAssignmentCalculator(AcmgEvidenceAssigner acmgEvidenceAssigner, AcmgEvidenceClassifier acmgEvidenceClassifier) { + this.acmgEvidenceAssigner = acmgEvidenceAssigner; + this.acmgEvidenceClassifier = acmgEvidenceClassifier; + } + + /** + * @param modeOfInheritance + * @param gene + * @param contributingVariants + * @param compatibleDiseaseMatches + * @return + */ + public List calculateAcmgAssignments(ModeOfInheritance modeOfInheritance, Gene gene, List contributingVariants, List> compatibleDiseaseMatches) { + Disease disease = findTopDiseaseMatch(compatibleDiseaseMatches); + + List knownDiseases = findKnownDiseasesCompatibleWithMoi(modeOfInheritance, gene); + + // TODO: implement criteria assignment and classification of structural/copy-number variants! + return contributingVariants.stream() + .sorted(VariantEvaluation::compareByRank) + .map(assignVariantAcmg(modeOfInheritance, gene, contributingVariants, knownDiseases, compatibleDiseaseMatches, disease)) + .collect(Collectors.toUnmodifiableList()); + } + + private Disease findTopDiseaseMatch(List> compatibleDiseaseMatches) { + return compatibleDiseaseMatches.stream() + .sorted(ModelPhenotypeMatch::compareTo) + .map(ModelPhenotypeMatch::getModel) + .findFirst() + .orElse(EMPTY_DISEASE); + } + + private List findKnownDiseasesCompatibleWithMoi(ModeOfInheritance modeOfInheritance, Gene gene) { + return gene.getAssociatedDiseases().stream() + .filter(disease -> disease.getInheritanceMode().isCompatibleWith(modeOfInheritance)) + .collect(Collectors.toUnmodifiableList()); + } + + private Function assignVariantAcmg(ModeOfInheritance modeOfInheritance, Gene gene, List contributingVariants, List knownDiseases, List> compatibleDiseaseMatches, Disease disease) { + return variantEvaluation -> { + AcmgEvidence acmgEvidence = acmgEvidenceAssigner.assignVariantAcmgEvidence(variantEvaluation, modeOfInheritance, contributingVariants, knownDiseases, compatibleDiseaseMatches); + AcmgClassification acmgClassification = acmgEvidenceClassifier.classify(acmgEvidence); + return AcmgAssignment.of(variantEvaluation, gene.getGeneIdentifier(), modeOfInheritance, disease, acmgEvidence, acmgClassification); + }; + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgClassification.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgClassification.java new file mode 100644 index 000000000..f6254693a --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgClassification.java @@ -0,0 +1,28 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +/** + * @since 13.1.0 + */ +public enum AcmgClassification { + PATHOGENIC, LIKELY_PATHOGENIC, UNCERTAIN_SIGNIFICANCE, LIKELY_BENIGN, BENIGN, NOT_AVAILABLE; +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterion.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterion.java new file mode 100644 index 000000000..2949baeb8 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterion.java @@ -0,0 +1,145 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.Evidence.*; +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.Impact.BENIGN; +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.Impact.PATHOGENIC; + +/** + * @since 13.1.0 + */ +public enum AcmgCriterion { + + // PATHOGENIC - Table 3 of https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf + PVS1(PATHOGENIC, VERY_STRONG, "null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease"), + + PS1(PATHOGENIC, STRONG, "Same amino acid change as a previously established pathogenic variant regardless of nucleotide change"), + PS2(PATHOGENIC, STRONG, "De novo (both maternity and paternity confirmed) in a patient with the disease and no family history"), + PS3(PATHOGENIC, STRONG, "Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product"), + PS4(PATHOGENIC, STRONG, "The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls"), + + PM1(PATHOGENIC, MODERATE, "Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation"), + PM2(PATHOGENIC, MODERATE, "Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium"), + PM3(PATHOGENIC, MODERATE, "For recessive disorders, detected in trans with a pathogenic variant"), + PM4(PATHOGENIC, MODERATE, "Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants"), + PM5(PATHOGENIC, MODERATE, "Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before"), + PM6(PATHOGENIC, MODERATE, "Assumed de novo, but without confirmation of paternity and maternity"), + + PP1(PATHOGENIC, SUPPORTING, "Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease"), + PP2(PATHOGENIC, SUPPORTING, "Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease"), + PP3(PATHOGENIC, SUPPORTING, "Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)"), + PP4(PATHOGENIC, SUPPORTING, "Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology"), + PP5(PATHOGENIC, SUPPORTING, "Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation"), + + // BENIGN - Table 4 of https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf + BA1(BENIGN, STAND_ALONE, "Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium"), + + BS1(BENIGN, STRONG, "Allele frequency is greater than expected for disorder"), + BS2(BENIGN, STRONG, "Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age"), + BS3(BENIGN, STRONG, "Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing"), + BS4(BENIGN, STRONG, "Lack of segregation in affected members of a family"), + + BP1(BENIGN, SUPPORTING, "Missense variant in a gene for which primarily truncating variants are known to cause disease"), + BP2(BENIGN, SUPPORTING, "Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern"), + BP3(BENIGN, SUPPORTING, "In-frame deletions/insertions in a repetitive region without a known function"), + BP4(BENIGN, SUPPORTING, "Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)"), + BP5(BENIGN, SUPPORTING, "Variant found in a case with an alternate molecular basis for disease"), + BP6(BENIGN, SUPPORTING, "Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation"), + BP7(BENIGN, SUPPORTING, "A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved"); + + public enum Impact { + PATHOGENIC, BENIGN; + } + + public enum Evidence { + STAND_ALONE, VERY_STRONG, STRONG, MODERATE, SUPPORTING; + + public static Evidence parseValue(String displayString) { + try { + return Evidence.valueOf(displayString); + } catch (IllegalArgumentException ex) { + // swallow and try the display string + } + switch (displayString) { + case "StandAlone": + return STAND_ALONE; + case "VeryStrong": + return VERY_STRONG; + case "Strong": + return STRONG; + case "Moderate": + return MODERATE; + case "Supporting": + return SUPPORTING; + default: + throw new IllegalArgumentException("Unrecognised evidence value '" + displayString + "'"); + } + } + + public String displayString() { + switch (this) { + case STAND_ALONE: + return "StandAlone"; + case VERY_STRONG: + return "VeryStrong"; + case STRONG: + return "Strong"; + case MODERATE: + return "Moderate"; + case SUPPORTING: + return "Supporting"; + } + return ""; + } + } + + private final Impact impact; + private final Evidence evidence; + private final String description; + + AcmgCriterion(Impact impact, Evidence evidence, String description) { + this.impact = impact; + this.evidence = evidence; + this.description = description; + } + + public Impact impact() { + return impact; + } + + public boolean isPathogenic() { + return impact == PATHOGENIC; + } + + public boolean isBenign() { + return impact == BENIGN; + } + + public Evidence evidence() { + return evidence; + } + + public String description() { + return description; + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidence.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidence.java new file mode 100644 index 000000000..01a578c74 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidence.java @@ -0,0 +1,209 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.Evidence; + +import javax.annotation.Nullable; +import java.util.*; + +/** + * @since 13.1.0 + */ +public class AcmgEvidence { + + private static final AcmgEvidence EMPTY = new AcmgEvidence(Map.of()); + + @JsonProperty + private final Map evidence; + + private int pvs = 0; + private int ps = 0; + private int pm = 0; + private int pp = 0; + + private int ba = 0; + private int bs = 0; + private int bp = 0; + + private AcmgEvidence(Map evidence) { + this.evidence = evidence == null || evidence.isEmpty() ? Map.of() : Collections.unmodifiableMap(new EnumMap<>(evidence)); + countCriteriaEvidence(this.evidence); + } + + @JsonCreator + public static AcmgEvidence of(Map evidence) { + return new AcmgEvidence(evidence); + } + + public static AcmgEvidence empty() { + return EMPTY; + } + + private void countCriteriaEvidence(Map evidence) { + for (Map.Entry entry : evidence.entrySet()) { + AcmgCriterion acmgCriterion = entry.getKey(); + Evidence evidenceStrength = entry.getValue(); + if (acmgCriterion.isPathogenic()) { + switch (evidenceStrength) { + case VERY_STRONG: + pvs++; + break; + case STRONG: + ps++; + break; + case MODERATE: + pm++; + break; + case SUPPORTING: + pp++; + break; + default: + // do nothing + break; + } + } + + if (acmgCriterion.isBenign()) { + switch (evidenceStrength) { + case STAND_ALONE: + ba++; + break; + case STRONG: + bs++; + break; + case SUPPORTING: + bp++; + break; + default: + // do nothing + break; + } + } + } + } + + public boolean hasCriterion(AcmgCriterion acmgCriterion) { + return evidence.containsKey(acmgCriterion); + } + + @Nullable + public Evidence criterionEvidence(AcmgCriterion acmgCriterion) { + return evidence.get(acmgCriterion); + } + + public int size() { + return evidence.size(); + } + + public boolean isEmpty() { + return evidence.isEmpty(); + } + + public Map evidence() { + return evidence; + } + + public int pvs() { + return pvs; + } + + public int ps() { + return ps; + } + + public int pm() { + return pm; + } + + public int pp() { + return pp; + } + + public int ba() { + return ba; + } + + public int bs() { + return bs; + } + + public int bp() { + return bp; + } + + public static AcmgEvidence.Builder builder() { + return new Builder(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + AcmgEvidence that = (AcmgEvidence) o; + return evidence.equals(that.evidence); + } + + @Override + public int hashCode() { + return Objects.hash(evidence); + } + + @Override + public String toString() { + StringJoiner stringJoiner = new StringJoiner(", "); + for (Map.Entry entry : evidence.entrySet()) { + AcmgCriterion acmgCriterion = entry.getKey(); + Evidence assignedEvidence = entry.getValue(); + if (acmgCriterion.evidence() != assignedEvidence) { + stringJoiner.add(acmgCriterion.toString() + '_' + assignedEvidence.displayString()); + } else { + stringJoiner.add(acmgCriterion.toString()); + } + } + return '[' + stringJoiner.toString() + ']'; + } + + public static class Builder { + + private final EnumMap evidence = new EnumMap<>(AcmgCriterion.class); + + public Builder add(AcmgCriterion acmgCriterion) { + evidence.put(acmgCriterion, acmgCriterion.evidence()); + return this; + } + + public Builder add(AcmgCriterion acmgCriterion, Evidence evidence) { + this.evidence.put(acmgCriterion, evidence); + return this; + } + + public boolean contains(AcmgCriterion acmgCriterion) { + return evidence.containsKey(acmgCriterion); + } + + public AcmgEvidence build() { + return evidence.isEmpty() ? EMPTY : new AcmgEvidence(evidence); + } + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceAssigner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceAssigner.java new file mode 100644 index 000000000..762ea52e8 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceAssigner.java @@ -0,0 +1,36 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; + +import java.util.List; + +/** + * @since 13.1.0 + */ +public interface AcmgEvidenceAssigner { + + AcmgEvidence assignVariantAcmgEvidence(VariantEvaluation variantEvaluation, ModeOfInheritance modeOfInheritance, List contributingVariants, List knownDiseases, List> compatibleDiseaseMatches); +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceClassifier.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceClassifier.java new file mode 100644 index 000000000..1219edd66 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceClassifier.java @@ -0,0 +1,29 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +/** + * @since 13.1.0 + */ +public interface AcmgEvidenceClassifier { + + AcmgClassification classify(AcmgEvidence acmgEvidence); +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/HgvsUtil.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/HgvsUtil.java index e2d155c3c..34eb65c1e 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/HgvsUtil.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/HgvsUtil.java @@ -97,7 +97,7 @@ private static String toDeletionString(Variant variant) { return getPrefix(variant) + (variant.start() + 1) + "del" + variant.ref() .substring(variant.alt().length()); } - int start = variant.startWithCoordinateSystem(CoordinateSystem.LEFT_OPEN) + length; + int start = variant.startWithCoordinateSystem(CoordinateSystem.zeroBased()) + length; int end = start + length - 1; // Need to adjust the start and end to report the DELETED section return getPrefix(variant) + start + "_" + end + "del" + variant.ref() diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarSmallVariantAnnotator.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarSmallVariantAnnotator.java index 4a2a7068d..d0e6089e9 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarSmallVariantAnnotator.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarSmallVariantAnnotator.java @@ -21,6 +21,7 @@ package org.monarchinitiative.exomiser.core.genome; import de.charite.compbio.jannovar.annotation.*; +import de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType; import de.charite.compbio.jannovar.data.JannovarData; import de.charite.compbio.jannovar.hgvs.AminoAcidCode; import de.charite.compbio.jannovar.reference.GenomeVariant; @@ -176,6 +177,7 @@ private List buildTranscriptAnnotations(List a } private TranscriptAnnotation toTranscriptAnnotation(Annotation annotation) { + AnnotationLocation annoLoc = annotation.getAnnoLoc(); return TranscriptAnnotation.builder() .variantEffect(getVariantEffectOrDefault(annotation.getMostPathogenicVarType(), VariantEffect.SEQUENCE_VARIANT)) .accession(TranscriptModelUtil.getTranscriptAccession(annotation.getTranscript())) @@ -183,10 +185,25 @@ private TranscriptAnnotation toTranscriptAnnotation(Annotation annotation) { .hgvsGenomic((annotation.getGenomicNTChange() == null) ? "" : annotation.getGenomicNTChangeStr()) .hgvsCdna(annotation.getCDSNTChangeStr()) .hgvsProtein(annotation.getProteinChangeStr(AminoAcidCode.THREE_LETTER)) + .rankType(annoLoc == null ? TranscriptAnnotation.RankType.UNDEFINED : getRankType(annoLoc.getRankType())) + .rankTotal(annoLoc == null ? -1 : annoLoc.getTotalRank()) + .rank(annoLoc == null ? -1 : annoLoc.getRank() + 1) .distanceFromNearestGene(getDistFromNearestGene(annotation)) .build(); } + private TranscriptAnnotation.RankType getRankType(RankType annoLocRankType) { + switch (annoLocRankType) { + case EXON: + return TranscriptAnnotation.RankType.EXON; + case INTRON: + return TranscriptAnnotation.RankType.INTRON; + case UNDEFINED: + return TranscriptAnnotation.RankType.UNDEFINED; + } + return TranscriptAnnotation.RankType.UNDEFINED; + } + private VariantEffect getVariantEffectOrDefault(VariantEffect annotatedEffect, VariantEffect defaultEffect) { return annotatedEffect == null ? defaultEffect : annotatedEffect; } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarVariantConverter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarVariantConverter.java index bf036609a..1243b87a6 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarVariantConverter.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/JannovarVariantConverter.java @@ -98,12 +98,12 @@ private GenomicRegion variantOrRightBreakend(Variant variant) { private GenomePosition startGenomePosition(GenomicRegion genomicRegion) { int chr = jannovarContigId(genomicRegion.contig()); - return new GenomePosition(referenceDictionary, genomicRegion.strand() == POSITIVE ? FWD : REV, chr, genomicRegion.startWithCoordinateSystem(CoordinateSystem.LEFT_OPEN), PositionType.ZERO_BASED); + return new GenomePosition(referenceDictionary, genomicRegion.strand() == POSITIVE ? FWD : REV, chr, genomicRegion.startWithCoordinateSystem(CoordinateSystem.zeroBased()), PositionType.ZERO_BASED); } private GenomePosition endGenomePosition(GenomicRegion genomicRegion) { int chr = jannovarContigId(genomicRegion.contig()); - return new GenomePosition(referenceDictionary, genomicRegion.strand() == POSITIVE ? FWD : REV, chr, genomicRegion.endWithCoordinateSystem(CoordinateSystem.LEFT_OPEN), PositionType.ZERO_BASED); + return new GenomePosition(referenceDictionary, genomicRegion.strand() == POSITIVE ? FWD : REV, chr, genomicRegion.endWithCoordinateSystem(CoordinateSystem.zeroBased()), PositionType.ZERO_BASED); } private int jannovarContigId(Contig contig) { diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/CaddDao.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/CaddDao.java index 8d239974a..f79ce9186 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/CaddDao.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/CaddDao.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -74,7 +74,7 @@ private PathogenicityData processResults(Variant variant) { return getCaddPathogenicityData(caddInDelTabixDataSource, chromosome, start, ref, alt); } - private PathogenicityData getCaddPathogenicityData(TabixDataSource tabixDataSource, String chromosome, int start, String ref, String alt) { + private synchronized PathogenicityData getCaddPathogenicityData(TabixDataSource tabixDataSource, String chromosome, int start, String ref, String alt) { try { TabixReader.Iterator results = tabixDataSource.query(chromosome, start, start); String line; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteList.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteList.java index 4adc72b2a..75d862ab1 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteList.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteList.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2019 Queen Mary University of London. + * Copyright (c) 2016-2021 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -20,7 +20,6 @@ package org.monarchinitiative.exomiser.core.genome.dao; -import com.google.common.collect.ImmutableSet; import org.monarchinitiative.exomiser.core.model.AlleleProtoAdaptor; import org.monarchinitiative.exomiser.core.model.Variant; import org.monarchinitiative.exomiser.core.proto.AlleleProto; @@ -54,7 +53,7 @@ public static VariantWhiteList of(Set whiteList) { } private InMemoryVariantWhiteList(Set whiteList) { - this.whiteList = ImmutableSet.copyOf(whiteList); + this.whiteList = Set.copyOf(whiteList); } @Override diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/LocalFrequencyDao.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/LocalFrequencyDao.java index 2a60a012f..dc486c0f3 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/LocalFrequencyDao.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/LocalFrequencyDao.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -64,7 +64,7 @@ private FrequencyData processResults(Variant variant) { return getPositionFrequencyData(chromosome, start, ref, alt); } - private FrequencyData getPositionFrequencyData(String chromosome, int start, String ref, String alt) { + private synchronized FrequencyData getPositionFrequencyData(String chromosome, int start, String ref, String alt) { //Local frequency file defined as tab-delimited lines in 'VCF-lite' format: //chr pos ref alt freq(%) //1 12345 A T 23.0 (an A->T SNP on chr1 at position 12345 with frequency of 23.0%) diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDao.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDao.java index e1c04b265..fab8dd440 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDao.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDao.java @@ -49,7 +49,7 @@ */ public class SvPathogenicityDao implements PathogenicityDao { - private static final Logger logger = LoggerFactory.getLogger(SvFrequencyDao.class); + private static final Logger logger = LoggerFactory.getLogger(SvPathogenicityDao.class); private final DataSource svDataSource; private final double minSimilarity = 0.80; @@ -152,7 +152,7 @@ private List runQuery(Variant variant) { int endMin = svDaoBoundaryCalculator.endMin(); int endMax = svDaoBoundaryCalculator.endMax(); - logger.debug("SELECT * FROM SV_FREQ WHERE CHROMOSOME = {} AND START >= {} and START <= {} and \"end\" >= {} and \"end\" <= {};", + logger.debug("SELECT * FROM SV_PATH WHERE CHROMOSOME = {} AND START >= {} and START <= {} and \"end\" >= {} and \"end\" <= {};", variant.contigId(), startMin, startMax, endMin, endMax diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/TabixReaderAdaptor.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/TabixReaderAdaptor.java index 1980bc2d1..33127b0b0 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/TabixReaderAdaptor.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/TabixReaderAdaptor.java @@ -56,7 +56,7 @@ private Map createChrIndex(Set tabixChromosomes) { * DATA BEING RETURNED DUE TO CHROMOSOME NAMING DIFFERENCES. */ @Override - public TabixReader.Iterator query(String query) { + public synchronized TabixReader.Iterator query(String query) { return tabixReader.query(query); } @@ -65,7 +65,7 @@ public TabixReader.Iterator query(String query) { * the tabix file. Requires fully-closed start and end coordinates. */ @Override - public TabixReader.Iterator query(String chromosome, int start, int end) { + public synchronized TabixReader.Iterator query(String chromosome, int start, int end) { String chr = chrIndex.get(chromosome); return tabixReader.query(tabixReader.chr2tid(chr), start - 1, end); } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java index 67eb3cc5a..e393307c4 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java @@ -31,6 +31,7 @@ import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey; import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties; import org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar; +import org.monarchinitiative.svart.Variant; import java.util.*; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/ChromosomalRegionIndex.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/ChromosomalRegionIndex.java index 5f54885cd..e06510871 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/ChromosomalRegionIndex.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/ChromosomalRegionIndex.java @@ -109,8 +109,8 @@ public boolean hasRegionContainingPosition(int chromosome, int position) { @Nonnull public List getRegionsContainingVariant(Variant variant) { int chromosome = variant.contigId(); - int start = variant.startOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.FULLY_CLOSED); - int end = variant.endOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.FULLY_CLOSED); + int start = variant.startOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.oneBased()); + int end = variant.endOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.oneBased()); List overlappingRegions = getRegionsOverlappingRegion(chromosome, start, end); List containingRegions = new ArrayList<>(); for (T overlapping : overlappingRegions) { @@ -122,13 +122,13 @@ public List getRegionsContainingVariant(Variant variant) { } private boolean regionContainsVariant(T region, Variant variant) { - return Coordinates.aContainsB(CoordinateSystem.FULLY_CLOSED, region.start(), region.end(), variant.coordinateSystem(), variant.start(), variant.end()); + return Coordinates.aContainsB(CoordinateSystem.oneBased(), region.start(), region.end(), variant.coordinateSystem(), variant.start(), variant.end()); } public List getRegionsOverlappingVariant(Variant variant) { int chromosome = variant.contigId(); - int start = variant.startOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.FULLY_CLOSED); - int end = variant.endOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.FULLY_CLOSED); + int start = variant.startOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.oneBased()); + int end = variant.endOnStrandWithCoordinateSystem(Strand.POSITIVE, CoordinateSystem.oneBased()); return getRegionsOverlappingRegion(chromosome, start, end); } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/Gene.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/Gene.java index 3248edfc9..36b2e9f82 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/Gene.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/Gene.java @@ -20,18 +20,21 @@ package org.monarchinitiative.exomiser.core.model; +import com.fasterxml.jackson.annotation.JsonGetter; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonPropertyOrder; -import com.google.common.collect.Sets; import de.charite.compbio.jannovar.mendel.ModeOfInheritance; import org.monarchinitiative.exomiser.core.filters.FilterResult; import org.monarchinitiative.exomiser.core.filters.FilterType; +import org.monarchinitiative.exomiser.core.prioritisers.OmimPriorityResult; import org.monarchinitiative.exomiser.core.prioritisers.Prioritiser; import org.monarchinitiative.exomiser.core.prioritisers.PriorityResult; import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; import javax.annotation.Nullable; import java.util.*; +import java.util.stream.Collectors; import static java.util.stream.Collectors.toList; @@ -67,7 +70,7 @@ * @author Jules Jacobsen * @version 0.21 (16 January, 2013) */ -@JsonPropertyOrder({"geneSymbol", "geneIdentifier", "combinedScore", "priorityScore", "variantScore", "filterResults", "priorityResults", "compatibleInheritanceModes", "geneScores", "variantEvaluations"}) +@JsonPropertyOrder({"geneSymbol", "geneIdentifier", "combinedScore", "priorityScore", "variantScore", "pValue", "filterResults", "priorityResults", "compatibleInheritanceModes", "geneScores", "variantEvaluations"}) public class Gene implements Comparable, Filterable, Inheritable { private final GeneIdentifier geneIdentifier; @@ -159,42 +162,6 @@ public int getNumberOfVariants() { return variantEvaluations.size(); } - /** - * Downrank gene because it has a large numbers of variants (under the - * assumption that such genes are unlikely to be be true disease genes, - * rather, by chance say 2 of 20 variants are score as highly pathogenic by - * polyphen, leading to a false positive call. This method downweights the - * {@link #variantScore} of this gene, which is the aggregate score for the - * variants. - * - * @param threshold Downweighting occurs for variants that have this number - * or more variants. - */ -//commented out as this was unused - use the GeneScorer for this sort of function. -// public void downWeightGeneWithManyVariants(int threshold) { -// if (this.variantList.size() < threshold) { -// return; -// } -// // Start with downweighting factor of 5% -// // For every additional variant, add half again to the factor -// int s = this.variantList.size(); -// float factor = 0.05f; -// float downweight = 0f; -// while (s > threshold) { -// downweight += factor; -// factor *= 1.5; -// s--; -// } -// if (downweight > 1f) { -// downweight = 1f; -// } -// this.variantScore = this.variantScore * (1f - downweight); -// /* -// * filterscore is now at least zero -// */ -// -// } - public boolean hasVariants() { return !variantEvaluations.isEmpty(); } @@ -203,18 +170,18 @@ public boolean hasVariants() { * This function adds additional variants to the current gene. The variants * have been identified by parsing the VCF file. * - * @param var A Variant affecting the current gene. + * @param variantEvaluation A Variant affecting the current gene. */ - public final void addVariant(VariantEvaluation var) { - Objects.requireNonNull(var); - addGeneFilterResultsToVariant(var); - variantEvaluations.add(var); + public final void addVariant(VariantEvaluation variantEvaluation) { + Objects.requireNonNull(variantEvaluation); + addGeneFilterResultsToVariant(variantEvaluation); + variantEvaluations.add(variantEvaluation); } - private void addGeneFilterResultsToVariant(VariantEvaluation var) { + private void addGeneFilterResultsToVariant(VariantEvaluation variantEvaluation) { for (FilterResult filterResult : filterResults.values()) { if (filterResult.getFilterType() != FilterType.INHERITANCE_FILTER) { - var.addFilterResult(filterResult); + variantEvaluation.addFilterResult(filterResult); } } } @@ -246,7 +213,7 @@ public Set getCompatibleInheritanceModes() { @Override public void setCompatibleInheritanceModes(Set inheritanceModes) { - this.inheritanceModes = Sets.immutableEnumSet(inheritanceModes); + this.inheritanceModes = Collections.unmodifiableSet(EnumSet.copyOf(inheritanceModes)); } /** @@ -334,6 +301,7 @@ public PriorityResult getPriorityResult(PriorityType type) { * @since 13.0.0 */ @Nullable + @SuppressWarnings("unchecked") public T getPriorityResult(Class clazz) { for (PriorityResult priorityResult : priorityResultsMap.values()) { if (clazz.isInstance(priorityResult)) { @@ -347,13 +315,17 @@ public T getPriorityResult(Class clazz) { * @return the map of {@code PriorityResult} objects that represent the * result of filtering */ -// @JsonIgnore public Map getPriorityResults() { return priorityResultsMap; } + public List getAssociatedDiseases() { + OmimPriorityResult omimPriorityResult = getPriorityResult(OmimPriorityResult.class); + // This is a bit silly. Known diseases should be added as part of Gene creation. + return omimPriorityResult == null ? List.of() : omimPriorityResult.getAssociatedDiseases(); + } + /** - * * @param geneScore * @throws NullPointerException if the argument is null * @since 10.0.0 @@ -364,6 +336,13 @@ public synchronized void addGeneScore(GeneScore geneScore) { topGeneScore = GeneScore.max(topGeneScore, geneScore); } + public synchronized void addGeneScores(Collection geneScores) { + Objects.requireNonNull(geneScores); + for (GeneScore geneScore : geneScores) { + addGeneScore(geneScore); + } + } + @JsonIgnore public GeneScore getTopGeneScore() { return topGeneScore; @@ -373,6 +352,19 @@ public List getGeneScores() { return List.copyOf(geneScoreMap.values()); } + /** + * Returns a list of GeneScores with inheritance modes compatible with the filtered variants compatible modes of + * inheritance. This will only return a (potentially) populated list once a GeneScorer has been applied to the Gene + * @since 13.1.0 + * @return A list of {@link GeneScore} with a compatible mode of inheritance. + */ + public List getCompatibleGeneScores() { + return this.geneScoreMap.entrySet().stream() + .filter(entry -> this.inheritanceModes.contains(entry.getKey())) + .map(Map.Entry::getValue) + .collect(Collectors.toUnmodifiableList()); + } + public GeneScore getGeneScoreForMode(ModeOfInheritance modeOfInheritance) { Objects.requireNonNull(modeOfInheritance); return geneScoreMap.getOrDefault(modeOfInheritance, GeneScore.builder() @@ -421,6 +413,11 @@ public double getCombinedScore() { return topGeneScore.getCombinedScore(); } + @JsonGetter + public double pValue() { + return topGeneScore.pValue(); + } + /** * Return the combined score of this gene based on the relevance of the gene * (priorityScore) and the predicted effects of the variants (variantScore). diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/GeneScore.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/GeneScore.java index b13b46039..fa18f0d81 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/GeneScore.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/GeneScore.java @@ -20,7 +20,10 @@ package org.monarchinitiative.exomiser.core.model; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgAssignment; import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; @@ -43,17 +46,22 @@ public final class GeneScore implements Comparable { private final double combinedScore; private final double phenotypeScore; private final double variantScore; + @JsonProperty + private final double pValue; private final List contributingVariants; private final List> compatibleDiseaseMatches; + private final List acmgAssignments; private GeneScore(Builder builder) { this.geneIdentifier = builder.geneIdentifier; this.modeOfInheritance = builder.modeOfInheritance; + this.pValue = builder.pValue; this.combinedScore = builder.combinedScore; this.phenotypeScore = builder.phenotypeScore; this.variantScore = builder.variantScore; this.contributingVariants = List.copyOf(builder.contributingVariants); this.compatibleDiseaseMatches = List.copyOf(builder.compatibleDiseaseMatches); + this.acmgAssignments = List.copyOf(builder.acmgAssignments); } public GeneIdentifier getGeneIdentifier() { @@ -64,6 +72,10 @@ public ModeOfInheritance getModeOfInheritance() { return modeOfInheritance; } + public double pValue() { + return pValue; + } + public double getCombinedScore() { return combinedScore; } @@ -90,14 +102,31 @@ public boolean hasContributingVariants() { return !contributingVariants.isEmpty(); } + /** + * @return A list of diseases associated with the Gene under the mode of inheritance for the GeneScore. + * @since 13.0.0 + */ public List> getCompatibleDiseaseMatches() { return compatibleDiseaseMatches; } + /** + * @return true if there is a disease associated with the Gene under the mode of inheritance for the GeneScore. + * @since 13.0.0 + */ public boolean hasCompatibleDiseaseMatches() { return !compatibleDiseaseMatches.isEmpty(); } + /** + * @return A list of {@link AcmgAssignment} for variants associated with the Gene under the mode of inheritance for + * the GeneScore. + * @since 13.1.0 + */ + public List getAcmgAssignments() { + return acmgAssignments; + } + /** * Compares the combined score of two {@code GeneScore} objects. Will return the {@code GeneScore} with the highest * numerical value or the first if equal. @@ -127,27 +156,30 @@ public int compareTo(GeneScore anotherGeneScore) { /** * Compares two specified {@code GeneScore} objects. The natural ordering of these objects is the reverse numerical - * ordering of their {@code combinedScore} or if this value is equal to 0, the natural order of their {@code GeneSymbol}. + * ordering of their {@code combinedScore}, then reverse numerical ordering of {@code phenotypeScore} + * or if this value is equal to 0, the natural order of their {@code GeneSymbol}. * * @param s1 the fist score to be compared. * @param s2 the second score to be compared. * @return a value less than {@code 0} if this {@code s1.combinedScore} is numerically greater than * {@code s2.combinedScore}; and a value greater than {@code 0} if {@code s1.combinedScore} is numerically * less than {@code s2.combinedScore}. Should {@code s1.combinedScore} be numerically equal to - * {@code s2.combinedScore} the return value will be equivalent to the comparison of the {@code GeneIdentifier}. + * {@code s2.combinedScore} the scores will be compared reverse order of phenotypeScore or if equal + * the return value will be equivalent to the comparison of the {@code GeneIdentifier}. * @throws NullPointerException if an argument is null */ public static int compare(GeneScore s1, GeneScore s2) { - double s1CombinedScore = s1.getCombinedScore(); - double s2CombinedScore = s2.getCombinedScore(); - if (s1CombinedScore < s2CombinedScore) { - return 1; + int result; + // n.b. these are *reversed* compared to their natural order + result = Double.compare(s2.combinedScore, s1.combinedScore); + if (result == 0) { + result = Double.compare(s2.phenotypeScore, s1.phenotypeScore); } - if (s1CombinedScore > s2CombinedScore) { - return -1; + if (result == 0) { + //if the scores are equal then return an alphabetised list based on gene symbol + result = GeneIdentifier.compare(s1.getGeneIdentifier(), s2.getGeneIdentifier()); } - //if the scores are equal then return an alphabetised list based on gene symbol - return GeneIdentifier.compare(s1.getGeneIdentifier(), s2.getGeneIdentifier()); + return result; } @Override @@ -176,6 +208,7 @@ public String toString() { ", combinedScore=" + combinedScore + ", phenotypeScore=" + phenotypeScore + ", variantScore=" + variantScore + + ", pValue=" + pValue + ", contributingVariants=" + contributingVariants + '}'; } @@ -191,11 +224,13 @@ public static Builder builder() { public static class Builder { private GeneIdentifier geneIdentifier = GeneIdentifier.builder().build(); private ModeOfInheritance modeOfInheritance = ModeOfInheritance.ANY; + private double pValue = 1.0; private double combinedScore; private double phenotypeScore; private double variantScore; private List contributingVariants = List.of(); private List> compatibleDiseaseMatches = List.of(); + private List acmgAssignments = List.of(); public Builder geneIdentifier(GeneIdentifier geneIdentifier) { this.geneIdentifier = geneIdentifier; @@ -207,6 +242,11 @@ public Builder modeOfInheritance(ModeOfInheritance modeOfInheritance) { return this; } + public Builder pValue(double pValue) { + this.pValue = pValue; + return this; + } + public Builder combinedScore(double combinedScore) { this.combinedScore = combinedScore; return this; @@ -235,5 +275,10 @@ public Builder compatibleDiseaseMatches(List> compa public GeneScore build() { return new GeneScore(this); } + + public Builder acmgAssignments(List acmgAssignments) { + this.acmgAssignments = Objects.requireNonNull(acmgAssignments); + return this; + } } } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/SampleGenotype.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/SampleGenotype.java index 14916a9f3..e78ad520a 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/SampleGenotype.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/SampleGenotype.java @@ -21,7 +21,6 @@ package org.monarchinitiative.exomiser.core.model; import com.fasterxml.jackson.annotation.JsonIgnore; -import com.google.common.collect.ImmutableList; import java.util.Arrays; import java.util.List; @@ -174,7 +173,7 @@ private static AlleleCall[] parseAlleleCalls(boolean phased, String genotype) { } public List getCalls() { - return ImmutableList.copyOf(alleleCalls); + return List.of(alleleCalls); } /** diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotation.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotation.java index 053cf4134..7ba62d7af 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotation.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotation.java @@ -22,6 +22,7 @@ import de.charite.compbio.jannovar.annotation.VariantEffect; +import javax.annotation.Nonnull; import java.util.Objects; /** @@ -29,6 +30,10 @@ */ public class TranscriptAnnotation { + public enum RankType { + EXON, INTRON, UNDEFINED + } + private static final TranscriptAnnotation EMPTY = TranscriptAnnotation.builder().build(); private final VariantEffect variantEffect; @@ -40,6 +45,13 @@ public class TranscriptAnnotation { private final String hgvsCdna; private final String hgvsProtein; + // exon / intron 'rank' e.g. lies in Exon (rank) 3 of (totalRank) 4 + private final RankType rankType; + // 1-based intron/exon rank + private final int rank; + // total number of introns/exons for this transcript + private final int rankTotal; + private final int distanceFromNearestGene; private TranscriptAnnotation(Builder builder) { @@ -49,6 +61,9 @@ private TranscriptAnnotation(Builder builder) { this.hgvsGenomic = builder.hgvsGenomic; this.hgvsCdna = builder.hgvsCdna; this.hgvsProtein = builder.hgvsProtein; + this.rankType = builder.rankType; + this.rank = builder.rank; + this.rankTotal = builder.rankTotal; this.distanceFromNearestGene = builder.distanceFromNearestGene; } @@ -80,6 +95,18 @@ public String getHgvsProtein() { return hgvsProtein; } + public RankType getRankType() { + return rankType; + } + + public int getRank() { + return rank; + } + + public int getRankTotal() { + return rankTotal; + } + public int getDistanceFromNearestGene() { return distanceFromNearestGene; } @@ -89,18 +116,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; TranscriptAnnotation that = (TranscriptAnnotation) o; - return distanceFromNearestGene == that.distanceFromNearestGene && - variantEffect == that.variantEffect && - Objects.equals(geneSymbol, that.geneSymbol) && - Objects.equals(accession, that.accession) && - Objects.equals(hgvsGenomic, that.hgvsGenomic) && - Objects.equals(hgvsCdna, that.hgvsCdna) && - Objects.equals(hgvsProtein, that.hgvsProtein); + return rank == that.rank && rankTotal == that.rankTotal && distanceFromNearestGene == that.distanceFromNearestGene && variantEffect == that.variantEffect && geneSymbol.equals(that.geneSymbol) && accession.equals(that.accession) && hgvsGenomic.equals(that.hgvsGenomic) && hgvsCdna.equals(that.hgvsCdna) && hgvsProtein.equals(that.hgvsProtein) && rankType == that.rankType; } @Override public int hashCode() { - return Objects.hash(variantEffect, geneSymbol, accession, hgvsGenomic, hgvsCdna, hgvsProtein, distanceFromNearestGene); + return Objects.hash(variantEffect, geneSymbol, accession, hgvsGenomic, hgvsCdna, hgvsProtein, rankType, rank, rankTotal, distanceFromNearestGene); } @Override @@ -112,6 +133,9 @@ public String toString() { ", hgvsGenomic='" + hgvsGenomic + '\'' + ", hgvsCdna='" + hgvsCdna + '\'' + ", hgvsProtein='" + hgvsProtein + '\'' + + ", rankType='" + rankType + '\'' + + ", rank='" + rank + '\'' + + ", rankTotal='" + rankTotal + '\'' + ", distanceFromNearestGene=" + distanceFromNearestGene + '}'; } @@ -131,9 +155,13 @@ public static class Builder { private String hgvsCdna = ""; private String hgvsProtein = ""; + private RankType rankType = RankType.UNDEFINED; + private int rank = -1; + private int rankTotal = -1; + private int distanceFromNearestGene = Integer.MIN_VALUE; - public Builder variantEffect(VariantEffect variantEffect) { + public Builder variantEffect(@Nonnull VariantEffect variantEffect) { this.variantEffect = variantEffect; return this; } @@ -163,6 +191,21 @@ public Builder hgvsProtein(String hgvsProtein) { return this; } + public Builder rankType(RankType rankType) { + this.rankType = rankType; + return this; + } + + public Builder rankTotal(int rankTotal) { + this.rankTotal = rankTotal; + return this; + } + + public Builder rank(int rank) { + this.rank = rank; + return this; + } + public Builder distanceFromNearestGene(int distanceFromNearestGene) { this.distanceFromNearestGene = distanceFromNearestGene; return this; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java index 91a630864..0a1e3f0bd 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java @@ -84,6 +84,7 @@ public class VariantEvaluation extends AbstractVariant implements Comparable contributingModes; private Set compatibleInheritanceModes; + private VariantEvaluation(Builder builder) { super(builder); @@ -174,14 +175,14 @@ public String toGnomad() { if (isSymbolic()) { // can be searched for in gnomad like so: // https://gnomad.broadinstitute.org/region/4-65216746-65216746-G-?dataset=gnomad_sv_r2_1 - return contig().name() + '-' + start() + '-' + end() + '-' + ref() + '-' + alt() + ' ' + unitLength(); + return contig().name() + '-' + start() + '-' + end() + '-' + ref() + '-' + alt(); } // can be searched for in gnomad like so: // https://gnomad.broadinstitute.org/variant/X-31517201-T-C return contig().name() + '-' + start() + '-' + ref() + '-' + alt(); } - private String unitLength() { + public String changeLengthString() { int length = Math.abs(changeLength()); if (length < 1000) { return length + "bp"; @@ -531,17 +532,26 @@ public boolean equals(Object obj) { return Objects.equals(this.ref(), other.ref()) && Objects.equals(this.alt(), other.alt()); } + @Override public String toString() { // expose frequency and pathogenicity scores? if (contributesToGeneScore()) { //Add a star to the output string between the variantEffect and the score - return "VariantEvaluation{assembly=" + genomeAssembly + " chr=" + contigId() + " strand=" + strand() + " start=" + start() + " end=" + end() + " length=" + length() + " ref=" + ref() + " alt=" + alt() + " id=" + id() + " qual=" + phredScore + " " + variantType() + " " + variantEffect + " gene=" + geneSymbol + " * score=" + getVariantScore() + " " + getFilterStatus() + " failedFilters=" + failedFilterTypes + " passedFilters=" + passedFilterTypes + return "VariantEvaluation{assembly=" + genomeAssembly + " chr=" + contigId() + " strand=" + strand() + " start=" + start() + " end=" + end() + " length=" + length() + " ref=" + ref() + " alt=" + alt() + " id=" + id() + " qual=" + phredScore + " " + variantType() + " " + variantEffect + " gene=" + geneSymbol + " * score=" + getVariantScore() + " freqScore=" + getFrequencyScore() + " pathScore=" + getPathogenicityScore() + " " + getFilterStatus() + " failedFilters=" + failedFilterTypes + " passedFilters=" + passedFilterTypes + " compatibleWith=" + compatibleInheritanceModes + " sampleGenotypes=" + sampleGenotypes + "}"; } - return "VariantEvaluation{assembly=" + genomeAssembly + " chr=" + contigId() + " strand=" + strand() + " start=" + start() + " end=" + end() + " length=" + length() + " ref=" + ref() + " alt=" + alt() + " id=" + id() + " qual=" + phredScore + " " + variantType() + " " + variantEffect + " gene=" + geneSymbol + " score=" + getVariantScore() + " " + getFilterStatus() + " failedFilters=" + failedFilterTypes + " passedFilters=" + passedFilterTypes + return "VariantEvaluation{assembly=" + genomeAssembly + " chr=" + contigId() + " strand=" + strand() + " start=" + start() + " end=" + end() + " length=" + length() + " ref=" + ref() + " alt=" + alt() + " id=" + id() + " qual=" + phredScore + " " + variantType() + " " + variantEffect + " gene=" + geneSymbol + " score=" + getVariantScore() + " freqScore=" + getFrequencyScore() + " pathScore=" + getPathogenicityScore() + " " + getFilterStatus() + " failedFilters=" + failedFilterTypes + " passedFilters=" + passedFilterTypes + " compatibleWith=" + compatibleInheritanceModes + " sampleGenotypes=" + sampleGenotypes + "}"; } + // TODO - Will Composition make Breakends work? + // VariantEvaluation implements Variant, VariantAnnotations, + // Variant + // VariantContext + // VariantAnnotations + // pass/fail filters & priorityResults... + // TODO: Delete AbstractVariant add variantAnnotations to Builder + /** * @return * @since 13.0.0 @@ -662,7 +672,7 @@ Builder passedFilters(Set passedFilterTypes) { return this; } - Builder compatibleInheritanceModes(Set compatibleInheritanceModes) { + public Builder compatibleInheritanceModes(Set compatibleInheritanceModes) { this.compatibleInheritanceModes = Objects.requireNonNull(compatibleInheritanceModes); return this; } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java index 178b456c7..1eb8c83eb 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java @@ -260,6 +260,31 @@ public float getMaxFreq() { return max; } + /** + * + * @return The maximum {@link Frequency} or null + * @since 13.1.0 + */ + @JsonIgnore + @Nullable + public Frequency getMaxFrequency() { + if (this.size == 0) { + return null; + } + float max = 0.0f; + int maxSource = 0; + + for(int i = 0; i < this.size; ++i) { + float value = this.values[i]; + if (value > max) { + max = value; + maxSource = i; + } + } + + return Frequency.of(this.sources[maxSource], max); + } + /** * @return returns a numerical value that is closer to one, the rarer * the variant is. If a variant is not entered in any of the data diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarData.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarData.java index a1fd30ecf..7c9c4232a 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarData.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarData.java @@ -65,6 +65,50 @@ public enum ClinSig { private final String reviewStatus; private final Map includedAlleles; + // https://www.medschool.umaryland.edu/Genetic_Variant_Interpretation_Tool1.html/ + // BP1, Missense variant in a gene for which primarily truncating variants are known to cause disease + // BP2, Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern + // BP6, * Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation + // BS1, Allele frequency is greater than expected for disorder + // --- + // PS1, Same amino acid change as a previously established pathogenic variant regardless of nucleotide change + // PM5, Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before + // PP2, Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease + // PP5, * Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation + // + // - needs link to gene, disease and amino acid change on variant. Could run 2*+ through Jannovar and annotation pipeline. + // Need to collect hets and homs for variant in gene + // TODO: add GENEINFO (geneSymbol:ncbiGeneId) and + // CLNDISDB=MedGen:C0006142,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:C0027672,SNOMED_CT:699346009 + // 22 29130684 460820 G C . . ALLELEID=471879;CLNDISDB=MedGen:C0006142,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:C0027672,SNOMED_CT:699346009;CLNDN=Familial_cancer_of_breast|Hereditary_cancer-predisposing_syndrome;CLNHGVS=NC_000022.10:g.29130684G>C;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Uncertain_significance;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=CHEK2:11200;MC=SO:0001583|missense_variant,SO:0001623|5_prime_UTR_variant;ORIGIN=1;RS=1456931393 + // 10 123357783 299024 G T . . AF_TGP=0.01717;ALLELEID=320947;CLNDISDB=Human_Phenotype_Ontology:HP:0001363,MedGen:C1849943|Human_Phenotype_Ontology:HP:0004439,MeSH:D003394,MedGen:C2931196,OMIM:123500,Orphanet:ORPHA207,SNOMED_CT:28861008|MedGen:C0001193,OMIM:101200,Orphanet:ORPHA87,SNOMED_CT:205258009|MedGen:C0175699,OMIM:101400,Orphanet:ORPHA794,SNOMED_CT:83015004|MedGen:C0220658,OMIM:101600,Orphanet:ORPHA710,Orphanet:ORPHA93258,Orphanet:ORPHA93259|MedGen:C0265269,OMIM:149730,Orphanet:ORPHA2363,SNOMED_CT:23817003|MedGen:C0795998,OMIM:123150,Orphanet:ORPHA1540|MedGen:C1852406,OMIM:123790,Orphanet:ORPHA1555|MedGen:CN043619;CLNDN=Craniosynostosis|Crouzon_syndrome|Acrocephalosyndactyly_type_I|Saethre-Chotzen_syndrome|Pfeiffer_syndrome|Levy-Hollister_syndrome|Jackson-Weiss_syndrome|Cutis_Gyrata_syndrome_of_Beare_and_Stevenson|Isolated_coronal_synostosis;CLNHGVS=NC_000010.10:g.123357783G>T;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;CLNVI=Illumina_Clinical_Services_Laboratory,Illumina:288098;GENEINFO=FGFR2:2263;MC=SO:0001619|non-coding_transcript_variant,SO:0001623|5_prime_UTR_variant;ORIGIN=1;RS=41301043 + // ##fileformat=VCFv4.1 + //##fileDate=2020-03-02 + //##source=ClinVar + //##reference=GRCh37 + //##ID= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= + //##INFO= private ClinVarData(Builder builder) { this.alleleId = builder.alleleId; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhiveOptions.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhiveOptions.java index 5dc3968dd..0076138b5 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhiveOptions.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhiveOptions.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -133,13 +133,12 @@ private boolean isBenchmarkHit(GeneModel model) { } private boolean matchesCandidateGeneSymbol(GeneModel model) { - return model.getHumanGeneSymbol() == null ? candidateGeneSymbol == null : model.getHumanGeneSymbol() - .equals(candidateGeneSymbol); + return model.getHumanGeneSymbol() != null && model.getHumanGeneSymbol().equals(candidateGeneSymbol); } private boolean matchesDisease(Model model) { // human model ID is now disease plus entrezgene to ensure uniqueness in HiPhive code - return model.getId() == null ? diseaseId == null : model.getId().split("_")[0].equals(diseaseId); + return model.getId() != null && model.getId().split("_")[0].equals(diseaseId); } public Set getOrganismsToRun() { diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhivePriorityResult.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhivePriorityResult.java index c250fdb98..8590cf617 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhivePriorityResult.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/HiPhivePriorityResult.java @@ -311,7 +311,7 @@ public String getHTMLCode() { } for (GeneModelPhenotypeMatch geneModelPhenotypeMatch : ppiEvidence) { - String stringDbLink = "http://string-db.org/newstring_cgi/show_network_section.pl?identifiers=" + geneSymbol + "%0D" + geneModelPhenotypeMatch + String stringDbLink = "http://version10.string-db.org/newstring_cgi/show_network_section.pl?identifiers=" + geneSymbol + "%0D" + geneModelPhenotypeMatch .getHumanGeneSymbol() + "&required_score=700&network_flavor=evidence&species=9606&limit=20"; switch (geneModelPhenotypeMatch.getOrganism()) { diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/OmimPriority.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/OmimPriority.java index c3b50d497..1a43562cb 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/OmimPriority.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/OmimPriority.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2021 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -122,8 +122,8 @@ private double calculateknownDiseaseInheritanceModeModifier(Gene gene, ModeOfInh // if we're still here check the compatibility of the gene against the known modes for the disease // under the current mode of inheritance return knownAssociatedDiseases.stream() - .filter(disease -> disease.getInheritanceMode() != InheritanceMode.UNKNOWN) .map(Disease::getInheritanceMode) + .filter(inheritanceMode -> inheritanceMode != InheritanceMode.UNKNOWN) .mapToDouble(scoreInheritanceMode(gene, modeOfInheritance)) .max() .orElse(1); diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDao.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDao.java index 45ac8be76..9d9240d4c 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDao.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDao.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -31,15 +31,13 @@ import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.cache.annotation.Cacheable; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.RowMapper; import org.springframework.stereotype.Repository; import javax.sql.DataSource; -import java.sql.Connection; -import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Collections; import java.util.List; import java.util.Set; @@ -51,28 +49,17 @@ public class DefaultDiseaseDao implements DiseaseDao { private final Logger logger = LoggerFactory.getLogger(DefaultDiseaseDao.class); - private final DataSource dataSource; + private final JdbcTemplate jdbcTemplate; public DefaultDiseaseDao(@Qualifier("phenotypeDataSource") DataSource phenotypeDataSource) { - this.dataSource = phenotypeDataSource; + this.jdbcTemplate = new JdbcTemplate(phenotypeDataSource); } @Cacheable(value = "diseaseHp") @Override public Set getHpoIdsForDiseaseId(String diseaseId) { - try (Connection connection = dataSource.getConnection()) { - try (PreparedStatement statement = connection.prepareStatement("SELECT hp_id FROM disease_hp WHERE disease_id = ?")) { - statement.setString(1, diseaseId); - ResultSet rs = statement.executeQuery(); - Set diseaseHpoIds = parseHpoIds(rs); - logger.info("{} HPO ids retrieved for disease {} - {}", diseaseHpoIds.size(), diseaseId, diseaseHpoIds); - return diseaseHpoIds; - - } - } catch (SQLException e) { - logger.error("Unable to retrieve HPO terms for disease {}", diseaseId, e); - } - return Collections.emptySet(); + String query = "SELECT hp_id FROM disease_hp WHERE disease_id = ?"; + return jdbcTemplate.query(query, this::parseHpoIds, diseaseId); } private Set parseHpoIds(ResultSet rs) throws SQLException { @@ -81,7 +68,7 @@ private Set parseHpoIds(ResultSet rs) throws SQLException { String[] hpoArray = hpoListString.split(","); return ImmutableSet.copyOf(hpoArray); } - return Collections.emptySet(); + return Set.of(); } @Cacheable(value = "diseases") @@ -100,37 +87,21 @@ public List getDiseaseDataAssociatedWithGeneId(int geneId) { "AND e.entrezid = d.gene_id " + "AND d.type in ('D', 'C', 'S', '?')" + "AND d.gene_id = ?"; - - try (Connection connection = dataSource.getConnection()) { - try (PreparedStatement statement = connection.prepareStatement(query)) { - statement.setInt(1, geneId); - ResultSet rs = statement.executeQuery(); - return processDiseaseResults(rs); - - } - } catch (SQLException e) { - logger.error("Unable to execute query '{}' for geneId: '{}'", query, geneId, e); - } - return Collections.emptyList(); + return jdbcTemplate.query(query, diseaseRowMapper, geneId); } - private List processDiseaseResults(ResultSet rs) throws SQLException { - List listBuilder = new ArrayList<>(); - while (rs.next()) { - List phenotypes = List.of(rs.getString("pheno_ids").split(",")); - Disease disease = Disease.builder() - .diseaseId(rs.getString("disease_id")) - .diseaseName(rs.getString("disease_name")) - .associatedGeneId(rs.getInt("entrez_id")) - .associatedGeneSymbol(rs.getString("human_gene_symbol")) - .inheritanceModeCode(formatInheritanceCode(rs.getString("inheritance_code"))) - .diseaseTypeCode(rs.getString("disease_type")) - .phenotypeIds(phenotypes) - .build(); - listBuilder.add(disease); - } - return List.copyOf(listBuilder); - } + private final RowMapper diseaseRowMapper = (ResultSet rs, int rowNum) -> { + List phenotypes = List.of(rs.getString("pheno_ids").split(",")); + return Disease.builder() + .diseaseId(rs.getString("disease_id")) + .diseaseName(rs.getString("disease_name")) + .associatedGeneId(rs.getInt("entrez_id")) + .associatedGeneSymbol(rs.getString("human_gene_symbol")) + .inheritanceModeCode(formatInheritanceCode(rs.getString("inheritance_code"))) + .diseaseTypeCode(rs.getString("disease_type")) + .phenotypeIds(phenotypes) + .build(); + }; // work-around for the inheritance code being defined as a char and interpreted as a char2 which will contain whitespace // this should be set to varchar(2). Not trimming the inheritanceCode results in all inheritance modes being UNKNOWN. diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceMode.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceMode.java index 7c0a4519e..56d96d5dc 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceMode.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceMode.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2021 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -142,6 +142,9 @@ public Set toModeOfInheritance() { } public boolean isCompatibleWith(ModeOfInheritance modeOfInheritance) { + if (modeOfInheritance == ModeOfInheritance.ANY) { + return true; + } switch (this) { case AUTOSOMAL_DOMINANT: return modeOfInheritance == ModeOfInheritance.AUTOSOMAL_DOMINANT; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriter.java index 895bc4742..985788a03 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriter.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriter.java @@ -29,6 +29,9 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import java.util.EnumSet; import java.util.Set; @@ -56,28 +59,67 @@ public static void writeToFile(AnalysisResults analysisResults, OutputProto.Outp public static void writeToFile(AnalysisResults analysisResults, OutputSettings outputSettings) { logger.debug("Writing results..."); + createOutputDirectoriesIfNotExists(outputSettings); + + if (outputSettings.getOutputFormats().isEmpty()) { + ResultsWriter resultsWriter = new HtmlResultsWriter(); + resultsWriter.writeFile(ModeOfInheritance.ANY, analysisResults, outputSettings); + } + Set outputFormatsForAnyMoi = EnumSet.noneOf(OutputFormat.class); for (OutputFormat outputFormat : outputSettings.getOutputFormats()) { if (outputFormat == OutputFormat.HTML || outputFormat == OutputFormat.JSON) { - writeResultsToFileForMoiWithFormat(ModeOfInheritance.ANY, outputFormat, analysisResults, outputSettings); + ResultsWriter resultsWriter = ResultsWriterFactory.getResultsWriter(outputFormat); + resultsWriter.writeFile(ModeOfInheritance.ANY, analysisResults, outputSettings); } else { outputFormatsForAnyMoi.add(outputFormat); } } + // eventually most of this will be superfluous and only the analysisResults and outputSettings will be required, + // here we're using these output formats twice - once for the new unified output (here) and then the original + // multiple-file output later + if (outputFormatsForAnyMoi.contains(OutputFormat.TSV_GENE)) { + logger.debug("Writing TSV_GENE results"); + ResultsWriter resultsWriter = new TsvGeneAllMoiResultsWriter(); + resultsWriter.writeFile(ModeOfInheritance.ANY, analysisResults, outputSettings); + } + + if (outputFormatsForAnyMoi.contains(OutputFormat.TSV_VARIANT)) { + logger.debug("Writing TSV_VARIANT results"); + ResultsWriter resultsWriter = new TsvVariantAllMoiResultsWriter(); + resultsWriter.writeFile(ModeOfInheritance.ANY, analysisResults, outputSettings); + } + + if (outputFormatsForAnyMoi.contains(OutputFormat.VCF)) { + logger.debug("Writing VCF results"); + ResultsWriter resultsWriter = new VcfAllMoiResultsWriter(); + resultsWriter.writeFile(ModeOfInheritance.ANY, analysisResults, outputSettings); + } + Analysis analysis = analysisResults.getAnalysis(); InheritanceModeOptions inheritanceModeOptions = analysis.getInheritanceModeOptions(); - if (inheritanceModeOptions.isEmpty()) { - writeForInheritanceMode(ModeOfInheritance.ANY, outputFormatsForAnyMoi, analysisResults, outputSettings); - } else { for (ModeOfInheritance modeOfInheritance : inheritanceModeOptions.getDefinedModes()) { - logger.debug("Writing {} results:", modeOfInheritance); - // Can't do this in parallel because theses are mutated each time for a different mode here. - // AnalysisResults could return a view for a ModeOfInheritance which can be called by the Writer - // without interfering with other writes for different modes. Check RAM requirements. - // Will only save a few seconds, so is not a rate-limiting step. - analysisResults.getGenes().sort(Gene.comparingScoreForInheritanceMode(modeOfInheritance)); - writeForInheritanceMode(modeOfInheritance, outputFormatsForAnyMoi, analysisResults, outputSettings); + if (modeOfInheritance != ModeOfInheritance.ANY) { + logger.debug("Writing {} results:", modeOfInheritance); + // Can't do this in parallel because theses are mutated each time for a different mode here. + // AnalysisResults could return a view for a ModeOfInheritance which can be called by the Writer + // without interfering with other writes for different modes. Check RAM requirements. + // Will only save a few seconds, so is not a rate-limiting step. + // TODO: For removal in v14.0 - analysisResults.getGenes() will be immutable in v14.0.0 + analysisResults.getGenes().sort(Gene.comparingScoreForInheritanceMode(modeOfInheritance)); + writeForInheritanceMode(modeOfInheritance, outputFormatsForAnyMoi, analysisResults, outputSettings); + } + } + } + + private static void createOutputDirectoriesIfNotExists(OutputSettings outputSettings) { + Path outputDir = ResultsWriterUtils.resolveOutputDir(outputSettings.getOutputPrefix()); + if (Files.notExists(outputDir)) { + try { + Files.createDirectories(outputDir); + } catch (IOException e) { + throw new IllegalStateException("Unable to create Exomiser output path due to " + e.getMessage()); } } } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/GeneScoreRanker.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/GeneScoreRanker.java new file mode 100644 index 000000000..65f0e76cf --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/GeneScoreRanker.java @@ -0,0 +1,187 @@ +package org.monarchinitiative.exomiser.core.writers; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.monarchinitiative.exomiser.core.analysis.AnalysisResults; +import org.monarchinitiative.exomiser.core.model.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.function.Function; +import java.util.stream.Stream; + +import static java.util.stream.Collectors.partitioningBy; +import static java.util.stream.Collectors.toUnmodifiableMap; + +class GeneScoreRanker { + + private static final Logger logger = LoggerFactory.getLogger(GeneScoreRanker.class); + + private final OutputSettings outputSettings; + private final boolean contributingVariantsOnly; + + private final List filteredGenesForOutput; + private final Map genesById; + + GeneScoreRanker(AnalysisResults analysisResults, OutputSettings outputSettings) { + this.outputSettings = outputSettings; + this.contributingVariantsOnly = outputSettings.outputContributingVariantsOnly(); + this.filteredGenesForOutput = outputSettings.filterGenesForOutput(analysisResults.getGenes()); + this.genesById = filteredGenesForOutput.stream().collect(toUnmodifiableMap(Gene::getGeneIdentifier, Function.identity())); + } + + Map mapGenesByGeneIdentifier() { + return genesById; + } + + private List calculateRankedGeneScores() { + Map> rankedAndUnrankedGeneScores = filteredGenesForOutput.stream() + .flatMap(gene -> { + List compatibleGeneScores = new ArrayList<>(gene.getCompatibleGeneScores()); + if (gene.getVariantEvaluations().stream().anyMatch(ve -> ve.getFilterStatus() == FilterStatus.FAILED)) { + // create a failed gene score placeholder for when run in FULL mode + GeneScore geneScore = GeneScore.builder() + .geneIdentifier(gene.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.ANY) + .combinedScore(0) + .phenotypeScore(gene.getPriorityScore()) + .variantScore(0) + .build(); + compatibleGeneScores.add(geneScore); + } + return compatibleGeneScores.stream(); + }) + .sorted() + .collect(partitioningBy(o -> o.getCombinedScore() != 0)); + + if (outputSettings.outputContributingVariantsOnly()) { + return rankedAndUnrankedGeneScores.get(true); + } else { + List rankedGeneScores = new ArrayList<>(rankedAndUnrankedGeneScores.get(true).size() + rankedAndUnrankedGeneScores.get(false).size()); + rankedGeneScores.addAll(rankedAndUnrankedGeneScores.get(true)); + rankedGeneScores.addAll(rankedAndUnrankedGeneScores.get(false)); + return List.copyOf(rankedGeneScores); + } + } + + Stream rankedGenes() { + ScoreRanker scoreRanker = new ScoreRanker(4); + return calculateRankedGeneScores().stream() + .map(geneScore -> { + int rank = scoreRanker.rank(geneScore.getCombinedScore()); + return new RankedGene(rank, genesById.get(geneScore.getGeneIdentifier()), geneScore); + }); + } + + Stream rankedVariants() { + return rankedGenes().flatMap(rankedGene -> { + int rank = rankedGene.rank(); + GeneScore geneScore = rankedGene.geneScore(); + ModeOfInheritance modeOfInheritance = geneScore.getModeOfInheritance(); + logger.debug("{} {} {} {} {} {}", rank, geneScore.getGeneIdentifier().getGeneSymbol(), modeOfInheritance.getAbbreviation(), geneScore.getCombinedScore(), geneScore.getPhenotypeScore(), geneScore.getVariantScore()); + // a GeneScore only contains the contributing variants so can't be used directly to get the variants involved, hence the requirement for the Gene. + return rankedGene.gene() + .getVariantEvaluations().stream() + .filter(variantEvaluation -> !contributingVariantsOnly || variantEvaluation.contributesToGeneScoreUnderMode(modeOfInheritance)) + .filter(variantEvaluation -> variantEvaluation.isCompatibleWith(modeOfInheritance)) + .filter(variantEvaluation -> (geneScore.getCombinedScore() == 0) != variantEvaluation.passedFilters()) + .sorted(VariantEvaluation::compareByRank) + .map(ve -> new RankedVariant(rank, ve, geneScore)); + }); + } + + static class RankedGene { + private final int rank; + private final Gene gene; + private final GeneScore geneScore; + + public RankedGene(int rank, Gene gene, GeneScore geneScore) { + this.rank = rank; + this.gene = Objects.requireNonNull(gene); + this.geneScore = Objects.requireNonNull(geneScore); + } + + public int rank() { + return rank; + } + + public Gene gene() { + return gene; + } + + public GeneScore geneScore() { + return geneScore; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + RankedGene that = (RankedGene) o; + return rank == that.rank && gene.equals(that.gene) && geneScore.equals(that.geneScore); + } + + @Override + public int hashCode() { + return Objects.hash(rank, gene, geneScore); + } + + @Override + public String toString() { + return "RankedGene{" + + "rank=" + rank + + ", gene=" + gene + + ", geneScore=" + geneScore + + '}'; + } + } + + static class RankedVariant { + private final int rank; + private final VariantEvaluation variantEvaluation; + private final GeneScore geneScore; + + public RankedVariant(int rank, VariantEvaluation variantEvaluation, GeneScore geneScore) { + this.rank = rank; + this.variantEvaluation = Objects.requireNonNull(variantEvaluation); + this.geneScore = Objects.requireNonNull(geneScore); + } + + public int rank() { + return rank; + } + + public VariantEvaluation variantEvaluation() { + return variantEvaluation; + } + + public GeneScore geneScore() { + return geneScore; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + RankedVariant that = (RankedVariant) o; + return rank == that.rank && variantEvaluation.equals(that.variantEvaluation) && geneScore.equals(that.geneScore); + } + + @Override + public int hashCode() { + return Objects.hash(rank, variantEvaluation, geneScore); + } + + @Override + public String toString() { + return "RankedVariant{" + + "rank=" + rank + + ", variantEvaluation=" + variantEvaluation + + ", geneScore=" + geneScore + + '}'; + } + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java index 3b7cdfbad..44118c43f 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/HtmlResultsWriter.java @@ -43,6 +43,7 @@ import org.monarchinitiative.exomiser.core.analysis.sample.SampleProtoConverter; import org.monarchinitiative.exomiser.core.filters.FilterReport; import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation; import org.monarchinitiative.exomiser.core.model.VariantEvaluation; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -55,6 +56,7 @@ import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.text.DecimalFormat; import java.util.List; import java.util.Locale; @@ -132,8 +134,24 @@ private Context buildContext(ModeOfInheritance modeOfInheritance, AnalysisResult // For the time being we're going to maintain the original behaviour (UCSC) // Need to wire it up through the system or it might be easiest to autodetect this from the transcripts of passed variants. // One of UCSC, ENSEMBL or REFSEQ - context.setVariable("transcriptDb", "ENSEMBL"); + var transcriptDb = analysisResults.getContributingVariants().stream() + .flatMap(variantEvaluation -> variantEvaluation.getTranscriptAnnotations().stream()) + .findFirst() + .map(TranscriptAnnotation::getAccession) + .map(value -> { + if (value.startsWith("ENST")) { + return "ENSEMBL"; + } else if (value.startsWith("uc")) { + return "UCSC"; + } else if (value.startsWith("NM") || value.startsWith("NR") || value.startsWith("XM") || value.startsWith("XR")) { + return "REFSEQ"; + } + return ""; + }) + .orElse("ENSEMBL"); + context.setVariable("transcriptDb", transcriptDb); context.setVariable("variantRankComparator", new VariantEvaluation.RankBasedComparator()); + context.setVariable("pValueFormatter", new DecimalFormat("0.0E0")); return context; } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/OutputSettings.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/OutputSettings.java index 2752e77b7..f73e00503 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/OutputSettings.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/OutputSettings.java @@ -39,6 +39,7 @@ import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.function.Predicate; +import java.util.stream.Stream; import static java.util.stream.Collectors.toUnmodifiableList; @@ -103,9 +104,7 @@ public String getOutputPrefix() { * @since 13.0.0 */ public List filterGenesForOutput(List genes) { - return genes.stream() - .filter(gene -> gene.getCombinedScore() >= minExomiserGeneScore) - .filter(withinNumberOfGenesToShow(numberOfGenesToShow)) + return applyOutputSettings(genes) .collect(toUnmodifiableList()); } @@ -118,13 +117,26 @@ public List filterGenesForOutput(List genes) { * @since 13.0.0 */ public List filterPassedGenesForOutput(List genes) { - return genes.stream() + return applyOutputSettings(genes) .filter(Gene::passedFilters) - .filter(gene -> gene.getCombinedScore() >= minExomiserGeneScore) - .filter(withinNumberOfGenesToShow(numberOfGenesToShow)) .collect(toUnmodifiableList()); } + /** + * Filters the input genes for those meeting the criteria defined in the {@link OutputSettings}. + * This method DOES NOT filter the contributing variants and will return all genes irrespective of their PASS/FAIL + * status. + * + * @param genes Input list to filter + * @return A {@link Stream} of genes meeting the output options criteria. + * @since 13.1.0 + */ + public Stream applyOutputSettings(List genes) { + return genes.stream() + .filter(gene -> gene.getCombinedScore() >= minExomiserGeneScore) + .filter(withinNumberOfGenesToShow(numberOfGenesToShow)); + } + private Predicate withinNumberOfGenesToShow(int limit) { AtomicInteger count = new AtomicInteger(1); return gene -> { diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtils.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtils.java index ade8947fc..d5f40326d 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtils.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtils.java @@ -37,8 +37,10 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.nio.file.Files; import java.nio.file.Path; import java.util.List; +import java.util.Objects; import java.util.Set; import java.util.stream.Collectors; @@ -58,6 +60,17 @@ private ResultsWriterUtils() { //Empty - this is a static class. } + public static Path resolveOutputDir(String outputPrefix) { + if (outputPrefix.isEmpty()) { + return Path.of(DEFAULT_OUTPUT_DIR); + } + Path outputPrefixPath = Path.of(outputPrefix); + if (Files.isDirectory(outputPrefixPath)) { + return outputPrefixPath; + } + return Objects.requireNonNullElse(outputPrefixPath.getParent(), Path.of("")); + } + /** * Determines the correct file extension for a file given that was specified by the user, or a sensible default if not. * @@ -69,18 +82,14 @@ private ResultsWriterUtils() { */ public static String makeOutputFilename(Path vcfPath, String outputPrefix, OutputFormat outputFormat, ModeOfInheritance modeOfInheritance) { String moiAbbreviation = moiAbbreviation(modeOfInheritance); - if (outputPrefix.isEmpty() && vcfPath == null) { - String defaultOutputPrefix = String.format("%s/exomiser", ResultsWriterUtils.DEFAULT_OUTPUT_DIR); - logger.debug("Output prefix and VCF was unspecified. Will write out to: {}", defaultOutputPrefix); - return String.format("%s%s.%s", defaultOutputPrefix, moiAbbreviation, outputFormat.getFileExtension()); - } - if (outputPrefix.isEmpty()) { - String fileName = vcfPath.getFileName().toString().replace(".vcf", "").replace(".gz", ""); - String defaultOutputPrefix = String.format("%s/%s_exomiser", ResultsWriterUtils.DEFAULT_OUTPUT_DIR, fileName); - logger.debug("Output prefix was unspecified. Will write out to: {}", defaultOutputPrefix); - return String.format("%s%s.%s", defaultOutputPrefix, moiAbbreviation, outputFormat.getFileExtension()); + String baseFileName = Path.of(outputPrefix).getFileName().toString(); + if (baseFileName.isEmpty() && vcfPath == null) { + baseFileName = "exomiser"; + } else if (baseFileName.isEmpty()) { + String vcfFileName = vcfPath.getFileName().toString().replace(".vcf", "").replace(".gz", ""); + baseFileName = vcfFileName + "-exomiser"; } - return String.format("%s%s.%s", outputPrefix, moiAbbreviation, outputFormat.getFileExtension()); + return resolveOutputDir(outputPrefix).normalize().resolve(baseFileName + moiAbbreviation + '.' + outputFormat.getFileExtension()).toString(); } private static String moiAbbreviation(ModeOfInheritance modeOfInheritance) { @@ -112,7 +121,7 @@ public static List makeVariantEffectCounters(List sa VariantEffect.INITIATOR_CODON_VARIANT, VariantEffect.SYNONYMOUS_VARIANT, VariantEffect.FIVE_PRIME_UTR_TRUNCATION, VariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT, - VariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT, + VariantEffect.FIVE_PRIME_UTR_EXON_VARIANT, VariantEffect.THREE_PRIME_UTR_TRUNCATION, VariantEffect.THREE_PRIME_UTR_INTRON_VARIANT, VariantEffect.THREE_PRIME_UTR_EXON_VARIANT, diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ScoreRanker.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ScoreRanker.java new file mode 100644 index 000000000..2f4603119 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/ScoreRanker.java @@ -0,0 +1,71 @@ +package org.monarchinitiative.exomiser.core.writers; + +import java.math.BigDecimal; +import java.math.RoundingMode; + +class ScoreRanker { + + /** Positive zero. */ + private static final double POSITIVE_ZERO = 0d; + + private final int scale; + + private int rank = 0; + private double currentScore = Double.MAX_VALUE; + private int count = 0; + + ScoreRanker(int scale) { + this.scale = scale; + } + + /** + * Expects scores to be sorted in descending numerical order. + * + * @param score a score from a series of descending values where the highest score is ranked first. + * @return the running rank of the input score + */ + int rank(double score) { + double round = round(score, scale, RoundingMode.HALF_EVEN); + if (round > currentScore) { + throw new IllegalStateException("Input score " + score + " greater than previous score of " + currentScore+ ". Scores must be provided in reverse numerical order i.e. highest to lowest."); + } + count++; + if (currentScore == round) { + return rank; + } + currentScore = round; + rank = count; + return rank; + } + + + /** + * Rounds the given value to the specified number of decimal places. + * The value is rounded using the given method which is any method defined + * in {@link BigDecimal}. + * If {@code x} is infinite or {@code NaN}, then the value of {@code x} is + * returned unchanged, regardless of the other parameters. + * + * @param x Value to round. + * @param scale Number of digits to the right of the decimal point. + * @param roundingMethod Rounding method as defined in {@link BigDecimal}. + * @return the rounded value. + * @throws ArithmeticException if {@code roundingMethod} is + * {@link RoundingMode#UNNECESSARY} and the specified scaling operation + * would require rounding. + */ + private static double round(double x, int scale, RoundingMode roundingMethod) { + try { + final double rounded = (new BigDecimal(Double.toString(x)) + .setScale(scale, roundingMethod)) + .doubleValue(); + // MATH-1089: negative values rounded to zero should result in negative zero + return rounded == POSITIVE_ZERO ? POSITIVE_ZERO * x : rounded; + } catch (NumberFormatException ex) { + if (Double.isInfinite(x)) { + return x; + } + return Double.NaN; + } + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvGeneAllMoiResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvGeneAllMoiResultsWriter.java new file mode 100644 index 000000000..2ef4895dc --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvGeneAllMoiResultsWriter.java @@ -0,0 +1,162 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2022 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.writers; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; +import org.monarchinitiative.exomiser.core.analysis.AnalysisResults; +import org.monarchinitiative.exomiser.core.analysis.sample.Sample; +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.model.GeneScore; +import org.monarchinitiative.exomiser.core.prioritisers.HiPhivePriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.OmimPriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; +import java.nio.file.Path; +import java.text.DecimalFormat; +import java.util.ArrayList; +import java.util.List; +import java.util.Locale; +import java.util.function.Consumer; + +/** + * @since 13.1.0 + */ +public class TsvGeneAllMoiResultsWriter implements ResultsWriter { + private static final Logger logger = LoggerFactory.getLogger(TsvGeneAllMoiResultsWriter.class); + private static final OutputFormat OUTPUT_FORMAT = OutputFormat.TSV_GENE; + private final CSVFormat csvFormat = CSVFormat.newFormat('\t') + .withQuote(null) + .withRecordSeparator("\n") + .withIgnoreSurroundingSpaces(true) + .withHeader("#RANK", "ID", "GENE_SYMBOL", "ENTREZ_GENE_ID", "MOI", "P-VALUE", "EXOMISER_GENE_COMBINED_SCORE", "EXOMISER_GENE_PHENO_SCORE", "EXOMISER_GENE_VARIANT_SCORE", "HUMAN_PHENO_SCORE", "MOUSE_PHENO_SCORE", "FISH_PHENO_SCORE", "WALKER_SCORE", "PHIVE_ALL_SPECIES_SCORE", "OMIM_SCORE", "MATCHES_CANDIDATE_GENE", "HUMAN_PHENO_EVIDENCE", "MOUSE_PHENO_EVIDENCE", "FISH_PHENO_EVIDENCE", "HUMAN_PPI_EVIDENCE", "MOUSE_PPI_EVIDENCE", "FISH_PPI_EVIDENCE"); + + private final DecimalFormat decimalFormat = new DecimalFormat("0.0000"); + + public TsvGeneAllMoiResultsWriter() { + Locale.setDefault(Locale.UK); + } + + public void writeFile(ModeOfInheritance modeOfInheritance, AnalysisResults analysisResults, OutputSettings outputSettings) { + Sample sample = analysisResults.getSample(); + String outFileName = ResultsWriterUtils.makeOutputFilename(sample.getVcfPath(), outputSettings.getOutputPrefix(), OUTPUT_FORMAT, ModeOfInheritance.ANY); + Path outFile = Path.of(outFileName); + + try (CSVPrinter printer = new CSVPrinter(Files.newBufferedWriter(outFile, StandardCharsets.UTF_8), this.csvFormat)){ + writeData(analysisResults, outputSettings, printer); + } catch (Exception e) { + logger.error("Unable to write results to file {}", outFileName, e); + } + + logger.debug("{} {} results written to file {}", OUTPUT_FORMAT, ModeOfInheritance.ANY.getAbbreviation(), outFileName); + } + + public String writeString(ModeOfInheritance modeOfInheritance, AnalysisResults analysisResults, OutputSettings outputSettings) { + StringBuilder stringBuilder = new StringBuilder(); + + try (CSVPrinter printer = new CSVPrinter(stringBuilder, this.csvFormat)) { + this.writeData(analysisResults, outputSettings, printer); + } catch (IOException e) { + logger.error("Unable to write results to string {}", stringBuilder, e); + } + + return stringBuilder.toString(); + } + + private void writeData(AnalysisResults analysisResults, OutputSettings outputSettings, CSVPrinter printer) { + GeneScoreRanker geneScoreRanker = new GeneScoreRanker(analysisResults, outputSettings); + geneScoreRanker.rankedGenes() + .map(rankedGene -> makeGeneScoreRecord(rankedGene.rank(), rankedGene.gene(), rankedGene.geneScore())) + .forEach(printRecord(printer)); + } + + Consumer> printRecord(CSVPrinter printer) { + return strings -> { + try { + printer.printRecord(strings); + } catch (IOException e) { + // cross fingers and swallow? + throw new IllegalStateException(e); + } + }; + } + + private List makeGeneScoreRecord(int rank, Gene gene, GeneScore geneScore) { + double humanPhenScore = 0.0; + double mousePhenScore = 0.0; + double fishPhenScore = 0.0; + double walkerScore = 0.0; + double phiveAllSpeciesScore = 0.0; + double omimScore = 0.0; + String phenoEvidence = ""; + int matchesCandidateGene = 0; + + for (PriorityResult prioritiserResult : gene.getPriorityResults().values()) { + PriorityType type = prioritiserResult.getPriorityType(); + if (type == PriorityType.HIPHIVE_PRIORITY) { + HiPhivePriorityResult phenoScore = (HiPhivePriorityResult) prioritiserResult; + phiveAllSpeciesScore = phenoScore.getScore(); + humanPhenScore = phenoScore.getHumanScore(); + mousePhenScore = phenoScore.getMouseScore(); + fishPhenScore = phenoScore.getFishScore(); + walkerScore = phenoScore.getPpiScore(); + phenoEvidence = phenoScore.getPhenotypeEvidenceText(); + if (phenoScore.isCandidateGeneMatch()) { + matchesCandidateGene = 1; + } + } else if (type == PriorityType.OMIM_PRIORITY) { + OmimPriorityResult omimPriorityResult = (OmimPriorityResult) prioritiserResult; + omimScore = omimPriorityResult.getScoreForMode(geneScore.getModeOfInheritance()); + } else if (type == PriorityType.EXOMEWALKER_PRIORITY) { + walkerScore = prioritiserResult.getScore(); + } + } + List values = new ArrayList<>(16); + ModeOfInheritance modeOfInheritance = geneScore.getModeOfInheritance(); + String moiAbbreviation = modeOfInheritance.getAbbreviation() == null ? "ANY" : modeOfInheritance.getAbbreviation(); + values.add(Integer.toString(rank)); + String geneSymbol = gene.getGeneSymbol(); + values.add(geneSymbol + "_" + moiAbbreviation); + values.add(geneSymbol); + values.add(Integer.toString(gene.getEntrezGeneID())); + values.add(moiAbbreviation); + values.add(decimalFormat.format(geneScore.pValue())); + values.add(decimalFormat.format(geneScore.getCombinedScore())); + values.add(decimalFormat.format(geneScore.getPhenotypeScore())); + values.add(decimalFormat.format(geneScore.getVariantScore())); + values.add(decimalFormat.format(humanPhenScore)); + values.add(decimalFormat.format(mousePhenScore)); + values.add(decimalFormat.format(fishPhenScore)); + values.add(decimalFormat.format(walkerScore)); + values.add(decimalFormat.format(phiveAllSpeciesScore)); + values.add(decimalFormat.format(omimScore)); + values.add(Integer.toString(matchesCandidateGene)); + values.add(phenoEvidence); + return values; + } +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantAllMoiResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantAllMoiResultsWriter.java new file mode 100644 index 000000000..754c10726 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantAllMoiResultsWriter.java @@ -0,0 +1,238 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2022 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.writers; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; +import java.nio.file.Path; +import java.text.DecimalFormat; +import java.util.ArrayList; +import java.util.List; +import java.util.Locale; +import java.util.Optional; +import java.util.Set; +import java.util.StringJoiner; +import java.util.function.Consumer; + +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; +import org.monarchinitiative.exomiser.core.analysis.AnalysisResults; +import org.monarchinitiative.exomiser.core.analysis.sample.Sample; +import org.monarchinitiative.exomiser.core.analysis.util.GeneConstraint; +import org.monarchinitiative.exomiser.core.analysis.util.GeneConstraints; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgAssignment; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgClassification; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgEvidence; +import org.monarchinitiative.exomiser.core.filters.FilterType; +import org.monarchinitiative.exomiser.core.model.GeneIdentifier; +import org.monarchinitiative.exomiser.core.model.GeneScore; +import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.model.frequency.Frequency; +import org.monarchinitiative.exomiser.core.model.frequency.FrequencyData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.ClinVarData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityScore; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import static java.util.stream.Collectors.*; + +/** + * @since 13.1.0 + */ +public class TsvVariantAllMoiResultsWriter implements ResultsWriter { + private static final Logger logger = LoggerFactory.getLogger(TsvVariantAllMoiResultsWriter.class); + private static final OutputFormat OUTPUT_FORMAT = OutputFormat.TSV_VARIANT; + private final CSVFormat csvFormat = CSVFormat.newFormat('\t') + .withQuote(null) + .withRecordSeparator("\n") + .withIgnoreSurroundingSpaces(true) + .withHeader("#RANK", "ID", "GENE_SYMBOL", "ENTREZ_GENE_ID", "MOI", "P-VALUE", "EXOMISER_GENE_COMBINED_SCORE", "EXOMISER_GENE_PHENO_SCORE", "EXOMISER_GENE_VARIANT_SCORE", "EXOMISER_VARIANT_SCORE", "CONTRIBUTING_VARIANT", "WHITELIST_VARIANT", "VCF_ID", "RS_ID", "CONTIG", "START", "END", "REF", "ALT", "CHANGE_LENGTH", "QUAL", "FILTER", "GENOTYPE", "FUNCTIONAL_CLASS", "HGVS", "EXOMISER_ACMG_CLASSIFICATION", "EXOMISER_ACMG_EVIDENCE", "EXOMISER_ACMG_DISEASE_ID", "EXOMISER_ACMG_DISEASE_NAME", "CLINVAR_ALLELE_ID", "CLINVAR_PRIMARY_INTERPRETATION", "CLINVAR_STAR_RATING", "GENE_CONSTRAINT_LOEUF", "GENE_CONSTRAINT_LOEUF_LOWER", "GENE_CONSTRAINT_LOEUF_UPPER", "MAX_FREQ_SOURCE", "MAX_FREQ", "ALL_FREQ", "MAX_PATH_SOURCE", "MAX_PATH", "ALL_PATH"); + private final DecimalFormat decimalFormat = new DecimalFormat("0.0000"); + + public TsvVariantAllMoiResultsWriter() { + Locale.setDefault(Locale.UK); + } + + public void writeFile(ModeOfInheritance modeOfInheritance, AnalysisResults analysisResults, OutputSettings outputSettings) { + Sample sample = analysisResults.getSample(); + String outFileName = ResultsWriterUtils.makeOutputFilename(sample.getVcfPath(), outputSettings.getOutputPrefix(), OUTPUT_FORMAT, ModeOfInheritance.ANY); + Path outFile = Path.of(outFileName); + + try (CSVPrinter printer = new CSVPrinter(Files.newBufferedWriter(outFile, StandardCharsets.UTF_8), this.csvFormat)) { + this.writeData(analysisResults, outputSettings, printer); + } catch (Exception var12) { + logger.error("Unable to write results to file {}", outFileName, var12); + } + + logger.debug("{} {} results written to file {}", OUTPUT_FORMAT, ModeOfInheritance.ANY.getAbbreviation(), outFileName); + } + + public String writeString(ModeOfInheritance modeOfInheritance, AnalysisResults analysisResults, OutputSettings outputSettings) { + StringBuilder output = new StringBuilder(); + + try (CSVPrinter printer = new CSVPrinter(output, this.csvFormat)) { + this.writeData(analysisResults, outputSettings, printer); + } catch (Exception var10) { + logger.error("Unable to write results to string {}", output, var10); + } + + return output.toString(); + } + + private void writeData(AnalysisResults analysisResults, OutputSettings outputSettings, CSVPrinter printer) { + GeneScoreRanker geneScoreRanker = new GeneScoreRanker(analysisResults, outputSettings); + geneScoreRanker.rankedVariants() + .map(rankedVariant -> buildVariantRecord(rankedVariant.rank(), rankedVariant.variantEvaluation(), rankedVariant.geneScore())) + .forEach(printRecord(printer)); + } + + Consumer> printRecord(CSVPrinter printer) { + return list -> { + try { + printer.printRecord(list); + } catch (IOException e) { + // cross fingers and swallow? + throw new IllegalStateException(e); + } + }; + } + + private List buildVariantRecord(int rank, VariantEvaluation ve, GeneScore geneScore) { + List fields = new ArrayList<>(csvFormat.getHeader().length); + GeneIdentifier geneIdentifier = geneScore.getGeneIdentifier(); + ModeOfInheritance modeOfInheritance = geneScore.getModeOfInheritance(); + String moiAbbreviation = modeOfInheritance.getAbbreviation() == null ? "ANY" : modeOfInheritance.getAbbreviation(); + List acmgAssignments = geneScore.getAcmgAssignments(); + Optional assignment = acmgAssignments.stream().filter(acmgAssignment -> acmgAssignment.variantEvaluation().equals(ve)).findFirst(); + fields.add(rank); + String gnomadString = ve.toGnomad(); + fields.add(gnomadString + "_" + moiAbbreviation); + fields.add(geneIdentifier.getGeneSymbol()); + fields.add(geneIdentifier.getEntrezId()); + fields.add(moiAbbreviation); + fields.add(decimalFormat.format(geneScore.pValue())); + fields.add(decimalFormat.format(geneScore.getCombinedScore())); + fields.add(decimalFormat.format(geneScore.getPhenotypeScore())); + fields.add(decimalFormat.format(geneScore.getVariantScore())); + fields.add(decimalFormat.format(ve.getVariantScore())); + fields.add(ve.contributesToGeneScoreUnderMode(modeOfInheritance) ? "1" : "0"); + fields.add(ve.isWhiteListed() ? "1" : "0"); + fields.add(ve.id()); + FrequencyData frequencyData = ve.getFrequencyData(); + fields.add(frequencyData.getRsId()); + fields.add(ve.contigName()); + fields.add(ve.start()); + fields.add(ve.end()); + fields.add(ve.ref()); + fields.add(ve.alt()); + fields.add(ve.changeLength()); + fields.add(this.decimalFormat.format(ve.getPhredScore())); + fields.add(this.makeFiltersField(modeOfInheritance, ve)); + fields.add(ve.getGenotypeString()); + fields.add(ve.getVariantEffect().getSequenceOntologyTerm()); + fields.add(this.getRepresentativeAnnotation(ve.getTranscriptAnnotations())); + fields.add(assignment.map(AcmgAssignment::acmgClassification).orElse(AcmgClassification.NOT_AVAILABLE)); + fields.add(assignment.map(acmgAssignment -> toVcfAcmgInfo(acmgAssignment.acmgEvidence())).orElse("")); + fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseId()).orElse("")); + fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseName()).orElse("")); + PathogenicityData pathogenicityData = ve.getPathogenicityData(); + ClinVarData clinVarData = pathogenicityData.getClinVarData(); + fields.add(clinVarData.getAlleleId()); + fields.add(clinVarData.getPrimaryInterpretation()); + fields.add(clinVarData.starRating()); + GeneConstraint geneConstraint = GeneConstraints.geneContraint(geneIdentifier.getGeneSymbol()); + fields.add(geneConstraint == null ? "" : geneConstraint.loeuf()); + fields.add(geneConstraint == null ? "" : geneConstraint.loeufLower()); + fields.add(geneConstraint == null ? "" : geneConstraint.loeufUpper()); + Frequency maxFreq = frequencyData.getMaxFrequency(); + fields.add(maxFreq == null ? "" : maxFreq.getSource()); + fields.add(maxFreq == null ? "" : maxFreq.getFrequency()); + fields.add(toVcfFreqInfo(frequencyData.getKnownFrequencies())); + PathogenicityScore maxPath = pathogenicityData.getMostPathogenicScore(); + fields.add(maxPath == null ? "" : maxPath.getSource()); + fields.add(maxPath == null ? "" : maxPath.getScore()); + fields.add(toVcfPathInfo(pathogenicityData.getPredictedPathogenicityScores())); + return fields; + } + + private String toVcfAcmgInfo(AcmgEvidence acmgEvidence) { + return acmgEvidence.evidence().entrySet().stream() + .map(entry -> { + AcmgCriterion acmgCriterion = entry.getKey(); + AcmgCriterion.Evidence evidence = entry.getValue(); + return (acmgCriterion.evidence() == evidence) ? acmgCriterion.toString() : acmgCriterion + "_" + evidence.displayString(); + }) + .collect(joining(",")); + } + private String toVcfFreqInfo(List frequencies) { + return frequencies.stream() + .map(frequency -> frequency.getSource() + "=" + frequency.getFrequency()) + .collect(joining(",")); + } + + private String toVcfPathInfo(List predictedPathogenicityScores) { + return predictedPathogenicityScores.stream() + .map(pathScore -> pathScore.getSource() + "=" + pathScore.getScore()) + .collect(joining(",")); + } + + private String makeFiltersField(ModeOfInheritance modeOfInheritance, VariantEvaluation variantEvaluation) { + switch (variantEvaluation.getFilterStatusForMode(modeOfInheritance)) { + case FAILED: + Set failedFilterTypes = variantEvaluation.getFailedFilterTypesForMode(modeOfInheritance); + return this.formatFailedFilters(failedFilterTypes); + case PASSED: + return "PASS"; + case UNFILTERED: + default: + return "."; + } + } + + private String formatFailedFilters(Set failedFilters) { + StringJoiner stringJoiner = new StringJoiner(";"); + for (FilterType filterType : failedFilters) { + stringJoiner.add(filterType.vcfValue()); + } + return stringJoiner.toString(); + } + + private String getRepresentativeAnnotation(List annotations) { + if (annotations.isEmpty()) { + return ""; + } else { + TranscriptAnnotation anno = annotations.get(0); + StringJoiner stringJoiner = new StringJoiner(":"); + stringJoiner.add(anno.getGeneSymbol()); + stringJoiner.add(anno.getAccession()); + stringJoiner.add(anno.getHgvsCdna()); + stringJoiner.add(anno.getHgvsProtein()); + return stringJoiner.toString(); + } + } + +} diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/VcfAllMoiResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/VcfAllMoiResultsWriter.java new file mode 100644 index 000000000..3e71c35f8 --- /dev/null +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/VcfAllMoiResultsWriter.java @@ -0,0 +1,248 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.writers; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextComparator; +import htsjdk.variant.variantcontext.writer.Options; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; +import htsjdk.variant.vcf.*; +import org.monarchinitiative.exomiser.core.analysis.AnalysisResults; +import org.monarchinitiative.exomiser.core.analysis.sample.Sample; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgAssignment; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgClassification; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgEvidence; +import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; +import org.monarchinitiative.exomiser.core.genome.VcfFiles; +import org.monarchinitiative.exomiser.core.model.*; +import org.monarchinitiative.svart.Contig; +import org.monarchinitiative.svart.GenomicAssembly; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.ByteArrayOutputStream; +import java.nio.charset.StandardCharsets; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.text.DecimalFormat; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; + +import static java.util.stream.Collectors.*; + +/** + * Generate results in VCF format using HTS-JDK. + * + * @author Jules Jacobsen + * @author Manuel Holtgrewe + * @see VCF Standard + * @since 13.1.0 + */ +public class VcfAllMoiResultsWriter implements ResultsWriter { + private static final Logger logger = LoggerFactory.getLogger(VcfAllMoiResultsWriter.class); + + private static final String EXOMISER_INFO_KEY = "Exomiser"; + private static final VCFHeaderLine EXOMISER_VCF_HEADER_METADATA_LINE = new VCFInfoHeaderLine(EXOMISER_INFO_KEY, + VCFHeaderLineCount.UNBOUNDED, + VCFHeaderLineType.String, + "A pipe-separated set of values for the proband allele(s) from the record with one per compatible MOI following the format: {RANK|ID|GENE_SYMBOL|ENTREZ_GENE_ID|MOI|P-VALUE|EXOMISER_GENE_COMBINED_SCORE|EXOMISER_GENE_PHENO_SCORE|EXOMISER_GENE_VARIANT_SCORE|EXOMISER_VARIANT_SCORE|CONTRIBUTING_VARIANT|WHITELIST_VARIANT|FUNCTIONAL_CLASS|HGVS|EXOMISER_ACMG_CLASSIFICATION|EXOMISER_ACMG_EVIDENCE|EXOMISER_ACMG_DISEASE_ID|EXOMISER_ACMG_DISEASE_NAME}" + ); + + private static final OutputFormat OUTPUT_FORMAT = OutputFormat.VCF; + + private final DecimalFormat decimalFormat = new DecimalFormat("0.0000"); + + /** + * Initialize the object, given the original {@link VCFFileReader} from the + * input. + */ + public VcfAllMoiResultsWriter() { + Locale.setDefault(Locale.UK); + } + + @Override + public void writeFile(ModeOfInheritance modeOfInheritance, AnalysisResults analysisResults, OutputSettings settings) { + // create a VariantContextWriter writing to the output file path + Sample sample = analysisResults.getSample(); + Path vcfPath = sample.getVcfPath(); + if (vcfPath == null) { + logger.info("Skipping writing VCF results as no input VCF has been defined"); + return; + } + String outFileName = ResultsWriterUtils.makeOutputFilename(vcfPath, settings.getOutputPrefix(), OUTPUT_FORMAT, ModeOfInheritance.ANY); + Path outPath = Paths.get(outFileName + ".gz"); + try (VariantContextWriter writer = variantContextWriterBuilder().setOutputPath(outPath).build()) { + writeData(analysisResults, settings, vcfPath, writer); + } + logger.debug("{} {} results written to file {}.", OUTPUT_FORMAT, ModeOfInheritance.ANY.getAbbreviation(), outFileName); + } + + @Override + public String writeString(ModeOfInheritance modeOfInheritance, AnalysisResults analysisResults, OutputSettings settings) { + Sample sample = analysisResults.getSample(); + Path vcfPath = sample.getVcfPath(); + if (vcfPath == null) { + logger.info("Skipping writing VCF results as no input VCF has been defined. Returning empty string."); + return ""; + } + // create a VariantContextWriter writing to a buffer + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + try (VariantContextWriter writer = variantContextWriterBuilder().setOutputStream(baos).build()) { + writeData(analysisResults, settings, vcfPath, writer); + } + logger.debug("{} results written to string buffer", OUTPUT_FORMAT); + return baos.toString(StandardCharsets.UTF_8); + } + + private VariantContextWriterBuilder variantContextWriterBuilder() { + return new VariantContextWriterBuilder() + .setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER); + } + + private void writeData(AnalysisResults analysisResults, OutputSettings outputSettings, Path vcfPath, VariantContextWriter writer){ + // n.b. identity is key here as VariantContext doesn't override equals() or hashCode() so don't change the implementation of this map + Map> variantContextAlleleInfoMap = new IdentityHashMap<>(); + + GeneScoreRanker geneScoreRanker = new GeneScoreRanker(analysisResults, outputSettings); + geneScoreRanker.rankedVariants().forEach(rankedVariant -> { + VariantEvaluation ve = rankedVariant.variantEvaluation(); + String alleleInfo = this.buildVariantRecord(rankedVariant.rank(), ve, rankedVariant.geneScore()); + if (variantContextAlleleInfoMap.containsKey(ve.getVariantContext())) { + variantContextAlleleInfoMap.get(ve.getVariantContext()).add(alleleInfo); + } else { + var alleleInfoList = new ArrayList(); + alleleInfoList.add(alleleInfo); + variantContextAlleleInfoMap.put(ve.getVariantContext(), alleleInfoList); + } + }); + + VCFHeader vcfHeader = VcfFiles.readVcfHeader(vcfPath); + vcfHeader.addMetaDataLine(EXOMISER_VCF_HEADER_METADATA_LINE); + + SAMSequenceDictionary samSequenceDictionary = vcfHeader.getSequenceDictionary(); + Map genesById = geneScoreRanker.mapGenesByGeneIdentifier(); + if (samSequenceDictionary == null) { + var genomicAssembly = genesById.values().stream() + .filter(Gene::hasVariants) + .flatMap(gene -> gene.getVariantEvaluations().stream()) + .findFirst() + .map(Variant::getGenomeAssembly) + .orElse(GenomeAssembly.UNKNOWN) + .genomicAssembly(); + samSequenceDictionary = createSamSequenceDictionary(genomicAssembly, variantContextAlleleInfoMap.keySet()); + vcfHeader.setSequenceDictionary(samSequenceDictionary); + } + writer.writeHeader(vcfHeader); + + if (variantContextAlleleInfoMap.isEmpty() || samSequenceDictionary.isEmpty()) { + // don't try sorting and writing as the VariantContextComparator will throw an error + // with no contigs in the samSequenceDictionary + return; + } + + variantContextAlleleInfoMap.entrySet().stream() + .map(entry -> new VariantContextBuilder(entry.getKey()) + .attribute(EXOMISER_INFO_KEY, String.join(",", entry.getValue())) + .make()) + .sorted(new VariantContextComparator(samSequenceDictionary)) + .forEach(writer::add); + } + + private SAMSequenceDictionary createSamSequenceDictionary(GenomicAssembly genomicAssembly, Set variantContexts) { + var unknownContigId = new AtomicInteger(genomicAssembly.contigs().size()); + var contigs = variantContexts.stream() + .map(VariantContext::getContig) + .distinct() + .map(contigName -> { + // it's possible that there are other non-canonical contigs, in which case we'll make some new ids for the sequence index + Contig contig = genomicAssembly.contigByName(contigName); + SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord(contigName, contig.length()); + samSequenceRecord.setSequenceIndex(contig.isUnknown() ? unknownContigId.incrementAndGet() : contig.id()); + samSequenceRecord.setAssembly(genomicAssembly.name()); + samSequenceRecord.setAlternativeSequenceName(contig.isUnknown() ? List.of() : List.of(contig.ucscName(), contig.name(), contig.genBankAccession())); + return samSequenceRecord; + }) + .sorted(Comparator.comparingInt(SAMSequenceRecord::getSequenceIndex)) + .collect(toList()); + + return new SAMSequenceDictionary(contigs); + } + + private String buildVariantRecord(int rank, VariantEvaluation ve, GeneScore geneScore) { + List fields = new ArrayList<>(); + GeneIdentifier geneIdentifier = geneScore.getGeneIdentifier(); + ModeOfInheritance modeOfInheritance = geneScore.getModeOfInheritance(); + String moiAbbreviation = modeOfInheritance.getAbbreviation() == null ? "ANY" : modeOfInheritance.getAbbreviation(); + List acmgAssignments = geneScore.getAcmgAssignments(); + Optional assignment = acmgAssignments.stream().filter(acmgAssignment -> acmgAssignment.variantEvaluation().equals(ve)).findFirst(); + fields.add(String.valueOf(rank)); + String gnomadString = ve.toGnomad(); + fields.add(gnomadString + "_" + moiAbbreviation); + fields.add(geneIdentifier.getGeneSymbol()); + fields.add(geneIdentifier.getEntrezId()); + fields.add(moiAbbreviation); + fields.add(decimalFormat.format(geneScore.pValue())); + fields.add(decimalFormat.format(geneScore.getCombinedScore())); + fields.add(decimalFormat.format(geneScore.getPhenotypeScore())); + fields.add(decimalFormat.format(geneScore.getVariantScore())); + fields.add(decimalFormat.format(ve.getVariantScore())); + fields.add(ve.contributesToGeneScoreUnderMode(modeOfInheritance) ? "1" : "0"); + fields.add(ve.isWhiteListed() ? "1" : "0"); + fields.add(ve.getVariantEffect().getSequenceOntologyTerm()); + fields.add(this.getRepresentativeAnnotation(ve.getTranscriptAnnotations())); + fields.add(assignment.map(AcmgAssignment::acmgClassification).orElse(AcmgClassification.NOT_AVAILABLE).toString()); + fields.add(assignment.map(acmgAssignment -> toVcfAcmgInfo(acmgAssignment.acmgEvidence())).orElse("")); + fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseId()).orElse("")); + fields.add('"' + assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseName()).orElse("") + '"'); + return "{"+ String.join("|", fields) + "}"; + } + + private String toVcfAcmgInfo(AcmgEvidence acmgEvidence) { + return acmgEvidence.evidence().entrySet().stream() + .map(entry -> { + AcmgCriterion acmgCriterion = entry.getKey(); + AcmgCriterion.Evidence evidence = entry.getValue(); + return (acmgCriterion.evidence() == evidence) ? acmgCriterion.toString() : acmgCriterion + "_" + evidence.displayString(); + }) + .collect(Collectors.joining(",")); + } + + private String getRepresentativeAnnotation(List annotations) { + if (annotations.isEmpty()) { + return ""; + } else { + TranscriptAnnotation anno = annotations.get(0); + StringJoiner stringJoiner = new StringJoiner(":"); + stringJoiner.add(anno.getGeneSymbol()); + stringJoiner.add(anno.getAccession()); + stringJoiner.add(anno.getHgvsCdna()); + stringJoiner.add(anno.getHgvsProtein()); + return stringJoiner.toString(); + } + } +} diff --git a/exomiser-core/src/main/resources/gnomad.v2.1.1.gene-constraints.tsv b/exomiser-core/src/main/resources/gnomad.v2.1.1.gene-constraints.tsv new file mode 100644 index 000000000..1914e2604 --- /dev/null +++ b/exomiser-core/src/main/resources/gnomad.v2.1.1.gene-constraints.tsv @@ -0,0 +1,19726 @@ +## created with command: +## bgzip -d -c gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz | cut -f 1,2,21,24,29,30 > gnomad.v2.1.1.gene-constraints.tsv +## pLI (probability of being loss-of-function intolerant) +## pLI scores closer to one indicate more intolerance to protein-truncating variation. For a set of transcripts +## intolerant of protein-truncating variation, we suggest pLI ≥ 0.9. +## +## Observed / expected (oe) +## The constraint score shown in gnomAD is the ratio of the observed / expected (oe) number of loss-of-function variants +## in that gene. The expected counts are based on a mutational model that takes sequence context, coverage and methylation +## into account. +## Interpretation +## Observed/expected (oe) is a continuous measure of how tolerant a gene is to a certain class of variation +## (e.g. loss-of-function). When a gene has a low oe value, it is under stronger selection for that class of variation +## than a gene with a higher value. Because counts depend on gene size and sample size, the precision of the oe values +## varies a lot from one gene to the next. Therefore in addition to the oe value, we also display the 90% confidence +## interval (CI) for each of the oe values. When evaluating how constrained a gene is, it is essential to take the 90% +## CI into consideration. +## Although oe is a continuous value, we understand that it can be useful to use a threshold for certain applications. In +## particular, for the interpretation of Mendelian diseases cases, we suggest using the upper bound of the oe CI < 0.35 +## as a threshold if needed. Again, ideally oe should be used as a continuous value rather than a cutoff and evaluating +## the oe 90% CI is a must. +#gene transcript pLI oe_lof oe_lof_lower oe_lof_upper +MED13 ENST00000397786 1.0000e+00 0.0000e+00 0.0000e+00 3.0000e-02 +NIPBL ENST00000282516 1.0000e+00 6.6527e-03 1.0000e-03 3.2000e-02 +SMC3 ENST00000361804 1.0000e+00 0.0000e+00 0.0000e+00 3.7000e-02 +CNOT1 ENST00000317147 1.0000e+00 7.9978e-03 2.0000e-03 3.8000e-02 +RLF ENST00000372771 1.0000e+00 0.0000e+00 0.0000e+00 4.0000e-02 +PCF11 ENST00000298281 1.0000e+00 0.0000e+00 0.0000e+00 4.0000e-02 +FNDC3B ENST00000336824 1.0000e+00 0.0000e+00 0.0000e+00 4.2000e-02 +TAF1 ENST00000276072 1.0000e+00 0.0000e+00 0.0000e+00 4.3000e-02 +RSF1 ENST00000308488 1.0000e+00 0.0000e+00 0.0000e+00 4.4000e-02 +NCKAP1 ENST00000360982 1.0000e+00 0.0000e+00 0.0000e+00 4.4000e-02 +KDM2A ENST00000529006 1.0000e+00 0.0000e+00 0.0000e+00 4.5000e-02 +BRD4 ENST00000263377 1.0000e+00 0.0000e+00 0.0000e+00 4.8000e-02 +HELZ ENST00000358691 1.0000e+00 1.0152e-02 3.0000e-03 4.8000e-02 +FBN1 ENST00000316623 1.0000e+00 1.8895e-02 8.0000e-03 4.9000e-02 +XPO1 ENST00000401558 1.0000e+00 0.0000e+00 0.0000e+00 5.1000e-02 +PRR12 ENST00000418929 1.0000e+00 0.0000e+00 0.0000e+00 5.1000e-02 +USP9X ENST00000324545 1.0000e+00 1.0698e-02 3.0000e-03 5.1000e-02 +POLA1 ENST00000379059 1.0000e+00 0.0000e+00 0.0000e+00 5.1000e-02 +SYNGAP1 ENST00000418600 1.0000e+00 0.0000e+00 0.0000e+00 5.2000e-02 +PRKDC ENST00000314191 1.0000e+00 2.4934e-02 1.2000e-02 5.2000e-02 +HDAC4 ENST00000345617 1.0000e+00 0.0000e+00 0.0000e+00 5.2000e-02 +SMG1 ENST00000446231 1.0000e+00 2.3202e-02 1.0000e-02 5.3000e-02 +ZC3H4 ENST00000253048 1.0000e+00 0.0000e+00 0.0000e+00 5.4000e-02 +COL5A1 ENST00000371817 1.0000e+00 1.7445e-02 6.0000e-03 5.5000e-02 +SMARCA4 ENST00000429416 1.0000e+00 1.1662e-02 3.0000e-03 5.5000e-02 +TNPO1 ENST00000337273 1.0000e+00 0.0000e+00 0.0000e+00 5.6000e-02 +AGO1 ENST00000373204 1.0000e+00 0.0000e+00 0.0000e+00 5.7000e-02 +ARHGAP35 ENST00000404338 1.0000e+00 0.0000e+00 0.0000e+00 5.7000e-02 +LRP1 ENST00000243077 1.0000e+00 3.2397e-02 1.8000e-02 5.8000e-02 +TOP1 ENST00000361337 1.0000e+00 0.0000e+00 0.0000e+00 5.9000e-02 +TRIP12 ENST00000283943 1.0000e+00 1.8956e-02 7.0000e-03 6.0000e-02 +KMT2E ENST00000311117 1.0000e+00 1.2722e-02 4.0000e-03 6.0000e-02 +HCFC1 ENST00000310441 1.0000e+00 0.0000e+00 0.0000e+00 6.0000e-02 +UBTF ENST00000302904 1.0000e+00 0.0000e+00 0.0000e+00 6.0000e-02 +HUWE1 ENST00000342160 1.0000e+00 2.6088e-02 1.2000e-02 6.0000e-02 +KDM3B ENST00000314358 1.0000e+00 1.2543e-02 3.0000e-03 6.0000e-02 +TRRAP ENST00000359863 1.0000e+00 3.0535e-02 1.6000e-02 6.0000e-02 +GRIN2B ENST00000609686 1.0000e+00 0.0000e+00 0.0000e+00 6.1000e-02 +USP7 ENST00000344836 1.0000e+00 1.2958e-02 4.0000e-03 6.1000e-02 +ATP1A3 ENST00000545399 1.0000e+00 0.0000e+00 0.0000e+00 6.2000e-02 +ASH1L ENST00000392403 1.0000e+00 2.3938e-02 1.0000e-02 6.2000e-02 +ANKRD17 ENST00000358602 1.0000e+00 1.9796e-02 7.0000e-03 6.2000e-02 +SMC1A ENST00000322213 1.0000e+00 0.0000e+00 0.0000e+00 6.2000e-02 +NPEPPS ENST00000322157 1.0000e+00 0.0000e+00 0.0000e+00 6.2000e-02 +CHERP ENST00000546361 1.0000e+00 0.0000e+00 0.0000e+00 6.2000e-02 +MED13L ENST00000281928 1.0000e+00 2.0314e-02 7.0000e-03 6.4000e-02 +RPRD2 ENST00000369068 1.0000e+00 0.0000e+00 0.0000e+00 6.4000e-02 +KMT2A ENST00000534358 1.0000e+00 3.1118e-02 1.5000e-02 6.5000e-02 +CREBBP ENST00000262367 1.0000e+00 2.5349e-02 1.1000e-02 6.6000e-02 +SF3B1 ENST00000335508 1.0000e+00 1.3864e-02 4.0000e-03 6.6000e-02 +EIF3B ENST00000360876 1.0000e+00 0.0000e+00 0.0000e+00 6.7000e-02 +PPFIA1 ENST00000253925 1.0000e+00 1.4130e-02 4.0000e-03 6.7000e-02 +ZSWIM6 ENST00000252744 1.0000e+00 0.0000e+00 0.0000e+00 6.7000e-02 +PRPF3 ENST00000324862 1.0000e+00 0.0000e+00 0.0000e+00 6.8000e-02 +KAT6A ENST00000396930 1.0000e+00 2.1841e-02 8.0000e-03 6.9000e-02 +KMT2B ENST00000222270 1.0000e+00 2.6915e-02 1.1000e-02 7.0000e-02 +SIN3A ENST00000394947 1.0000e+00 1.4832e-02 4.0000e-03 7.0000e-02 +CHD2 ENST00000394196 1.0000e+00 2.7031e-02 1.1000e-02 7.0000e-02 +ARID1A ENST00000324856 1.0000e+00 2.2463e-02 8.0000e-03 7.1000e-02 +GLTSCR1L ENST00000314073 1.0000e+00 0.0000e+00 0.0000e+00 7.1000e-02 +SCN1A ENST00000303395 1.0000e+00 2.2602e-02 8.0000e-03 7.1000e-02 +MED12 ENST00000374080 1.0000e+00 2.2555e-02 8.0000e-03 7.1000e-02 +TJP1 ENST00000346128 1.0000e+00 2.2625e-02 8.0000e-03 7.1000e-02 +SPEN ENST00000375759 1.0000e+00 3.1010e-02 1.4000e-02 7.1000e-02 +WDFY3 ENST00000295888 1.0000e+00 3.7990e-02 2.1000e-02 7.1000e-02 +HDAC6 ENST00000334136 1.0000e+00 0.0000e+00 0.0000e+00 7.2000e-02 +EHMT1 ENST00000460843 1.0000e+00 1.5126e-02 4.0000e-03 7.2000e-02 +JMJD1C ENST00000399262 1.0000e+00 2.7844e-02 1.2000e-02 7.2000e-02 +MAP3K12 ENST00000547035 1.0000e+00 0.0000e+00 0.0000e+00 7.2000e-02 +GGNBP2 ENST00000304718 1.0000e+00 0.0000e+00 0.0000e+00 7.3000e-02 +CASK ENST00000378166 1.0000e+00 0.0000e+00 0.0000e+00 7.3000e-02 +TLE3 ENST00000558939 1.0000e+00 0.0000e+00 0.0000e+00 7.3000e-02 +CHD6 ENST00000373233 1.0000e+00 3.1735e-02 1.5000e-02 7.3000e-02 +UBR5 ENST00000520539 1.0000e+00 3.7137e-02 1.9000e-02 7.3000e-02 +EIF4G1 ENST00000424196 1.0000e+00 2.3611e-02 9.0000e-03 7.4000e-02 +NBEA ENST00000400445 1.0000e+00 3.5174e-02 1.7000e-02 7.4000e-02 +SMARCA5 ENST00000283131 1.0000e+00 1.5690e-02 5.0000e-03 7.4000e-02 +TSC2 ENST00000219476 1.0000e+00 2.3406e-02 9.0000e-03 7.4000e-02 +SUPT5H ENST00000599117 1.0000e+00 1.5513e-02 5.0000e-03 7.4000e-02 +GREB1L ENST00000580732 1.0000e+00 2.3739e-02 9.0000e-03 7.5000e-02 +PTCH1 ENST00000331920 1.0000e+00 1.5809e-02 5.0000e-03 7.5000e-02 +CHD7 ENST00000423902 1.0000e+00 3.6285e-02 1.8000e-02 7.6000e-02 +RAD54L2 ENST00000409535 1.0000e+00 1.6026e-02 5.0000e-03 7.6000e-02 +CNOT3 ENST00000406403 1.0000e+00 0.0000e+00 0.0000e+00 7.6000e-02 +AHDC1 ENST00000374011 1.0000e+00 0.0000e+00 0.0000e+00 7.6000e-02 +U2SURP ENST00000473835 1.0000e+00 1.6335e-02 5.0000e-03 7.7000e-02 +RBM25 ENST00000261973 1.0000e+00 1.6196e-02 5.0000e-03 7.7000e-02 +GIGYF2 ENST00000409451 1.0000e+00 2.9970e-02 1.3000e-02 7.7000e-02 +MBTD1 ENST00000586178 1.0000e+00 0.0000e+00 0.0000e+00 7.7000e-02 +DCAF5 ENST00000341516 1.0000e+00 0.0000e+00 0.0000e+00 7.8000e-02 +SUV420H1 ENST00000304363 1.0000e+00 0.0000e+00 0.0000e+00 7.8000e-02 +RABGAP1 ENST00000373647 1.0000e+00 1.6372e-02 5.0000e-03 7.8000e-02 +KHSRP ENST00000398148 1.0000e+00 0.0000e+00 0.0000e+00 7.8000e-02 +TM9SF2 ENST00000376387 1.0000e+00 0.0000e+00 0.0000e+00 7.9000e-02 +MATR3 ENST00000394805 1.0000e+00 0.0000e+00 0.0000e+00 7.9000e-02 +PHF21A ENST00000418153 1.0000e+00 0.0000e+00 0.0000e+00 8.0000e-02 +NAV1 ENST00000367296 1.0000e+00 2.5417e-02 9.0000e-03 8.0000e-02 +HIVEP2 ENST00000367603 1.0000e+00 2.5372e-02 9.0000e-03 8.0000e-02 +OGT ENST00000373719 1.0000e+00 0.0000e+00 0.0000e+00 8.0000e-02 +RBBP6 ENST00000319715 1.0000e+00 2.5497e-02 9.0000e-03 8.0000e-02 +GTPBP4 ENST00000360803 1.0000e+00 0.0000e+00 0.0000e+00 8.0000e-02 +MYBL1 ENST00000522677 1.0000e+00 0.0000e+00 0.0000e+00 8.0000e-02 +TEX11 ENST00000395889 1.0000e+00 0.0000e+00 0.0000e+00 8.0000e-02 +DYNC1H1 ENST00000360184 1.0000e+00 4.8236e-02 2.9000e-02 8.0000e-02 +SBNO1 ENST00000420886 1.0000e+00 2.5601e-02 9.0000e-03 8.1000e-02 +THOC2 ENST00000245838 1.0000e+00 1.6971e-02 5.0000e-03 8.1000e-02 +PRKCB ENST00000303531 1.0000e+00 0.0000e+00 0.0000e+00 8.1000e-02 +INO80 ENST00000361937 1.0000e+00 3.1343e-02 1.3000e-02 8.1000e-02 +TAF4 ENST00000252996 1.0000e+00 0.0000e+00 0.0000e+00 8.1000e-02 +FLNA ENST00000369850 1.0000e+00 2.6140e-02 1.0000e-02 8.2000e-02 +TRIM28 ENST00000253024 1.0000e+00 0.0000e+00 0.0000e+00 8.2000e-02 +CHD8 ENST00000399982 1.0000e+00 3.8764e-02 1.9000e-02 8.2000e-02 +RBM33 ENST00000401878 1.0000e+00 1.7334e-02 5.0000e-03 8.2000e-02 +SNRNP200 ENST00000323853 1.0000e+00 3.5815e-02 1.7000e-02 8.2000e-02 +XPO6 ENST00000304658 1.0000e+00 1.7294e-02 5.0000e-03 8.2000e-02 +SMARCAD1 ENST00000359052 1.0000e+00 1.7414e-02 5.0000e-03 8.3000e-02 +FRMPD4 ENST00000380682 1.0000e+00 0.0000e+00 0.0000e+00 8.3000e-02 +MACF1 ENST00000545844 1.0000e+00 5.6465e-02 3.8000e-02 8.4000e-02 +WAC ENST00000354911 1.0000e+00 0.0000e+00 0.0000e+00 8.4000e-02 +BRWD3 ENST00000373275 1.0000e+00 2.6535e-02 1.0000e-02 8.4000e-02 +C17orf104 ENST00000409122 1.0000e+00 0.0000e+00 0.0000e+00 8.4000e-02 +ATP2B1 ENST00000428670 1.0000e+00 1.7765e-02 5.0000e-03 8.4000e-02 +EIF4G2 ENST00000526148 1.0000e+00 1.7981e-02 5.0000e-03 8.5000e-02 +ZNF462 ENST00000277225 1.0000e+00 3.2888e-02 1.4000e-02 8.5000e-02 +WDR26 ENST00000414423 1.0000e+00 0.0000e+00 0.0000e+00 8.5000e-02 +CUL4B ENST00000404115 1.0000e+00 0.0000e+00 0.0000e+00 8.5000e-02 +TRIM33 ENST00000358465 1.0000e+00 1.8203e-02 5.0000e-03 8.6000e-02 +STXBP1 ENST00000373302 1.0000e+00 0.0000e+00 0.0000e+00 8.6000e-02 +TOPBP1 ENST00000260810 1.0000e+00 2.7431e-02 1.0000e-02 8.6000e-02 +NF2 ENST00000338641 1.0000e+00 0.0000e+00 0.0000e+00 8.6000e-02 +TET3 ENST00000409262 1.0000e+00 1.8143e-02 5.0000e-03 8.6000e-02 +MN1 ENST00000302326 9.9999e-01 0.0000e+00 0.0000e+00 8.7000e-02 +SUPT6H ENST00000314616 1.0000e+00 3.7832e-02 1.8000e-02 8.7000e-02 +RP11-762I7.5 ENST00000546837 1.0000e+00 0.0000e+00 0.0000e+00 8.7000e-02 +NHS ENST00000380060 9.9999e-01 0.0000e+00 0.0000e+00 8.7000e-02 +RPS6KA3 ENST00000379565 9.9999e-01 0.0000e+00 0.0000e+00 8.7000e-02 +MYT1L ENST00000428368 1.0000e+00 1.8386e-02 6.0000e-03 8.7000e-02 +UBP1 ENST00000283629 9.9999e-01 0.0000e+00 0.0000e+00 8.8000e-02 +PLCL2 ENST00000418129 9.9999e-01 0.0000e+00 0.0000e+00 8.8000e-02 +SPTBN1 ENST00000356805 1.0000e+00 4.1887e-02 2.1000e-02 8.8000e-02 +MYH9 ENST00000216181 1.0000e+00 3.8313e-02 1.8000e-02 8.8000e-02 +ZDHHC5 ENST00000287169 9.9999e-01 0.0000e+00 0.0000e+00 8.8000e-02 +LUC7L3 ENST00000505658 9.9999e-01 0.0000e+00 0.0000e+00 8.9000e-02 +COPB2 ENST00000333188 1.0000e+00 1.8746e-02 6.0000e-03 8.9000e-02 +DNAJC14 ENST00000357606 9.9999e-01 0.0000e+00 0.0000e+00 8.9000e-02 +RNF17 ENST00000255324 1.0000e+00 3.4290e-02 1.5000e-02 8.9000e-02 +ANK3 ENST00000280772 1.0000e+00 4.9308e-02 2.8000e-02 8.9000e-02 +F8 ENST00000360256 1.0000e+00 2.8416e-02 1.1000e-02 8.9000e-02 +TM9SF3 ENST00000371142 9.9999e-01 0.0000e+00 0.0000e+00 9.0000e-02 +DLG3 ENST00000374360 9.9999e-01 0.0000e+00 0.0000e+00 9.0000e-02 +MGA ENST00000219905 1.0000e+00 4.2833e-02 2.1000e-02 9.0000e-02 +ANKRD52 ENST00000267116 1.0000e+00 1.8933e-02 6.0000e-03 9.0000e-02 +STAG2 ENST00000218089 1.0000e+00 1.8923e-02 6.0000e-03 9.0000e-02 +SATB2 ENST00000417098 9.9999e-01 0.0000e+00 0.0000e+00 9.1000e-02 +USP34 ENST00000398571 1.0000e+00 5.4952e-02 3.4000e-02 9.1000e-02 +MAP3K2 ENST00000409947 9.9999e-01 0.0000e+00 0.0000e+00 9.1000e-02 +PREX1 ENST00000371941 1.0000e+00 3.5185e-02 1.5000e-02 9.1000e-02 +MED14 ENST00000324817 1.0000e+00 1.9330e-02 6.0000e-03 9.2000e-02 +CYFIP2 ENST00000521420 1.0000e+00 2.9307e-02 1.1000e-02 9.2000e-02 +ZNF407 ENST00000299687 1.0000e+00 2.9252e-02 1.1000e-02 9.2000e-02 +KPNB1 ENST00000290158 1.0000e+00 1.9307e-02 6.0000e-03 9.2000e-02 +ETV5 ENST00000306376 9.9999e-01 0.0000e+00 0.0000e+00 9.2000e-02 +CUL2 ENST00000537177 1.0000e+00 1.9602e-02 6.0000e-03 9.3000e-02 +HNRNPM ENST00000325495 9.9999e-01 0.0000e+00 0.0000e+00 9.3000e-02 +PIAS1 ENST00000249636 9.9999e-01 0.0000e+00 0.0000e+00 9.4000e-02 +DAAM2 ENST00000398904 1.0000e+00 1.9827e-02 6.0000e-03 9.4000e-02 +EFTUD2 ENST00000426333 1.0000e+00 1.9846e-02 6.0000e-03 9.4000e-02 +YTHDC1 ENST00000344157 1.0000e+00 1.9789e-02 6.0000e-03 9.4000e-02 +NCBP1 ENST00000375147 1.0000e+00 1.9877e-02 6.0000e-03 9.4000e-02 +TCF20 ENST00000359486 1.0000e+00 3.0129e-02 1.1000e-02 9.5000e-02 +DLL1 ENST00000366756 9.9999e-01 0.0000e+00 0.0000e+00 9.5000e-02 +UBR4 ENST00000375254 1.0000e+00 6.2772e-02 4.2000e-02 9.5000e-02 +STAT3 ENST00000264657 1.0000e+00 1.9945e-02 6.0000e-03 9.5000e-02 +IGF2BP3 ENST00000258729 9.9999e-01 0.0000e+00 0.0000e+00 9.5000e-02 +NSD1 ENST00000439151 1.0000e+00 4.5197e-02 2.3000e-02 9.5000e-02 +SRCAP ENST00000262518 1.0000e+00 4.8453e-02 2.6000e-02 9.6000e-02 +ZNF777 ENST00000247930 9.9998e-01 0.0000e+00 0.0000e+00 9.6000e-02 +HNRNPK ENST00000376263 9.9998e-01 0.0000e+00 0.0000e+00 9.6000e-02 +SCAF8 ENST00000367178 1.0000e+00 3.0519e-02 1.1000e-02 9.6000e-02 +ARID2 ENST00000334344 1.0000e+00 3.7297e-02 1.6000e-02 9.6000e-02 +CCT3 ENST00000295688 9.9998e-01 0.0000e+00 0.0000e+00 9.7000e-02 +COL5A2 ENST00000374866 1.0000e+00 4.2311e-02 2.0000e-02 9.7000e-02 +PHC3 ENST00000495893 1.0000e+00 2.0360e-02 6.0000e-03 9.7000e-02 +GATAD2B ENST00000368655 9.9998e-01 0.0000e+00 0.0000e+00 9.7000e-02 +FBXO11 ENST00000403359 1.0000e+00 2.0460e-02 6.0000e-03 9.7000e-02 +NOTCH1 ENST00000277541 1.0000e+00 4.6153e-02 2.3000e-02 9.7000e-02 +COL3A1 ENST00000304636 1.0000e+00 4.2706e-02 2.0000e-02 9.8000e-02 +PPP3CB ENST00000394829 9.9998e-01 0.0000e+00 0.0000e+00 9.8000e-02 +ILF3 ENST00000449870 1.0000e+00 2.0650e-02 6.0000e-03 9.8000e-02 +PLEKHA5 ENST00000429027 1.0000e+00 3.7955e-02 1.6000e-02 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0.0000e+00 3.4300e-01 +RUNX2 ENST00000371438 9.4884e-01 1.3282e-01 5.9000e-02 3.4300e-01 +ALKBH5 ENST00000399138 9.4974e-01 7.2360e-02 2.5000e-02 3.4300e-01 +PFDN6 ENST00000395131 9.3592e-01 0.0000e+00 0.0000e+00 3.4300e-01 +SNX1 ENST00000261889 9.3179e-01 1.6346e-01 8.4000e-02 3.4400e-01 +ASIC1 ENST00000228468 9.3017e-01 1.6382e-01 8.5000e-02 3.4400e-01 +COPZ1 ENST00000262061 9.4896e-01 7.2587e-02 2.5000e-02 3.4400e-01 +MTUS2 ENST00000431530 7.9549e-01 2.0294e-01 1.2400e-01 3.4400e-01 +IRF8 ENST00000268638 9.4807e-01 1.3307e-01 6.0000e-02 3.4400e-01 +PCDHAC2 ENST00000289269 9.3114e-01 1.6361e-01 8.5000e-02 3.4400e-01 +POLR2B ENST00000381227 5.2372e-01 2.2035e-01 1.4500e-01 3.4400e-01 +CADPS2 ENST00000449022 3.6785e-01 2.2646e-01 1.5200e-01 3.4400e-01 +LYPLA2 ENST00000374514 9.4955e-01 7.2416e-02 2.5000e-02 3.4400e-01 +LRRC1 ENST00000370888 9.3181e-01 1.6346e-01 8.4000e-02 3.4400e-01 +MAP3K13 ENST00000265026 8.0051e-01 2.0260e-01 1.2400e-01 3.4400e-01 +OXR1 ENST00000442977 8.4148e-01 1.9694e-01 1.1800e-01 3.4400e-01 +P4HA1 ENST00000412021 9.3166e-01 1.6349e-01 8.4000e-02 3.4400e-01 +NTN4 ENST00000343702 9.1585e-01 1.7447e-01 9.5000e-02 3.4400e-01 +AP3B1 ENST00000255194 6.1532e-01 2.1620e-01 1.4000e-01 3.4400e-01 +KIF3A ENST00000378746 8.9775e-01 1.8313e-01 1.0300e-01 3.4400e-01 +FNTA ENST00000302279 9.4721e-01 1.3334e-01 6.0000e-02 3.4500e-01 +ITGA5 ENST00000293379 4.2455e-01 2.2429e-01 1.4900e-01 3.4500e-01 +PI4KB ENST00000368875 8.6607e-01 1.9131e-01 1.1100e-01 3.4500e-01 +CXXC1 ENST00000412036 8.9506e-01 1.8350e-01 1.0300e-01 3.4500e-01 +CD86 ENST00000330540 9.4879e-01 7.2635e-02 2.5000e-02 3.4500e-01 +MAF1 ENST00000322428 9.4812e-01 7.2830e-02 2.5000e-02 3.4500e-01 +VASP ENST00000245932 9.4665e-01 1.3352e-01 6.0000e-02 3.4500e-01 +HERPUD2 ENST00000396081 9.4702e-01 1.3340e-01 6.0000e-02 3.4500e-01 +LARP4 ENST00000398473 8.6884e-01 1.9102e-01 1.1100e-01 3.4500e-01 +LCOR ENST00000371097 9.5022e-01 1.0956e-01 4.4000e-02 3.4500e-01 +C6orf136 ENST00000293604 9.4895e-01 1.0999e-01 4.4000e-02 3.4600e-01 +CCNT2 ENST00000264157 9.2681e-01 1.6455e-01 8.5000e-02 3.4600e-01 +ATG2A ENST00000377264 5.3526e-02 2.4209e-01 1.7200e-01 3.4600e-01 +USP49 ENST00000373006 9.3828e-01 1.5114e-01 7.3000e-02 3.4600e-01 +NUPL1 ENST00000381736 9.2697e-01 1.6452e-01 8.5000e-02 3.4600e-01 +ASUN ENST00000261191 8.6229e-01 1.9171e-01 1.1200e-01 3.4600e-01 +ATP8A1 ENST00000381668 1.9990e-01 2.3313e-01 1.6000e-01 3.4600e-01 +RNF214 ENST00000531452 9.0960e-01 1.7554e-01 9.5000e-02 3.4600e-01 +EIF3I ENST00000373586 9.4930e-01 1.0987e-01 4.4000e-02 3.4600e-01 +SGMS1 ENST00000361781 9.4507e-01 1.3401e-01 6.0000e-02 3.4600e-01 +TECPR2 ENST00000359520 5.8003e-01 2.1763e-01 1.4100e-01 3.4600e-01 +VPS4A ENST00000254950 9.4474e-01 1.3411e-01 6.0000e-02 3.4700e-01 +DHX36 ENST00000496811 4.7221e-01 2.2228e-01 1.4600e-01 3.4700e-01 +DROSHA ENST00000511367 9.3176e-02 2.3908e-01 1.6700e-01 3.4700e-01 +PER2 ENST00000254657 7.1480e-01 2.0948e-01 1.3100e-01 3.4700e-01 +NEO1 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4.8400e-01 +GIGYF1 ENST00000275732 3.4196e-06 3.3896e-01 2.4100e-01 4.8400e-01 +VPS13A ENST00000360280 9.3125e-22 3.9557e-01 3.2400e-01 4.8400e-01 +VPS26A ENST00000373382 6.1411e-01 1.8723e-01 8.4000e-02 4.8400e-01 +RBM46 ENST00000281722 4.7301e-01 2.1164e-01 1.0300e-01 4.8400e-01 +SLC20A1 ENST00000272542 6.7227e-02 2.6852e-01 1.5700e-01 4.8400e-01 +CDK2 ENST00000266970 6.1054e-01 1.8770e-01 8.4000e-02 4.8500e-01 +ZNF248 ENST00000395867 3.2621e-01 2.3086e-01 1.2000e-01 4.8500e-01 +FAM126A ENST00000432176 1.2103e-01 2.5816e-01 1.4600e-01 4.8500e-01 +B3GNT5 ENST00000326505 7.2579e-01 1.5412e-01 6.2000e-02 4.8500e-01 +HK2 ENST00000290573 4.5893e-03 2.9941e-01 1.9100e-01 4.8500e-01 +TAZ ENST00000299328 7.2591e-01 1.5410e-01 6.2000e-02 4.8500e-01 +CNTN5 ENST00000524871 6.1963e-05 3.2720e-01 2.2500e-01 4.8500e-01 +PRKAB2 ENST00000254101 7.2559e-01 1.5415e-01 6.2000e-02 4.8500e-01 +TPT1 ENST00000530705 8.0548e-01 1.0233e-01 3.5000e-02 4.8500e-01 +ASF1A ENST00000229595 8.0542e-01 1.0234e-01 3.5000e-02 4.8500e-01 +PAPPA2 ENST00000367662 7.7879e-08 3.5139e-01 2.5800e-01 4.8500e-01 +PFDN1 ENST00000261813 8.4732e-01 0.0000e+00 0.0000e+00 4.8500e-01 +GRM2 ENST00000395052 1.2019e-01 2.5836e-01 1.4600e-01 4.8500e-01 +STARD7 ENST00000337288 4.7179e-01 2.1178e-01 1.0300e-01 4.8500e-01 +RNF34 ENST00000392465 6.1057e-01 1.8769e-01 8.4000e-02 4.8500e-01 +PDE9A ENST00000291539 4.5595e-03 2.9954e-01 1.9100e-01 4.8500e-01 +TARBP2 ENST00000266987 4.6644e-01 2.1243e-01 1.0400e-01 4.8600e-01 +ABCA1 ENST00000374736 1.4525e-13 3.7761e-01 2.9600e-01 4.8600e-01 +RBMS1 ENST00000348849 1.1929e-01 2.5858e-01 1.4600e-01 4.8600e-01 +TADA2B ENST00000310074 7.2366e-01 1.5446e-01 6.2000e-02 4.8600e-01 +MSANTD1 ENST00000438480 8.0456e-01 1.0249e-01 3.5000e-02 4.8600e-01 +REPS2 ENST00000357277 2.0309e-01 2.4639e-01 1.3400e-01 4.8600e-01 +NPC1 ENST00000269228 6.5418e-06 3.3746e-01 2.3800e-01 4.8600e-01 +SMC5 ENST00000361138 3.1326e-06 3.4019e-01 2.4200e-01 4.8600e-01 +DENND1B ENST00000367396 2.0408e-01 2.4622e-01 1.3400e-01 4.8600e-01 +TLR8 ENST00000218032 3.2401e-01 2.3114e-01 1.2000e-01 4.8600e-01 +GAS6 ENST00000327773 3.4477e-02 2.7842e-01 1.6700e-01 4.8600e-01 +MROH1 ENST00000528919 2.0264e-01 2.4646e-01 1.3400e-01 4.8600e-01 +COPS8 ENST00000354371 7.2485e-01 1.5427e-01 6.2000e-02 4.8600e-01 +STK32C ENST00000298630 2.0408e-01 2.4622e-01 1.3400e-01 4.8600e-01 +GJB1 ENST00000374022 8.4627e-01 0.0000e+00 0.0000e+00 4.8600e-01 +RPL30 ENST00000521291 8.4674e-01 0.0000e+00 0.0000e+00 4.8600e-01 +TNF ENST00000449264 8.0330e-01 1.0271e-01 3.6000e-02 4.8700e-01 +UCK2 ENST00000367879 7.2131e-01 1.5483e-01 6.2000e-02 4.8700e-01 +RNF121 ENST00000361756 3.1902e-01 2.3180e-01 1.2000e-01 4.8700e-01 +KLHL11 ENST00000319121 2.0133e-01 2.4668e-01 1.3400e-01 4.8700e-01 +TBC1D9 ENST00000442267 2.8039e-05 3.3158e-01 2.3000e-01 4.8700e-01 +AFAP1L2 ENST00000304129 2.1581e-03 3.0614e-01 1.9800e-01 4.8700e-01 +WBSCR17 ENST00000333538 1.1671e-01 2.5921e-01 1.4600e-01 4.8700e-01 +ZNF624 ENST00000311331 3.2471e-02 2.7986e-01 1.6800e-01 4.8800e-01 +FAM91A1 ENST00000334705 2.4063e-04 3.2114e-01 2.1600e-01 4.8800e-01 +COPS7B ENST00000350033 6.0071e-01 1.8900e-01 8.5000e-02 4.8800e-01 +HAPLN1 ENST00000274341 6.0242e-01 1.8877e-01 8.5000e-02 4.8800e-01 +GPBP1L1 ENST00000355105 1.9902e-01 2.4708e-01 1.3400e-01 4.8800e-01 +SH3PXD2B ENST00000311601 4.1589e-03 3.0139e-01 1.9200e-01 4.8800e-01 +ENC1 ENST00000302351 4.6008e-01 2.1320e-01 1.0400e-01 4.8800e-01 +GALNT2 ENST00000366672 8.4175e-03 2.9489e-01 1.8500e-01 4.8800e-01 +NETO2 ENST00000562435 6.2704e-02 2.7032e-01 1.5800e-01 4.8800e-01 +STT3A ENST00000392708 2.0450e-03 3.0718e-01 1.9900e-01 4.8800e-01 +PPP1R13L ENST00000418234 3.2060e-02 2.8017e-01 1.6800e-01 4.8900e-01 +KIAA1731 ENST00000325212 2.3569e-13 3.7916e-01 2.9600e-01 4.8900e-01 +CNN3 ENST00000370206 5.9852e-01 1.8929e-01 8.5000e-02 4.8900e-01 +PIK3R2 ENST00000222254 1.6273e-02 2.8838e-01 1.7700e-01 4.8900e-01 +PPP4C ENST00000279387 4.5540e-01 2.1378e-01 1.0400e-01 4.8900e-01 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4.9000e-01 +PEX5L ENST00000467460 7.9927e-03 2.9600e-01 1.8500e-01 4.9000e-01 +NFYC ENST00000425457 1.0847e-01 2.6135e-01 1.4800e-01 4.9100e-01 +UGGT1 ENST00000259253 5.1934e-10 3.6709e-01 2.7700e-01 4.9100e-01 +RIMKLB ENST00000357529 5.9273e-01 1.9006e-01 8.6000e-02 4.9100e-01 +MCM3AP ENST00000397708 5.2400e-09 3.6210e-01 2.7000e-01 4.9100e-01 +LRRTM1 ENST00000295057 5.9450e-01 1.8982e-01 8.5000e-02 4.9100e-01 +ARMC5 ENST00000268314 1.0750e-01 2.6161e-01 1.4800e-01 4.9100e-01 +CACNB4 ENST00000539935 3.0679e-02 2.8123e-01 1.6900e-01 4.9100e-01 +NPRL3 ENST00000399953 1.9021e-01 2.4861e-01 1.3500e-01 4.9100e-01 +ITSN2 ENST00000355123 9.7511e-13 3.7828e-01 2.9400e-01 4.9100e-01 +LTBR ENST00000228918 3.0580e-01 2.3358e-01 1.2100e-01 4.9100e-01 +NUDCD3 ENST00000355451 4.4788e-01 2.1471e-01 1.0500e-01 4.9100e-01 +SPTA1 ENST00000368147 2.6001e-18 3.9414e-01 3.1800e-01 4.9100e-01 +ARC ENST00000356613 5.9433e-01 1.8984e-01 8.5000e-02 4.9100e-01 +RENBP ENST00000393700 4.4916e-01 2.1455e-01 1.0500e-01 4.9100e-01 +CXorf21 ENST00000378962 8.4298e-01 0.0000e+00 0.0000e+00 4.9200e-01 +NUDT4 ENST00000337179 7.9724e-01 1.0379e-01 3.6000e-02 4.9200e-01 +MAGOH ENST00000371470 7.9740e-01 1.0376e-01 3.6000e-02 4.9200e-01 +ATXN3 ENST00000393287 1.0575e-01 2.6209e-01 1.4800e-01 4.9200e-01 +WARS ENST00000355338 3.0288e-01 2.3398e-01 1.2100e-01 4.9200e-01 +UBE2M ENST00000253023 7.9769e-01 1.0371e-01 3.6000e-02 4.9200e-01 +ABCC4 ENST00000376887 1.0674e-07 3.5485e-01 2.5900e-01 4.9200e-01 +ARSE ENST00000381134 5.8982e-01 1.9045e-01 8.6000e-02 4.9200e-01 +UNC5C ENST00000453304 8.8130e-04 3.1478e-01 2.0700e-01 4.9200e-01 +KHDRBS3 ENST00000355849 4.4237e-01 2.1540e-01 1.0500e-01 4.9300e-01 +DENND6A ENST00000311128 1.7721e-03 3.0999e-01 2.0100e-01 4.9300e-01 +MCTP1 ENST00000515393 9.3096e-05 3.2887e-01 2.2400e-01 4.9300e-01 +PSMC4 ENST00000157812 3.0101e-01 2.3424e-01 1.2100e-01 4.9300e-01 +TBCD ENST00000355528 1.0032e-07 3.5565e-01 2.6000e-01 4.9300e-01 +SPECC1 ENST00000261503 8.6772e-04 3.1507e-01 2.0700e-01 4.9300e-01 +LRRK1 ENST00000388948 4.5228e-10 3.6860e-01 2.7800e-01 4.9300e-01 +GRINA ENST00000313269 4.4203e-01 2.1544e-01 1.0500e-01 4.9300e-01 +ZNF207 ENST00000394670 1.0460e-01 2.6241e-01 1.4800e-01 4.9300e-01 +CRYBG3 ENST00000182096 9.2709e-05 3.2894e-01 2.2400e-01 4.9300e-01 +CXorf30 ENST00000378657 7.1001e-01 1.5662e-01 6.3000e-02 4.9300e-01 +C7orf43 ENST00000316937 1.8133e-01 2.5024e-01 1.3600e-01 4.9400e-01 +CNKSR3 ENST00000607772 2.8166e-02 2.8331e-01 1.7000e-01 4.9400e-01 +DNAJB12 ENST00000338820 4.4012e-01 2.1568e-01 1.0500e-01 4.9400e-01 +WNT5B ENST00000397196 5.8535e-01 1.9104e-01 8.6000e-02 4.9400e-01 +GLTSCR2 ENST00000246802 1.8147e-01 2.5022e-01 1.3600e-01 4.9400e-01 +HS3ST4 ENST00000331351 7.9575e-01 1.0405e-01 3.6000e-02 4.9400e-01 +GAREML ENST00000401533 4.3898e-01 2.1582e-01 1.0500e-01 4.9400e-01 +UST ENST00000367463 4.3933e-01 2.1578e-01 1.0500e-01 4.9400e-01 +CTD-2116N17.1 ENST00000606793 1.0265e-01 2.6297e-01 1.4900e-01 4.9400e-01 +FAM69A ENST00000370310 5.8405e-01 1.9122e-01 8.6000e-02 4.9400e-01 +SNAI2 ENST00000396822 7.9531e-01 1.0413e-01 3.6000e-02 4.9400e-01 +CARS ENST00000380525 4.0314e-04 3.2056e-01 2.1300e-01 4.9400e-01 +CCNYL1 ENST00000339882 5.8564e-01 1.9100e-01 8.6000e-02 4.9400e-01 +SRP72 ENST00000342756 1.7104e-03 3.1069e-01 2.0100e-01 4.9400e-01 +TMCC2 ENST00000358024 2.9466e-01 2.3514e-01 1.2200e-01 4.9400e-01 +YAF2 ENST00000442791 7.9482e-01 1.0421e-01 3.6000e-02 4.9400e-01 +SNRPB ENST00000438552 7.0858e-01 1.5685e-01 6.3000e-02 4.9400e-01 +UBE2J1 ENST00000435041 4.3658e-01 2.1613e-01 1.0500e-01 4.9500e-01 +DHX8 ENST00000262415 9.1546e-07 3.4960e-01 2.5100e-01 4.9500e-01 +B3GNT7 ENST00000287590 7.0639e-01 1.5720e-01 6.3000e-02 4.9500e-01 +SRPK3 ENST00000370101 2.9235e-01 2.3547e-01 1.2200e-01 4.9500e-01 +ZBTB8OS ENST00000468695 7.0542e-01 1.5735e-01 6.3000e-02 4.9500e-01 +ATP1A2 ENST00000361216 1.8093e-04 3.2613e-01 2.2000e-01 4.9500e-01 +GGH ENST00000260118 5.8132e-01 1.9158e-01 8.6000e-02 4.9500e-01 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6.5500e-01 +RAI2 ENST00000545871 6.1158e-01 1.3839e-01 4.8000e-02 6.5600e-01 +PTPN21 ENST00000556564 2.2052e-12 4.8336e-01 3.6100e-01 6.5600e-01 +FRMPD1 ENST00000539465 2.1898e-12 4.8350e-01 3.6100e-01 6.5600e-01 +RNF213 ENST00000582970 4.9078e-55 5.6562e-01 4.8900e-01 6.5600e-01 +NUDT3 ENST00000607016 4.2531e-01 2.0842e-01 8.4000e-02 6.5600e-01 +CIRH1A ENST00000314423 7.7093e-07 4.3730e-01 2.9800e-01 6.5600e-01 +TAP1 ENST00000354258 5.3431e-06 4.2574e-01 2.8400e-01 6.5600e-01 +NKAIN1 ENST00000373736 2.4678e-01 2.5389e-01 1.1500e-01 6.5600e-01 +KLHL5 ENST00000504108 5.2757e-06 4.2615e-01 2.8400e-01 6.5600e-01 +TCEAL4 ENST00000472745 7.4827e-01 0.0000e+00 0.0000e+00 6.5600e-01 +CD6 ENST00000313421 9.2695e-05 4.0492e-01 2.5800e-01 6.5600e-01 +SEMA3D ENST00000284136 4.0219e-08 4.5243e-01 3.1700e-01 6.5700e-01 +DPY19L3 ENST00000342179 2.8534e-07 4.4306e-01 3.0500e-01 6.5700e-01 +ECT2 ENST00000392692 8.0837e-10 4.6696e-01 3.3700e-01 6.5700e-01 +BRDT ENST00000362005 5.7616e-09 4.5997e-01 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3.1272e-01 1.6200e-01 6.5800e-01 +YPEL1 ENST00000339468 6.0986e-01 1.3875e-01 4.8000e-02 6.5800e-01 +CASP2 ENST00000310447 1.5026e-03 3.7719e-01 2.2600e-01 6.5800e-01 +NTRK1 ENST00000524377 1.9568e-06 4.3295e-01 2.9200e-01 6.5800e-01 +EHBP1L1 ENST00000309295 7.1163e-13 4.8857e-01 3.6600e-01 6.5900e-01 +GPR162 ENST00000311268 9.3905e-03 3.5060e-01 1.9800e-01 6.5900e-01 +TRIM36 ENST00000282369 3.4150e-05 4.1435e-01 2.6900e-01 6.5900e-01 +SCG3 ENST00000220478 1.4883e-03 3.7759e-01 2.2700e-01 6.5900e-01 +TRIM44 ENST00000299413 5.3808e-02 3.1363e-01 1.6300e-01 6.5900e-01 +TMED4 ENST00000457408 2.4339e-01 2.5494e-01 1.1500e-01 6.5900e-01 +HOMER2 ENST00000304231 9.3921e-03 3.5059e-01 1.9800e-01 6.5900e-01 +PRRX1 ENST00000239461 2.4291e-01 2.5509e-01 1.1500e-01 6.5900e-01 +TRABD ENST00000303434 2.2862e-02 3.3382e-01 1.8200e-01 6.5900e-01 +ENPP4 ENST00000321037 1.1941e-01 2.8858e-01 1.4100e-01 6.6000e-01 +CCM2 ENST00000381112 9.2809e-03 3.5116e-01 1.9900e-01 6.6000e-01 +HOXC13 ENST00000243056 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1.9319e-10 4.8097e-01 3.5000e-01 6.7200e-01 +MLX ENST00000246912 1.1032e-01 2.9361e-01 1.4400e-01 6.7200e-01 +SZRD1 ENST00000401088 5.9651e-01 1.4160e-01 4.9000e-02 6.7200e-01 +SDC2 ENST00000302190 4.0490e-01 2.1333e-01 8.6000e-02 6.7200e-01 +CRLF3 ENST00000324238 4.7973e-04 3.9659e-01 2.4400e-01 6.7300e-01 +TUBGCP5 ENST00000283645 1.2275e-12 4.9587e-01 3.7000e-01 6.7300e-01 +THOC6 ENST00000326266 4.7835e-04 3.9671e-01 2.4400e-01 6.7300e-01 +PNO1 ENST00000263657 2.2652e-01 2.6043e-01 1.1800e-01 6.7300e-01 +MED30 ENST00000297347 4.0259e-01 2.1390e-01 8.6000e-02 6.7300e-01 +TCEAL3 ENST00000372628 7.3954e-01 0.0000e+00 0.0000e+00 6.7300e-01 +DNAH11 ENST00000328843 2.5389e-58 5.8331e-01 5.0500e-01 6.7400e-01 +IFRD1 ENST00000403825 1.2141e-03 3.8641e-01 2.3200e-01 6.7400e-01 +C5orf42 ENST00000425232 5.8778e-36 5.6083e-01 4.6800e-01 6.7400e-01 +CPAMD8 ENST00000443236 6.9237e-23 5.3635e-01 4.2900e-01 6.7400e-01 +TUBB4A ENST00000264071 1.0910e-01 2.9432e-01 1.4400e-01 6.7400e-01 +DHRS3 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6.8100e-01 +APCDD1 ENST00000355285 7.3159e-03 3.6279e-01 2.0500e-01 6.8100e-01 +GPR19 ENST00000540510 1.0405e-01 2.9739e-01 1.4500e-01 6.8100e-01 +PCNXL2 ENST00000258229 1.7151e-23 5.4274e-01 4.3500e-01 6.8100e-01 +RNF14 ENST00000394520 1.1129e-03 3.9031e-01 2.3400e-01 6.8100e-01 +POU1F1 ENST00000344265 4.5046e-02 3.2372e-01 1.6800e-01 6.8100e-01 +ADCY3 ENST00000260600 1.9545e-11 4.9386e-01 3.6300e-01 6.8100e-01 +SNAI1 ENST00000244050 2.1754e-01 2.6357e-01 1.1900e-01 6.8100e-01 +DARS ENST00000264161 8.5360e-06 4.3645e-01 2.8700e-01 6.8200e-01 +ACKR3 ENST00000272928 3.9134e-01 2.1676e-01 8.8000e-02 6.8200e-01 +TLE2 ENST00000262953 1.6430e-07 4.5976e-01 3.1700e-01 6.8200e-01 +LIG3 ENST00000378526 1.4390e-10 4.8837e-01 3.5500e-01 6.8200e-01 +UBXN2B ENST00000399598 1.0316e-01 2.9796e-01 1.4600e-01 6.8200e-01 +TUBGCP2 ENST00000543663 2.2003e-08 4.6955e-01 3.2900e-01 6.8200e-01 +PTCHD4 ENST00000339488 1.6171e-04 4.1174e-01 2.5800e-01 6.8200e-01 +SCMH1 ENST00000402904 8.6107e-06 4.3613e-01 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ENST00000590071 6.6719e-05 5.7079e-01 3.4300e-01 9.9600e-01 +GCSAM ENST00000484193 6.4030e-02 3.8549e-01 1.7500e-01 9.9600e-01 +DCTN5 ENST00000300087 7.0514e-03 4.7379e-01 2.4700e-01 9.9600e-01 +CNIH4 ENST00000465271 2.1712e-02 4.3551e-01 2.1400e-01 9.9600e-01 +CRYBB1 ENST00000215939 7.0069e-04 5.3017e-01 3.0100e-01 9.9600e-01 +CD1D ENST00000368171 1.8805e-06 6.1447e-01 3.9300e-01 9.9600e-01 +OLFML2A ENST00000373580 1.2885e-09 6.7163e-01 4.6300e-01 9.9600e-01 +SYDE2 ENST00000341460 2.3083e-17 7.4224e-01 5.5900e-01 9.9700e-01 +KLK5 ENST00000336334 7.0149e-03 4.7436e-01 2.4700e-01 9.9700e-01 +SAAL1 ENST00000524803 4.3242e-09 6.6482e-01 4.5400e-01 9.9700e-01 +TMCO6 ENST00000394671 1.2724e-09 6.7228e-01 4.6400e-01 9.9700e-01 +TRPT1 ENST00000394546 2.2209e-03 5.0539e-01 2.7600e-01 9.9700e-01 +AKR1B1 ENST00000285930 2.0216e-05 5.8792e-01 3.6200e-01 9.9700e-01 +ASMTL ENST00000381317 1.2704e-09 6.7236e-01 4.6400e-01 9.9700e-01 +FBXO2 ENST00000354287 2.1527e-04 5.5272e-01 3.2300e-01 9.9700e-01 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9.9800e-01 +KIAA1614 ENST00000367588 1.1531e-15 7.3182e-01 5.4400e-01 9.9800e-01 +RNF217 ENST00000359704 2.0177e-05 5.8807e-01 3.6200e-01 9.9800e-01 +CCDC19 ENST00000368099 5.5417e-14 7.1911e-01 5.2600e-01 9.9800e-01 +MED6 ENST00000256379 6.5981e-05 5.7175e-01 3.4400e-01 9.9800e-01 +RPLP1 ENST00000260379 3.7039e-01 2.1124e-01 7.4000e-02 9.9800e-01 +TTC30A ENST00000355689 5.4588e-07 6.2862e-01 4.0800e-01 9.9900e-01 +DDX51 ENST00000397333 8.6133e-12 6.9952e-01 4.9900e-01 9.9900e-01 +CHAD ENST00000508540 6.9766e-03 4.7497e-01 2.4700e-01 9.9900e-01 +TMPRSS11F ENST00000356291 1.2382e-09 6.7369e-01 4.6500e-01 9.9900e-01 +EXD3 ENST00000340951 2.9843e-16 7.3687e-01 5.5000e-01 9.9900e-01 +TRPM5 ENST00000155858 4.4415e-22 7.6742e-01 5.9500e-01 9.9900e-01 +GJA8 ENST00000240986 2.2050e-03 5.0614e-01 2.7600e-01 9.9900e-01 +CAPN10 ENST00000391984 6.9206e-13 7.1026e-01 5.1300e-01 9.9900e-01 +B3GALNT1 ENST00000392781 2.2090e-03 5.0595e-01 2.7600e-01 9.9900e-01 +USB1 ENST00000219281 6.8700e-04 5.3209e-01 3.0200e-01 9.9900e-01 +TAF1A ENST00000350027 1.2350e-09 6.7382e-01 4.6500e-01 9.9900e-01 +NRAP ENST00000359988 3.2577e-50 8.3478e-01 7.0000e-01 9.9900e-01 +RAB34 ENST00000447716 5.4311e-07 6.2897e-01 4.0900e-01 1.0000e+00 +FAM71F2 ENST00000480462 2.1409e-02 4.3718e-01 2.1400e-01 1.0000e+00 +DNAAF1 ENST00000378553 8.4672e-12 7.0022e-01 4.9900e-01 1.0000e+00 +P2RY4 ENST00000374519 1.6870e-01 3.1817e-01 1.2900e-01 1.0000e+00 +DNAJC18 ENST00000302060 4.8219e-08 6.4931e-01 4.3300e-01 1.0000e+00 +SLC10A7 ENST00000335472 1.9761e-05 5.8977e-01 3.6300e-01 1.0000e+00 +OR2A7 ENST00000493325 3.6959e-01 2.1161e-01 7.4000e-02 1.0000e+00 +SLCO4A1 ENST00000217159 1.0328e-10 6.8797e-01 4.8300e-01 1.0000e+00 +GAP43 ENST00000393780 2.1461e-02 4.3690e-01 2.1400e-01 1.0000e+00 +TMEM53 ENST00000372237 2.1392e-02 4.3728e-01 2.1400e-01 1.0000e+00 +ZNF75A ENST00000574298 2.1966e-03 5.0653e-01 2.7600e-01 1.0000e+00 +ARL2 ENST00000246747 2.1417e-02 4.3714e-01 2.1400e-01 1.0000e+00 +NAT6 ENST00000354862 1.6865e-01 3.1820e-01 1.2900e-01 1.0000e+00 +ZNF3 ENST00000303915 1.9833e-05 5.8948e-01 3.6300e-01 1.0000e+00 +SPAG7 ENST00000206020 6.8490e-04 5.3239e-01 3.0200e-01 1.0000e+00 +SPSB2 ENST00000524270 2.1370e-02 4.3740e-01 2.1400e-01 1.0010e+00 +ACOT8 ENST00000217455 5.9662e-06 6.0467e-01 3.8000e-01 1.0010e+00 +ZNF615 ENST00000594083 8.3760e-12 7.0066e-01 5.0000e-01 1.0010e+00 +BPGM ENST00000393132 2.1313e-02 4.3772e-01 2.1500e-01 1.0010e+00 +LY6H ENST00000414417 1.6827e-01 3.1854e-01 1.2900e-01 1.0010e+00 +SH3BGR ENST00000333634 2.1831e-03 5.0718e-01 2.7700e-01 1.0010e+00 +C9orf114 ENST00000361256 4.1284e-09 6.6735e-01 4.5600e-01 1.0010e+00 +SRP19 ENST00000505459 6.9014e-03 4.7617e-01 2.4800e-01 1.0010e+00 +TYSND1 ENST00000287078 6.8197e-04 5.3281e-01 3.0200e-01 1.0010e+00 +GSAP ENST00000257626 2.5479e-23 7.7417e-01 6.0400e-01 1.0010e+00 +PLEKHG6 ENST00000396988 3.7173e-19 7.5472e-01 5.7500e-01 1.0010e+00 +ZNF804B ENST00000333190 5.3504e-18 7.4869e-01 5.6600e-01 1.0010e+00 +ACER1 ENST00000301452 2.1705e-03 5.0778e-01 2.7700e-01 1.0020e+00 +ASAH2C ENST00000426610 6.7646e-04 5.3360e-01 3.0200e-01 1.0020e+00 +SLCO6A1 ENST00000506729 2.8807e-11 6.9556e-01 4.9200e-01 1.0020e+00 +SIGIRR ENST00000431843 5.9288e-06 6.0515e-01 3.8000e-01 1.0020e+00 +FBXW9 ENST00000393261 4.0860e-09 6.6792e-01 4.5600e-01 1.0020e+00 +CORO2A ENST00000343933 3.4457e-10 6.8302e-01 4.7500e-01 1.0020e+00 +CRYBA1 ENST00000225387 6.4088e-05 5.7427e-01 3.4500e-01 1.0020e+00 +CNDP1 ENST00000358821 1.1834e-09 6.7602e-01 4.6600e-01 1.0020e+00 +CXCL10 ENST00000306602 3.6865e-01 2.1205e-01 7.4000e-02 1.0020e+00 +APOOL ENST00000373173 2.1234e-02 4.3817e-01 2.1500e-01 1.0020e+00 +TC2N ENST00000435962 1.1879e-09 6.7583e-01 4.6600e-01 1.0020e+00 +RGS20 ENST00000297313 6.4013e-05 5.7437e-01 3.4500e-01 1.0020e+00 +PRSS23 ENST00000280258 1.9421e-05 5.9119e-01 3.6400e-01 1.0030e+00 +C16orf11 ENST00000409413 2.1160e-02 4.3858e-01 2.1500e-01 1.0030e+00 +UBALD2 ENST00000327490 3.6820e-01 2.1226e-01 7.4000e-02 1.0030e+00 +CLMP ENST00000448775 1.5718e-07 6.4165e-01 4.2300e-01 1.0030e+00 +C2orf16 ENST00000408964 1.3435e-14 7.2762e-01 5.3500e-01 1.0030e+00 +CDRT1 ENST00000395906 4.9801e-14 7.2255e-01 5.2900e-01 1.0030e+00 +SMIM23 ENST00000330910 6.8348e-03 4.7725e-01 2.4800e-01 1.0030e+00 +CCDC147 ENST00000369704 9.4345e-23 7.7292e-01 6.0100e-01 1.0030e+00 +NKX6-1 ENST00000295886 6.2705e-02 3.8822e-01 1.7600e-01 1.0030e+00 +CAB39L ENST00000355854 6.3887e-05 5.7454e-01 3.4500e-01 1.0030e+00 +UTP3 ENST00000254803 1.9374e-05 5.9139e-01 3.6400e-01 1.0030e+00 +ZNF235 ENST00000291182 3.3787e-10 6.8398e-01 4.7600e-01 1.0040e+00 +ELTD1 ENST00000370742 2.7800e-11 6.9709e-01 4.9300e-01 1.0040e+00 +ATP6V0A4 ENST00000310018 2.1504e-20 7.6337e-01 5.8600e-01 1.0040e+00 +CBLN4 ENST00000064571 1.6726e-01 3.1944e-01 1.3000e-01 1.0040e+00 +CD59 ENST00000395850 6.0568e-01 0.0000e+00 0.0000e+00 1.0040e+00 +RXFP2 ENST00000298386 9.8971e-16 7.3598e-01 5.4700e-01 1.0040e+00 +PQLC2 ENST00000375153 6.3479e-05 5.7510e-01 3.4600e-01 1.0040e+00 +FAM118A ENST00000216214 6.3156e-05 5.7554e-01 3.4600e-01 1.0040e+00 +LIPK ENST00000404190 1.7565e-06 6.1942e-01 3.9600e-01 1.0040e+00 +C9orf78 ENST00000372447 1.9212e-05 5.9208e-01 3.6400e-01 1.0040e+00 +HIST1H3J ENST00000359303 6.0556e-01 0.0000e+00 0.0000e+00 1.0040e+00 +PIK3R3 ENST00000262741 3.3583e-10 6.8427e-01 4.7600e-01 1.0040e+00 +KLKB1 ENST00000264690 6.2893e-13 7.1372e-01 5.1600e-01 1.0040e+00 +DDX60L ENST00000260184 1.0665e-38 8.2034e-01 6.7300e-01 1.0050e+00 +C4orf21 ENST00000505019 2.1633e-42 8.2699e-01 6.8400e-01 1.0050e+00 +HHLA2 ENST00000357759 1.7284e-06 6.2060e-01 3.9700e-01 1.0050e+00 +PPA1 ENST00000373232 1.9170e-05 5.9226e-01 3.6400e-01 1.0050e+00 +YDJC ENST00000292778 6.2374e-02 3.8891e-01 1.7600e-01 1.0050e+00 +TMC4 ENST00000376591 1.7195e-13 7.1934e-01 5.2300e-01 1.0050e+00 +COL21A1 ENST00000244728 5.2336e-24 7.7974e-01 6.1000e-01 1.0050e+00 +SLC9B1 ENST00000296422 5.1677e-07 6.3239e-01 4.1100e-01 1.0050e+00 +DPYD ENST00000370192 3.3686e-22 7.7223e-01 5.9900e-01 1.0050e+00 +P4HTM ENST00000343546 3.9204e-09 6.7018e-01 4.5800e-01 1.0050e+00 +KBTBD11 ENST00000320248 6.2354e-02 3.8895e-01 1.7600e-01 1.0050e+00 +ZNF416 ENST00000196489 3.6706e-01 2.1280e-01 7.5000e-02 1.0050e+00 +TTC29 ENST00000325106 1.3375e-08 6.6194e-01 4.4700e-01 1.0050e+00 +ZXDC ENST00000389709 1.1449e-09 6.7773e-01 4.6700e-01 1.0050e+00 +DBH ENST00000393056 3.3352e-10 6.8461e-01 4.7700e-01 1.0050e+00 +BTC ENST00000395743 6.2276e-02 3.8912e-01 1.7600e-01 1.0050e+00 +TMPO ENST00000266732 1.5453e-07 6.4275e-01 4.2400e-01 1.0050e+00 +CDC6 ENST00000209728 1.1499e-09 6.7750e-01 4.6700e-01 1.0050e+00 +RSL1D1 ENST00000571133 5.1679e-07 6.3239e-01 4.1100e-01 1.0050e+00 +C16orf54 ENST00000329410 3.6686e-01 2.1289e-01 7.5000e-02 1.0060e+00 +ACTR5 ENST00000243903 1.1352e-09 6.7817e-01 4.6800e-01 1.0060e+00 +C6orf211 ENST00000367294 5.1190e-07 6.3304e-01 4.1100e-01 1.0060e+00 +PPP1R3A ENST00000284601 9.3122e-16 7.3763e-01 5.4800e-01 1.0060e+00 +C10orf129 ENST00000341686 1.5331e-07 6.4327e-01 4.2400e-01 1.0060e+00 +PALB2 ENST00000261584 3.0379e-19 7.5888e-01 5.7900e-01 1.0060e+00 +BMF ENST00000354670 6.7580e-03 4.7851e-01 2.4900e-01 1.0060e+00 +NUDCD1 ENST00000239690 2.6721e-11 6.9880e-01 4.9500e-01 1.0060e+00 +FAM71C ENST00000324341 1.6671e-01 3.1993e-01 1.3000e-01 1.0060e+00 +CCBE1 ENST00000439986 1.5315e-07 6.4334e-01 4.2400e-01 1.0060e+00 +AIM1 ENST00000369066 3.5143e-33 8.0864e-01 6.5400e-01 1.0060e+00 +DIS3 ENST00000377767 1.2694e-21 7.7053e-01 5.9600e-01 1.0060e+00 +TMEM209 ENST00000397622 6.0536e-13 7.1509e-01 5.1700e-01 1.0060e+00 +PLA2G4C ENST00000599111 1.6781e-13 7.2017e-01 5.2400e-01 1.0060e+00 +FAM175A ENST00000321945 5.0739e-07 6.3365e-01 4.1200e-01 1.0070e+00 +ADCK3 ENST00000366779 9.2856e-11 6.9284e-01 4.8600e-01 1.0070e+00 +C20orf196 ENST00000303142 1.6633e-01 3.2028e-01 1.3000e-01 1.0070e+00 +BLZF1 ENST00000367808 5.0879e-07 6.3346e-01 4.1100e-01 1.0070e+00 +FKBP3 ENST00000216330 6.6025e-04 5.3598e-01 3.0400e-01 1.0070e+00 +TTC22 ENST00000371276 1.7098e-06 6.2139e-01 3.9700e-01 1.0070e+00 +ESR2 ENST00000341099 4.4516e-08 6.5421e-01 4.3700e-01 1.0070e+00 +ZNF614 ENST00000270649 1.5117e-07 6.4418e-01 4.2400e-01 1.0070e+00 +ZPLD1 ENST00000306176 4.4480e-08 6.5426e-01 4.3700e-01 1.0070e+00 +HACL1 ENST00000321169 7.4827e-12 7.0524e-01 5.0300e-01 1.0070e+00 +NKIRAS2 ENST00000307641 6.7229e-03 4.7910e-01 2.4900e-01 1.0070e+00 +GEMIN4 ENST00000319004 5.8966e-13 7.1603e-01 5.1800e-01 1.0070e+00 +C16orf80 ENST00000262498 2.1100e-03 5.1074e-01 2.7900e-01 1.0080e+00 +MEIS3 ENST00000561293 3.7957e-09 6.7194e-01 4.5900e-01 1.0080e+00 +BSCL2 ENST00000433053 1.0981e-09 6.7988e-01 4.6900e-01 1.0080e+00 +TPD52L2 ENST00000217121 2.0188e-04 5.5864e-01 3.2700e-01 1.0080e+00 +FGL2 ENST00000248598 6.1472e-05 5.7790e-01 3.4700e-01 1.0080e+00 +RASSF2 ENST00000379400 5.0648e-07 6.3378e-01 4.1200e-01 1.0080e+00 +LAMB4 ENST00000388781 1.6140e-42 8.3001e-01 6.8600e-01 1.0080e+00 +ECE2 ENST00000402825 1.1756e-21 7.7190e-01 5.9700e-01 1.0080e+00 +KCTD12 ENST00000377474 6.1693e-02 3.9036e-01 1.7700e-01 1.0080e+00 +MTFMT ENST00000220058 1.4994e-07 6.4471e-01 4.2500e-01 1.0080e+00 +KCNN4 ENST00000262888 5.0256e-07 6.3431e-01 4.1200e-01 1.0080e+00 +MRPL33 ENST00000296102 3.6550e-01 2.1354e-01 7.5000e-02 1.0090e+00 +EMC1 ENST00000477853 6.7281e-26 7.8902e-01 6.2200e-01 1.0090e+00 +PTF1A ENST00000376504 1.6565e-01 3.2089e-01 1.3000e-01 1.0090e+00 +SCEL ENST00000349847 4.5807e-21 7.6950e-01 5.9300e-01 1.0090e+00 +GSG2 ENST00000325418 4.9913e-07 6.3479e-01 4.1200e-01 1.0090e+00 +HARBI1 ENST00000326737 6.4751e-04 5.3791e-01 3.0500e-01 1.0100e+00 +CREB3 ENST00000353704 1.8489e-05 5.9523e-01 3.6600e-01 1.0100e+00 +CX3CR1 ENST00000358309 6.1371e-02 3.9105e-01 1.7700e-01 1.0100e+00 +NHLRC3 ENST00000379600 1.8477e-05 5.9528e-01 3.6600e-01 1.0100e+00 +PWP1 ENST00000412830 1.9862e-12 7.1305e-01 5.1200e-01 1.0100e+00 +RPS20 ENST00000519807 2.0686e-02 4.4131e-01 2.1600e-01 1.0100e+00 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3.0500e-01 1.0110e+00 +MAN2B2 ENST00000285599 6.5570e-23 7.7910e-01 6.0600e-01 1.0110e+00 +CYP51A1 ENST00000003100 1.4563e-07 6.4661e-01 4.2600e-01 1.0110e+00 +RPL36A-HNRNPH2 ENST00000409170 3.6425e-01 2.1414e-01 7.5000e-02 1.0110e+00 +CTSH ENST00000220166 1.2518e-08 6.6577e-01 4.5000e-01 1.0110e+00 +CACNA2D4 ENST00000382722 1.4894e-34 8.1561e-01 6.6200e-01 1.0110e+00 +CTC-534A2.2 ENST00000510585 2.0609e-02 4.4177e-01 2.1700e-01 1.0110e+00 +ARHGAP19-SLIT1 ENST00000453547 6.9829e-12 7.0802e-01 5.0500e-01 1.0110e+00 +ATP8B3 ENST00000310127 1.4666e-26 7.9291e-01 6.2700e-01 1.0110e+00 +SNRNP27 ENST00000244227 1.9763e-04 5.6061e-01 3.2800e-01 1.0120e+00 +UNC50 ENST00000357765 1.9753e-04 5.6066e-01 3.2800e-01 1.0120e+00 +GHSR ENST00000241256 6.5825e-03 4.8147e-01 2.5100e-01 1.0120e+00 +POTEF ENST00000357462 5.4522e-06 6.1164e-01 3.8400e-01 1.0120e+00 +STAC ENST00000273183 1.4350e-07 6.4757e-01 4.2700e-01 1.0120e+00 +LOXHD1 ENST00000300591 5.5941e-26 7.9182e-01 6.2400e-01 1.0120e+00 +POLR1D ENST00000302979 3.6357e-01 2.1446e-01 7.5000e-02 1.0130e+00 +DNTT ENST00000371174 2.9548e-10 6.9046e-01 4.8100e-01 1.0130e+00 +LIMD2 ENST00000259006 1.6402e-01 3.2238e-01 1.3100e-01 1.0130e+00 +TRIM5 ENST00000380034 5.9675e-05 5.8049e-01 3.4900e-01 1.0130e+00 +COL6A6 ENST00000358511 8.4528e-46 8.3930e-01 6.9800e-01 1.0130e+00 +GSTM1 ENST00000309851 2.0641e-03 5.1306e-01 2.8000e-01 1.0130e+00 +GALNS ENST00000268695 2.9611e-10 6.9036e-01 4.8100e-01 1.0130e+00 +SLC7A2 ENST00000004531 2.3434e-11 7.0440e-01 4.9900e-01 1.0140e+00 +UBQLN3 ENST00000311659 1.7965e-05 5.9760e-01 3.6800e-01 1.0140e+00 +SCN10A ENST00000449082 9.9457e-38 8.2473e-01 6.7400e-01 1.0140e+00 +TMPRSS4 ENST00000437212 1.2055e-08 6.6794e-01 4.5100e-01 1.0140e+00 +SLC9A8 ENST00000417961 2.9146e-10 6.9112e-01 4.8100e-01 1.0140e+00 +SFI1 ENST00000400288 5.9369e-44 8.3672e-01 6.9300e-01 1.0140e+00 +FAM161A ENST00000404929 5.1034e-13 7.2117e-01 5.2100e-01 1.0140e+00 +RP11-758M4.1 ENST00000523118 1.6336e-01 3.2300e-01 1.3100e-01 1.0150e+00 +HMCN2 ENST00000428715 1.8027e-12 7.1669e-01 5.1500e-01 1.0150e+00 +EPB41L4A ENST00000261486 3.5133e-21 7.7441e-01 5.9700e-01 1.0150e+00 +PEX13 ENST00000295030 5.8959e-05 5.8155e-01 3.5000e-01 1.0150e+00 +PMS1 ENST00000441310 1.3178e-17 7.5531e-01 5.6900e-01 1.0150e+00 +SOSTDC1 ENST00000307068 1.6334e-01 3.2301e-01 1.3100e-01 1.0150e+00 +EFCAB3 ENST00000450662 3.4807e-09 6.7666e-01 4.6200e-01 1.0150e+00 +ZNF286B ENST00000545289 5.3381e-06 6.1329e-01 3.8500e-01 1.0150e+00 +TRMT61B ENST00000306108 4.1070e-08 6.5915e-01 4.4000e-01 1.0150e+00 +RIMKLA ENST00000431473 6.3057e-04 5.4054e-01 3.0600e-01 1.0150e+00 +TLR10 ENST00000308973 3.4787e-09 6.7669e-01 4.6200e-01 1.0150e+00 +ZNF302 ENST00000505242 1.9368e-04 5.6250e-01 3.2900e-01 1.0150e+00 +ZNF441 ENST00000357901 3.6240e-01 2.1503e-01 7.5000e-02 1.0150e+00 +ABT1 ENST00000274849 2.0296e-02 4.4362e-01 2.1700e-01 1.0150e+00 +C2orf82 ENST00000409230 6.0161e-01 0.0000e+00 0.0000e+00 1.0160e+00 +MED27 ENST00000292035 1.7718e-05 5.9874e-01 3.6800e-01 1.0160e+00 +TRDN ENST00000398178 8.3570e-22 7.7804e-01 6.0100e-01 1.0160e+00 +ANXA4 ENST00000394295 1.1858e-08 6.6890e-01 4.5200e-01 1.0160e+00 +C1orf198 ENST00000366663 6.2943e-04 5.4072e-01 3.0700e-01 1.0160e+00 +INHA ENST00000243786 6.4728e-03 4.8338e-01 2.5200e-01 1.0160e+00 +EDN2 ENST00000372587 6.0323e-02 3.9334e-01 1.7800e-01 1.0160e+00 +BHLHB9 ENST00000372735 2.0250e-02 4.4390e-01 2.1800e-01 1.0160e+00 +PARD6A ENST00000219255 6.4719e-03 4.8339e-01 2.5200e-01 1.0160e+00 +DBR1 ENST00000260803 1.1785e-08 6.6925e-01 4.5200e-01 1.0160e+00 +C7orf31 ENST00000409280 8.0549e-11 6.9929e-01 4.9100e-01 1.0160e+00 +KRT75 ENST00000252245 4.0410e-08 6.6014e-01 4.4100e-01 1.0160e+00 +RP11-155D18.14 ENST00000489595 1.6311e-01 3.2323e-01 1.3100e-01 1.0160e+00 +HYAL1 ENST00000266031 1.9112e-04 5.6374e-01 3.3000e-01 1.0170e+00 +KIAA0101 ENST00000300035 1.6276e-01 3.2355e-01 1.3100e-01 1.0170e+00 +APOBEC3H ENST00000401756 2.0200e-03 5.1535e-01 2.8100e-01 1.0170e+00 +ENTPD4 ENST00000358689 1.8146e-16 7.4958e-01 5.6000e-01 1.0170e+00 +TM2D2 ENST00000456397 6.4454e-03 4.8386e-01 2.5200e-01 1.0170e+00 +TM7SF2 ENST00000279263 1.3660e-07 6.5078e-01 4.2900e-01 1.0170e+00 +NLRP7 ENST00000588756 1.8058e-16 7.4971e-01 5.6000e-01 1.0170e+00 +BOK ENST00000318407 1.6279e-01 3.2353e-01 1.3100e-01 1.0170e+00 +CORO7 ENST00000251166 1.8292e-25 7.9309e-01 6.2400e-01 1.0170e+00 +HLA-C ENST00000376228 1.5695e-06 6.2766e-01 4.0100e-01 1.0170e+00 +PGP ENST00000333503 1.6263e-01 3.2368e-01 1.3100e-01 1.0170e+00 +TCHP ENST00000312777 1.8026e-16 7.4975e-01 5.6000e-01 1.0170e+00 +MICU3 ENST00000318063 3.4019e-09 6.7790e-01 4.6300e-01 1.0170e+00 +SEPN1 ENST00000361547 9.7863e-10 6.8577e-01 4.7300e-01 1.0170e+00 +C4orf47 ENST00000378850 6.2148e-04 5.4199e-01 3.0700e-01 1.0180e+00 +NFATC2IP ENST00000320805 1.7420e-05 6.0015e-01 3.6900e-01 1.0180e+00 +ZMAT3 ENST00000311417 1.9034e-04 5.6413e-01 3.3000e-01 1.0180e+00 +RALB ENST00000272519 2.0067e-02 4.4501e-01 2.1800e-01 1.0180e+00 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1.0190e+00 +CAPN8 ENST00000366872 1.2513e-13 7.2995e-01 5.3100e-01 1.0190e+00 +APOBEC3F ENST00000308521 1.3460e-07 6.5174e-01 4.2900e-01 1.0190e+00 +FUNDC2 ENST00000369498 5.9823e-02 3.9446e-01 1.7900e-01 1.0190e+00 +HPS3 ENST00000296051 2.9433e-21 7.7770e-01 5.9900e-01 1.0190e+00 +WBSCR27 ENST00000297873 5.9768e-02 3.9458e-01 1.7900e-01 1.0190e+00 +CCDC57 ENST00000392343 6.5038e-16 7.4721e-01 5.5500e-01 1.0190e+00 +TM9SF1 ENST00000530611 2.4599e-15 7.4311e-01 5.5000e-01 1.0190e+00 +RHOJ ENST00000316754 6.4012e-03 4.8464e-01 2.5200e-01 1.0190e+00 +FAM110A ENST00000304189 3.6091e-01 2.1576e-01 7.6000e-02 1.0190e+00 +SLC35B1 ENST00000240333 1.7301e-05 6.0072e-01 3.7000e-01 1.0190e+00 +HOXB4 ENST00000332503 5.9777e-02 3.9456e-01 1.7900e-01 1.0190e+00 +PODN ENST00000312553 9.5675e-10 6.8692e-01 4.7400e-01 1.0190e+00 +C3orf38 ENST00000318887 6.1331e-04 5.4332e-01 3.0800e-01 1.0200e+00 +CMTM8 ENST00000307526 5.9614e-02 3.9492e-01 1.7900e-01 1.0200e+00 +AIF1L ENST00000372309 6.3739e-03 4.8513e-01 2.5300e-01 1.0200e+00 +ZCCHC10 ENST00000324170 5.9669e-02 3.9480e-01 1.7900e-01 1.0200e+00 +VKORC1 ENST00000394975 1.6163e-01 3.2462e-01 1.3200e-01 1.0200e+00 +COG6 ENST00000455146 6.3567e-16 7.4782e-01 5.5600e-01 1.0200e+00 +JUN ENST00000371222 5.9620e-02 3.9491e-01 1.7900e-01 1.0200e+00 +MATN4 ENST00000537548 1.1311e-08 6.7162e-01 4.5400e-01 1.0200e+00 +GPALPP1 ENST00000361121 1.7222e-05 6.0110e-01 3.7000e-01 1.0200e+00 +NPY5R ENST00000515560 6.3686e-03 4.8523e-01 2.5300e-01 1.0200e+00 +SNAPC3 ENST00000380821 4.5455e-07 6.4125e-01 4.1700e-01 1.0200e+00 +TREH ENST00000264029 8.9579e-15 7.3968e-01 5.4400e-01 1.0200e+00 +MAP3K19 ENST00000375845 1.7574e-22 7.8362e-01 6.0800e-01 1.0200e+00 +CALB2 ENST00000302628 4.5423e-07 6.4130e-01 4.1700e-01 1.0200e+00 +CREB3L4 ENST00000368607 5.1401e-06 6.1624e-01 3.8700e-01 1.0200e+00 +PCDHAC1 ENST00000253807 7.5673e-11 7.0209e-01 4.9300e-01 1.0200e+00 +COA7 ENST00000371538 5.9686e-02 3.9476e-01 1.7900e-01 1.0200e+00 +HAUS8 ENST00000253669 1.5207e-06 6.2998e-01 4.0300e-01 1.0210e+00 +CDK7 ENST00000256443 4.4725e-07 6.4237e-01 4.1700e-01 1.0210e+00 +DYNLRB1 ENST00000357156 1.6147e-01 3.2477e-01 1.3200e-01 1.0210e+00 +ZWILCH ENST00000307897 1.1980e-13 7.3139e-01 5.3200e-01 1.0210e+00 +EARS2 ENST00000449606 1.1238e-08 6.7199e-01 4.5400e-01 1.0210e+00 +TSPAN17 ENST00000310032 1.5110e-06 6.3045e-01 4.0300e-01 1.0210e+00 +FGA ENST00000302053 1.2236e-13 7.3069e-01 5.3100e-01 1.0210e+00 +RGAG4 ENST00000545866 1.8633e-04 5.6613e-01 3.3100e-01 1.0210e+00 +STAP1 ENST00000265404 1.6993e-05 6.0221e-01 3.7100e-01 1.0210e+00 +EGR4 ENST00000545030 6.3486e-03 4.8559e-01 2.5300e-01 1.0210e+00 +NOMO1 ENST00000287667 1.7020e-19 7.7073e-01 5.8800e-01 1.0220e+00 +BCAT1 ENST00000539282 3.7984e-08 6.6393e-01 4.4300e-01 1.0220e+00 +SYCE3 ENST00000406915 5.9990e-01 0.0000e+00 0.0000e+00 1.0220e+00 +SLC22A11 ENST00000301891 1.2995e-07 6.5403e-01 4.3100e-01 1.0220e+00 +RP11-47I22.4 ENST00000556347 5.9327e-02 3.9557e-01 1.7900e-01 1.0220e+00 +SMPD4 ENST00000409031 1.7125e-19 7.7060e-01 5.8800e-01 1.0220e+00 +GEMIN2 ENST00000308317 1.4999e-06 6.3099e-01 4.0300e-01 1.0220e+00 +GYLTL1B ENST00000531526 1.6044e-12 7.2103e-01 5.1800e-01 1.0220e+00 +MARVELD1 ENST00000285605 3.5958e-01 2.1641e-01 7.6000e-02 1.0220e+00 +HTR5A ENST00000287907 6.2906e-03 4.8664e-01 2.5300e-01 1.0230e+00 +CCDC34 ENST00000328697 5.0130e-06 6.1820e-01 3.8800e-01 1.0230e+00 +GABRE ENST00000370328 1.8436e-04 5.6713e-01 3.3200e-01 1.0230e+00 +STX7 ENST00000367941 5.0273e-06 6.1797e-01 3.8800e-01 1.0230e+00 +METTL1 ENST00000324871 1.9620e-03 5.1847e-01 2.8300e-01 1.0230e+00 +ERMARD ENST00000366773 5.7789e-16 7.5033e-01 5.5800e-01 1.0230e+00 +MRPS18B ENST00000259873 5.6012e-05 5.8608e-01 3.5200e-01 1.0230e+00 +NBL1 ENST00000289749 5.9018e-02 3.9628e-01 1.7900e-01 1.0230e+00 +SLC30A7 ENST00000370112 4.4049e-07 6.4343e-01 4.1800e-01 1.0230e+00 +MYL10 ENST00000223167 6.2611e-03 4.8718e-01 2.5400e-01 1.0240e+00 +FANCI ENST00000310775 8.9116e-37 8.2993e-01 6.7700e-01 1.0240e+00 +SPHK2 ENST00000245222 1.2800e-07 6.5501e-01 4.3200e-01 1.0240e+00 +TREM1 ENST00000244709 6.2776e-03 4.8688e-01 2.5300e-01 1.0240e+00 +ERAL1 ENST00000254928 3.1095e-09 6.8276e-01 4.6600e-01 1.0240e+00 +CD34 ENST00000310833 4.9881e-06 6.1859e-01 3.8800e-01 1.0240e+00 +CCDC86 ENST00000227520 1.6652e-05 6.0390e-01 3.7200e-01 1.0240e+00 +THNSL2 ENST00000324166 1.4828e-06 6.3184e-01 4.0400e-01 1.0240e+00 +VSIG10L ENST00000335624 1.0860e-08 6.7396e-01 4.5500e-01 1.0240e+00 +CEBPB ENST00000303004 3.5809e-01 2.1714e-01 7.6000e-02 1.0250e+00 +ATP10B ENST00000327245 1.4073e-30 8.1504e-01 6.5300e-01 1.0250e+00 +ELP3 ENST00000256398 3.0115e-14 7.3835e-01 5.4000e-01 1.0250e+00 +HDGFL1 ENST00000510882 5.8681e-02 3.9705e-01 1.8000e-01 1.0250e+00 +ENPP3 ENST00000414305 3.4680e-23 7.9001e-01 6.1400e-01 1.0250e+00 +PLCZ1 ENST00000266505 1.5016e-12 7.2348e-01 5.2000e-01 1.0250e+00 +TAF1B ENST00000263663 7.9823e-15 7.4305e-01 5.4700e-01 1.0250e+00 +ARTN ENST00000414809 3.5793e-01 2.1723e-01 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1.4922e-18 7.7687e-01 5.8800e-01 1.0390e+00 +P2RY10 ENST00000171757 1.5542e-01 3.3068e-01 1.3400e-01 1.0390e+00 +ISLR ENST00000249842 1.8643e-02 4.5417e-01 2.2300e-01 1.0390e+00 +IL10 ENST00000423557 5.8874e-03 4.9433e-01 2.5700e-01 1.0390e+00 +MRPL1 ENST00000315567 4.4456e-06 6.2766e-01 3.9400e-01 1.0390e+00 +UQCC1 ENST00000374385 3.1978e-08 6.7446e-01 4.5000e-01 1.0390e+00 +UQCC2 ENST00000607484 1.8660e-02 4.5406e-01 2.2300e-01 1.0390e+00 +ZYX ENST00000322764 2.0307e-10 7.0825e-01 4.9300e-01 1.0390e+00 +ALOX12 ENST00000251535 1.4397e-15 7.5782e-01 5.6000e-01 1.0390e+00 +SGK494 ENST00000301037 7.2766e-10 7.0073e-01 4.8300e-01 1.0390e+00 +TDO2 ENST00000536354 2.0378e-10 7.0809e-01 4.9300e-01 1.0390e+00 +TRPM8 ENST00000324695 4.5964e-29 8.2117e-01 6.5300e-01 1.0390e+00 +PLTP ENST00000477313 8.9961e-09 6.8475e-01 4.6300e-01 1.0400e+00 +FAM114A2 ENST00000351797 7.2335e-10 7.0103e-01 4.8400e-01 1.0400e+00 +SI ENST00000264382 3.9353e-60 8.8020e-01 7.4700e-01 1.0400e+00 +PUS10 ENST00000316752 7.8796e-14 7.4493e-01 5.4200e-01 1.0400e+00 +CDCA2 ENST00000330560 1.5175e-11 7.2250e-01 5.1100e-01 1.0400e+00 +ABI3 ENST00000225941 5.0089e-05 5.9607e-01 3.5800e-01 1.0400e+00 +RTKN2 ENST00000373789 5.4633e-15 7.5398e-01 5.5500e-01 1.0400e+00 +HADHB ENST00000317799 1.5183e-11 7.2248e-01 5.1100e-01 1.0400e+00 +NIPA1 ENST00000337435 5.8703e-03 4.9468e-01 2.5800e-01 1.0400e+00 +TCTN3 ENST00000371217 4.1528e-12 7.2839e-01 5.1900e-01 1.0400e+00 +MYO3A ENST00000265944 1.8056e-45 8.5918e-01 7.1300e-01 1.0400e+00 +DCAF12L2 ENST00000538699 5.8713e-03 4.9466e-01 2.5800e-01 1.0400e+00 +IL7R ENST00000303115 3.7630e-07 6.5436e-01 4.2500e-01 1.0400e+00 +ZNF23 ENST00000393539 1.0831e-07 6.6590e-01 4.3900e-01 1.0410e+00 +TUBB6 ENST00000317702 1.6645e-04 5.7688e-01 3.3800e-01 1.0410e+00 +DDX20 ENST00000369702 7.7601e-14 7.4541e-01 5.4200e-01 1.0410e+00 +FIBP ENST00000338369 4.3854e-06 6.2874e-01 3.9500e-01 1.0410e+00 +VNN1 ENST00000367928 4.3868e-06 6.2871e-01 3.9500e-01 1.0410e+00 +DRC1 ENST00000288710 8.3157e-20 7.8539e-01 5.9900e-01 1.0410e+00 +LHFPL2 ENST00000380345 5.6209e-02 4.0295e-01 1.8300e-01 1.0410e+00 +FBXW12 ENST00000296438 7.0808e-10 7.0210e-01 4.8400e-01 1.0410e+00 +ZNF567 ENST00000585696 1.0840e-07 6.6585e-01 4.3900e-01 1.0410e+00 +DTD1 ENST00000377452 1.8054e-03 5.2752e-01 2.8800e-01 1.0410e+00 +C1orf127 ENST00000377004 1.4917e-11 7.2320e-01 5.1200e-01 1.0410e+00 +MYH4 ENST00000255381 1.0355e-55 8.7570e-01 7.3900e-01 1.0410e+00 +NDNL2 ENST00000332303 5.6212e-02 4.0294e-01 1.8300e-01 1.0410e+00 +LYAR ENST00000343470 3.7580e-07 6.5445e-01 4.2500e-01 1.0410e+00 +ZMYM5 ENST00000382905 1.6664e-04 5.7677e-01 3.3800e-01 1.0410e+00 +CD37 ENST00000323906 4.3887e-06 6.2868e-01 3.9500e-01 1.0410e+00 +INADL ENST00000371158 1.1917e-50 8.6950e-01 7.2800e-01 1.0420e+00 +MKS1 ENST00000393119 3.3768e-16 7.6431e-01 5.6800e-01 1.0420e+00 +LRRC48 ENST00000313838 2.5027e-09 6.9442e-01 4.7400e-01 1.0420e+00 +ZNF713 ENST00000429591 4.3462e-06 6.2945e-01 3.9500e-01 1.0420e+00 +CCDC181 ENST00000545005 1.9512e-10 7.1011e-01 4.9400e-01 1.0420e+00 +POMGNT1 ENST00000371992 1.9454e-20 7.8941e-01 6.0400e-01 1.0420e+00 +FANCC ENST00000289081 2.7921e-13 7.4194e-01 5.3600e-01 1.0430e+00 +BIRC5 ENST00000301633 5.5854e-02 4.0382e-01 1.8300e-01 1.0430e+00 +C16orf86 ENST00000403458 5.8052e-03 4.9599e-01 2.5800e-01 1.0430e+00 +MTX3 ENST00000512560 1.6475e-04 5.7787e-01 3.3800e-01 1.0430e+00 +TOM1 ENST00000411850 1.4544e-11 7.2423e-01 5.1300e-01 1.0430e+00 +GTF2H3 ENST00000543341 3.0414e-08 6.7752e-01 4.5200e-01 1.0430e+00 +INS-IGF2 ENST00000397270 5.5811e-02 4.0393e-01 1.8300e-01 1.0430e+00 +LGALSL ENST00000238875 1.8392e-02 4.5589e-01 2.2400e-01 1.0430e+00 +CCR6 ENST00000341935 5.7867e-03 4.9637e-01 2.5800e-01 1.0430e+00 +TRIM31 ENST00000376734 4.3248e-06 6.2984e-01 3.9500e-01 1.0430e+00 +FGF2 ENST00000264498 1.8400e-02 4.5584e-01 2.2400e-01 1.0430e+00 +KLHDC8B ENST00000332780 1.7910e-03 5.2840e-01 2.8800e-01 1.0430e+00 +TCP11 ENST00000311875 1.0587e-07 6.6738e-01 4.4000e-01 1.0430e+00 +AC003002.6 ENST00000596400 3.5010e-01 2.2119e-01 7.8000e-02 1.0430e+00 +OSTC ENST00000512478 1.8353e-02 4.5616e-01 2.2400e-01 1.0430e+00 +TNN ENST00000239462 1.5729e-28 8.2236e-01 6.5300e-01 1.0430e+00 +VSX2 ENST00000261980 1.6481e-04 5.7783e-01 3.3800e-01 1.0430e+00 +SDAD1 ENST00000356260 1.8319e-20 7.9062e-01 6.0500e-01 1.0440e+00 +SHBG ENST00000380450 1.2538e-06 6.4426e-01 4.1200e-01 1.0440e+00 +ETFDH ENST00000511912 2.7780e-13 7.4211e-01 5.3600e-01 1.0440e+00 +SLC17A5 ENST00000355773 6.8514e-10 7.0374e-01 4.8500e-01 1.0440e+00 +C1QB ENST00000314933 1.5392e-01 3.3220e-01 1.3500e-01 1.0440e+00 +CCL3 ENST00000225245 3.4981e-01 2.2134e-01 7.8000e-02 1.0440e+00 +AGA ENST00000264595 4.2802e-06 6.3066e-01 3.9600e-01 1.0440e+00 +BTNL8 ENST00000340184 1.4502e-05 6.1553e-01 3.7900e-01 1.0440e+00 +LRRC37A ENST00000320254 5.4349e-04 5.5561e-01 3.1500e-01 1.0440e+00 +NDUFB9 ENST00000276689 1.6312e-04 5.7883e-01 3.3900e-01 1.0440e+00 +ADHFE1 ENST00000396623 8.5168e-09 6.8788e-01 4.6500e-01 1.0450e+00 +SCARA3 ENST00000301904 2.9816e-08 6.7873e-01 4.5300e-01 1.0450e+00 +EPHA1 ENST00000275815 1.4624e-23 8.0508e-01 6.2600e-01 1.0450e+00 +S1PR2 ENST00000590320 1.8286e-02 4.5663e-01 2.2400e-01 1.0450e+00 +SIRT3 ENST00000382743 1.6261e-04 5.7913e-01 3.3900e-01 1.0450e+00 +CLEC18B ENST00000339953 1.2431e-06 6.4490e-01 4.1200e-01 1.0450e+00 +AC174470.1 ENST00000457257 1.5353e-01 3.3260e-01 1.3500e-01 1.0450e+00 +OXA1L ENST00000285848 1.8749e-10 7.1197e-01 4.9600e-01 1.0450e+00 +TTI2 ENST00000431156 3.6074e-07 6.5730e-01 4.2700e-01 1.0450e+00 +SPDYC ENST00000377185 4.8667e-05 5.9868e-01 3.6000e-01 1.0450e+00 +LLPH ENST00000266604 3.4929e-01 2.2161e-01 7.8000e-02 1.0450e+00 +ELAC2 ENST00000338034 1.7245e-20 7.9182e-01 6.0600e-01 1.0460e+00 +FAM65C ENST00000327979 7.0058e-20 7.8892e-01 6.0200e-01 1.0460e+00 +POM121C ENST00000453279 6.6064e-10 7.0555e-01 4.8700e-01 1.0460e+00 +RHBDL3 ENST00000269051 1.0358e-07 6.6881e-01 4.4100e-01 1.0460e+00 +SGCG ENST00000218867 4.8210e-05 5.9953e-01 3.6000e-01 1.0460e+00 +TM6SF1 ENST00000322019 1.0194e-07 6.6985e-01 4.4100e-01 1.0470e+00 +DESI1 ENST00000263256 5.7118e-03 4.9791e-01 2.5900e-01 1.0470e+00 +TIPIN ENST00000261881 1.6045e-04 5.8043e-01 3.4000e-01 1.0470e+00 +PABPC4L ENST00000529122 5.3305e-04 5.5762e-01 3.1600e-01 1.0470e+00 +SOCS4 ENST00000395472 1.4208e-05 6.1726e-01 3.8000e-01 1.0470e+00 +KRT222 ENST00000394052 1.4228e-05 6.1715e-01 3.8000e-01 1.0470e+00 +ARL6IP6 ENST00000326446 1.8099e-02 4.5794e-01 2.2500e-01 1.0470e+00 +CRELD1 ENST00000326434 1.3432e-11 7.2747e-01 5.1500e-01 1.0480e+00 +MYOD1 ENST00000250003 1.5239e-01 3.3378e-01 1.3500e-01 1.0480e+00 +ARL5B ENST00000377275 1.7521e-03 5.3083e-01 2.9000e-01 1.0480e+00 +SLC25A16 ENST00000609923 1.2089e-06 6.4697e-01 4.1400e-01 1.0480e+00 +TTC12 ENST00000529221 1.7871e-17 7.7653e-01 5.8300e-01 1.0480e+00 +MON1A ENST00000296473 2.2952e-09 6.9903e-01 4.7700e-01 1.0490e+00 +WNK4 ENST00000246914 6.8806e-25 8.1334e-01 6.3600e-01 1.0490e+00 +ABHD14A-ACY1 ENST00000463937 1.7689e-10 7.1467e-01 4.9800e-01 1.0490e+00 +ZDHHC12 ENST00000372663 5.2913e-04 5.5838e-01 3.1700e-01 1.0490e+00 +ZDHHC22 ENST00000319374 5.4892e-02 4.0625e-01 1.8400e-01 1.0490e+00 +TMEM101 ENST00000589334 1.7385e-03 5.3169e-01 2.9000e-01 1.0490e+00 +DKK3 ENST00000396505 4.1049e-06 6.3399e-01 3.9800e-01 1.0490e+00 +KRTAP17-1 ENST00000334202 5.9112e-01 0.0000e+00 0.0000e+00 1.0490e+00 +RBM23 ENST00000359890 4.8221e-11 7.2193e-01 5.0700e-01 1.0490e+00 +GNB1L ENST00000329517 4.7419e-05 6.0103e-01 3.6100e-01 1.0490e+00 +FAM149B1 ENST00000242505 2.4901e-13 7.4578e-01 5.3900e-01 1.0490e+00 +PROCR ENST00000216968 5.6256e-03 4.9972e-01 2.6000e-01 1.0500e+00 +AP000275.65 ENST00000553001 1.1868e-06 6.4834e-01 4.1400e-01 1.0500e+00 +SEC31B ENST00000370345 2.5856e-29 8.2981e-01 6.6000e-01 1.0500e+00 +TIGIT ENST00000486257 1.7915e-02 4.5925e-01 2.2500e-01 1.0500e+00 +ACADVL ENST00000543245 4.2385e-15 7.6119e-01 5.6000e-01 1.0500e+00 +METTL25 ENST00000248306 9.1880e-13 7.4123e-01 5.3200e-01 1.0500e+00 +PNPLA5 ENST00000216177 1.1936e-06 6.4792e-01 4.1400e-01 1.0500e+00 +PPM1J ENST00000309276 2.2494e-09 7.0009e-01 4.7800e-01 1.0500e+00 +NOX3 ENST00000159060 1.6320e-14 7.5689e-01 5.5400e-01 1.0500e+00 +TMPRSS5 ENST00000299882 2.2562e-09 6.9994e-01 4.7800e-01 1.0500e+00 +VIPR2 ENST00000262178 4.7180e-11 7.2287e-01 5.0800e-01 1.0500e+00 +LCA5L ENST00000358268 3.4560e-07 6.6029e-01 4.2900e-01 1.0500e+00 +GPR27 ENST00000304411 3.4682e-01 2.2291e-01 7.8000e-02 1.0510e+00 +PROM1 ENST00000510224 1.9485e-22 8.0468e-01 6.2200e-01 1.0510e+00 +CRELD2 ENST00000404488 2.7906e-08 6.8276e-01 4.5600e-01 1.0510e+00 +ACAT1 ENST00000265838 9.8525e-08 6.7207e-01 4.4300e-01 1.0510e+00 +ZAN ENST00000546292 1.6432e-62 8.9140e-01 7.5800e-01 1.0510e+00 +C9orf152 ENST00000400613 1.7887e-02 4.5945e-01 2.2500e-01 1.0510e+00 +EPDR1 ENST00000199448 1.7864e-02 4.5962e-01 2.2500e-01 1.0510e+00 +EMILIN2 ENST00000254528 1.6186e-14 7.5713e-01 5.5400e-01 1.0510e+00 +GNRH1 ENST00000276414 1.5146e-01 3.3475e-01 1.3600e-01 1.0510e+00 +FBXO4 ENST00000281623 4.0093e-06 6.3586e-01 3.9900e-01 1.0520e+00 +MRPL9 ENST00000368830 1.5633e-04 5.8296e-01 3.4100e-01 1.0520e+00 +C1orf167 ENST00000433342 9.1452e-34 8.4334e-01 6.8100e-01 1.0520e+00 +RAD9A ENST00000307980 4.0279e-06 6.3549e-01 3.9900e-01 1.0520e+00 +ATP4B ENST00000335288 4.6372e-05 6.0306e-01 3.6300e-01 1.0520e+00 +LYSMD1 ENST00000368908 1.7805e-02 4.6004e-01 2.2600e-01 1.0520e+00 +NMUR2 ENST00000255262 5.1924e-04 5.6035e-01 3.1800e-01 1.0520e+00 +IGSF8 ENST00000368086 4.6329e-11 7.2366e-01 5.0800e-01 1.0520e+00 +CXCR4 ENST00000409817 1.7804e-02 4.6005e-01 2.2600e-01 1.0520e+00 +IRAK4 ENST00000448290 7.8001e-09 6.9287e-01 4.6800e-01 1.0520e+00 +KIAA1191 ENST00000298569 1.1689e-06 6.4948e-01 4.1500e-01 1.0520e+00 +ZNF555 ENST00000334241 9.7445e-08 6.7279e-01 4.4300e-01 1.0520e+00 +ATOH1 ENST00000306011 1.7833e-02 4.5984e-01 2.2500e-01 1.0520e+00 +UGT2B17 ENST00000317746 9.6905e-08 6.7315e-01 4.4400e-01 1.0520e+00 +GSDMB ENST00000418519 3.3446e-07 6.6257e-01 4.3000e-01 1.0530e+00 +PDX1 ENST00000381033 1.7775e-02 4.6026e-01 2.2600e-01 1.0530e+00 +TRIM72 ENST00000322122 4.6320e-05 6.0317e-01 3.6300e-01 1.0530e+00 +RPL7L1 ENST00000493763 1.5563e-04 5.8339e-01 3.4100e-01 1.0530e+00 +ARMC9 ENST00000349938 6.2032e-17 7.7623e-01 5.8000e-01 1.0530e+00 +SLCO2A1 ENST00000310926 2.2804e-13 7.4872e-01 5.4100e-01 1.0530e+00 +CXorf40A ENST00000441248 5.9015e-01 0.0000e+00 0.0000e+00 1.0530e+00 +SLC22A7 ENST00000372585 4.5139e-11 7.2478e-01 5.0900e-01 1.0530e+00 +SLC16A4 ENST00000369779 9.6707e-08 6.7328e-01 4.4400e-01 1.0530e+00 +KIF17 ENST00000247986 3.7556e-18 7.8398e-01 5.9100e-01 1.0530e+00 +KANK3 ENST00000330915 2.7340e-08 6.8400e-01 4.5700e-01 1.0530e+00 +KCNJ12 ENST00000583088 5.4242e-02 4.0792e-01 1.8500e-01 1.0530e+00 +SLC15A2 ENST00000489711 5.4803e-20 7.9400e-01 6.0500e-01 1.0530e+00 +SOX18 ENST00000340356 1.5103e-01 3.3520e-01 1.3600e-01 1.0530e+00 +TVP23B ENST00000307767 5.1742e-04 5.6072e-01 3.1800e-01 1.0530e+00 +ARMC12 ENST00000288065 1.1597e-06 6.5006e-01 4.1600e-01 1.0530e+00 +FAAH ENST00000243167 4.4449e-11 7.2544e-01 5.0900e-01 1.0540e+00 +RP11-426L16.10 ENST00000606505 3.9563e-06 6.3692e-01 4.0000e-01 1.0540e+00 +CAT ENST00000241052 1.6263e-10 7.1855e-01 5.0000e-01 1.0540e+00 +SNX15 ENST00000377244 3.9700e-06 6.3665e-01 4.0000e-01 1.0540e+00 +C17orf53 ENST00000319977 4.4469e-11 7.2542e-01 5.0900e-01 1.0540e+00 +CNPPD1 ENST00000409789 7.6384e-09 6.9406e-01 4.6900e-01 1.0540e+00 +ITPRIPL2 ENST00000381440 1.5396e-04 5.8445e-01 3.4200e-01 1.0540e+00 +C15orf41 ENST00000566621 3.2889e-07 6.6374e-01 4.3100e-01 1.0550e+00 +TYW3 ENST00000370867 1.6927e-03 5.3467e-01 2.9200e-01 1.0550e+00 +GNG12 ENST00000370982 5.8936e-01 0.0000e+00 0.0000e+00 1.0550e+00 +C9orf43 ENST00000288462 4.3555e-11 7.2632e-01 5.1000e-01 1.0550e+00 +C8orf58 ENST00000289989 4.5689e-05 6.0442e-01 3.6300e-01 1.0550e+00 +LILRB1 ENST00000324602 5.6502e-14 7.5544e-01 5.5000e-01 1.0550e+00 +CGA ENST00000369582 3.4518e-01 2.2377e-01 7.8000e-02 1.0550e+00 +DMKN ENST00000339686 8.3445e-13 7.4464e-01 5.3500e-01 1.0550e+00 +ATP6C ENST00000569317 3.4533e-01 2.2370e-01 7.8000e-02 1.0550e+00 +ACSM3 ENST00000289416 1.4410e-14 7.6059e-01 5.5700e-01 1.0550e+00 +ZBBX ENST00000455345 2.9306e-21 8.0180e-01 6.1600e-01 1.0550e+00 +FAM188B2 ENST00000397891 3.2951e-07 6.6361e-01 4.3100e-01 1.0550e+00 +ZNF213 ENST00000396878 9.4572e-08 6.7473e-01 4.4500e-01 1.0550e+00 +DCP1B ENST00000280665 1.6028e-10 7.1922e-01 5.0100e-01 1.0550e+00 +ALOXE3 ENST00000318227 5.1284e-20 7.9538e-01 6.0600e-01 1.0550e+00 +LCN9 ENST00000277526 1.6951e-03 5.3451e-01 2.9200e-01 1.0550e+00 +SAMD7 ENST00000428432 1.1415e-06 6.5125e-01 4.1600e-01 1.0550e+00 +IL5RA ENST00000446632 2.6791e-08 6.8524e-01 4.5700e-01 1.0550e+00 +SLC25A10 ENST00000571730 5.8727e-10 7.1138e-01 4.9100e-01 1.0550e+00 +POLL ENST00000370162 1.5836e-10 7.1978e-01 5.0100e-01 1.0560e+00 +C11orf85 ENST00000301896 5.0954e-04 5.6232e-01 3.1900e-01 1.0560e+00 +PIGC ENST00000367728 5.5065e-03 5.0228e-01 2.6100e-01 1.0560e+00 +ZFAND4 ENST00000344646 1.1579e-11 7.3345e-01 5.1900e-01 1.0560e+00 +MPP4 ENST00000409474 3.4180e-18 7.8613e-01 5.9200e-01 1.0560e+00 +ANAPC10 ENST00000507656 5.5077e-03 5.0226e-01 2.6100e-01 1.0560e+00 +SYTL1 ENST00000543823 1.1537e-11 7.3360e-01 5.1900e-01 1.0560e+00 +QDPR ENST00000281243 1.5254e-04 5.8535e-01 3.4300e-01 1.0560e+00 +OLFML2B ENST00000294794 3.6491e-15 7.6542e-01 5.6300e-01 1.0560e+00 +TWIST1 ENST00000242261 3.4491e-01 2.2392e-01 7.9000e-02 1.0560e+00 +AL356356.1 ENST00000538795 3.4464e-01 2.2406e-01 7.9000e-02 1.0560e+00 +FAM153C ENST00000507848 5.3887e-02 4.0885e-01 1.8500e-01 1.0560e+00 +FSHB ENST00000417547 3.4452e-01 2.2412e-01 7.9000e-02 1.0560e+00 +OSM ENST00000215781 5.8916e-01 0.0000e+00 0.0000e+00 1.0560e+00 +PKHD1L1 ENST00000378402 1.3739e-109 9.3233e-01 8.2300e-01 1.0570e+00 +ENTHD1 ENST00000325157 3.2503e-07 6.6456e-01 4.3200e-01 1.0570e+00 +TRPV4 ENST00000418703 2.2370e-16 7.7491e-01 5.7600e-01 1.0570e+00 +USP45 ENST00000327681 1.3630e-17 7.8295e-01 5.8700e-01 1.0570e+00 +CCDC15 ENST00000344762 4.6882e-20 7.9724e-01 6.0800e-01 1.0570e+00 +C19orf12 ENST00000392278 3.4416e-01 2.2432e-01 7.9000e-02 1.0570e+00 +GHRH ENST00000373614 1.4964e-01 3.3668e-01 1.3700e-01 1.0570e+00 +LGALS8 ENST00000526589 3.8769e-06 6.3854e-01 4.0100e-01 1.0570e+00 +NRBF2 ENST00000277746 5.0432e-04 5.6340e-01 3.1900e-01 1.0580e+00 +PEF1 ENST00000373703 1.5066e-04 5.8657e-01 3.4300e-01 1.0580e+00 +SMIM19 ENST00000438528 3.4399e-01 2.2441e-01 7.9000e-02 1.0580e+00 +TOR1A ENST00000351698 5.0557e-04 5.6314e-01 3.1900e-01 1.0580e+00 +GPR146 ENST00000397095 1.4930e-01 3.3705e-01 1.3700e-01 1.0580e+00 +BROX ENST00000340934 4.2023e-11 7.2785e-01 5.1100e-01 1.0580e+00 +SFRP2 ENST00000274063 1.6693e-03 5.3623e-01 2.9300e-01 1.0580e+00 +C21orf59 ENST00000290155 1.1187e-06 6.5275e-01 4.1700e-01 1.0580e+00 +SPDYE3 ENST00000332397 1.5103e-04 5.8633e-01 3.4300e-01 1.0580e+00 +SIGLEC8 ENST00000321424 3.2193e-07 6.6523e-01 4.3200e-01 1.0580e+00 +BOLA3 ENST00000327428 1.4911e-01 3.3725e-01 1.3700e-01 1.0590e+00 +GMPR ENST00000259727 1.3075e-05 6.2435e-01 3.8400e-01 1.0590e+00 +PKP2 ENST00000070846 3.1147e-18 7.8826e-01 5.9400e-01 1.0590e+00 +PCDHB10 ENST00000239446 1.3058e-05 6.2446e-01 3.8400e-01 1.0590e+00 +POLG2 ENST00000539111 1.5280e-10 7.2141e-01 5.0200e-01 1.0590e+00 +CTGF ENST00000367976 5.0202e-04 5.6388e-01 3.2000e-01 1.0590e+00 +UGGT2 ENST00000376747 1.3209e-41 8.6645e-01 7.1300e-01 1.0590e+00 +SH3BGRL3 ENST00000270792 1.4900e-01 3.3737e-01 1.3700e-01 1.0590e+00 +HOXD4 ENST00000306324 5.4479e-03 5.0357e-01 2.6200e-01 1.0590e+00 +METTL17 ENST00000382985 4.0832e-11 7.2908e-01 5.1200e-01 1.0590e+00 +C1orf65 ENST00000366875 9.0420e-08 6.7765e-01 4.4700e-01 1.0590e+00 +C9orf142 ENST00000371620 5.4207e-03 5.0418e-01 2.6200e-01 1.0600e+00 +RIMS3 ENST00000372684 1.4932e-04 5.8744e-01 3.4400e-01 1.0600e+00 +FGFBP1 ENST00000382333 5.8794e-01 0.0000e+00 0.0000e+00 1.0600e+00 +RNLS ENST00000331772 3.7960e-06 6.4023e-01 4.0200e-01 1.0600e+00 +AQP5 ENST00000293599 5.3249e-02 4.1054e-01 1.8600e-01 1.0600e+00 +TAMM41 ENST00000273037 1.0996e-06 6.5404e-01 4.1800e-01 1.0600e+00 +KRT4 ENST00000551956 5.4962e-10 7.1463e-01 4.9300e-01 1.0600e+00 +FMO2 ENST00000441535 3.1430e-07 6.6690e-01 4.3300e-01 1.0600e+00 +TBC1D21 ENST00000300504 3.1602e-07 6.6652e-01 4.3300e-01 1.0600e+00 +VTN ENST00000226218 1.5014e-10 7.2222e-01 5.0300e-01 1.0600e+00 +ELP6 ENST00000296149 4.9822e-04 5.6468e-01 3.2000e-01 1.0610e+00 +DSCR3 ENST00000309117 1.4872e-04 5.8784e-01 3.4400e-01 1.0610e+00 +GPR183 ENST00000376414 1.7257e-02 4.6410e-01 2.2800e-01 1.0610e+00 +ABHD10 ENST00000273359 1.2865e-05 6.2574e-01 3.8500e-01 1.0610e+00 +MYH15 ENST00000273353 4.5499e-59 8.9556e-01 7.5800e-01 1.0610e+00 +MUC3A ENST00000319509 1.4752e-10 7.2303e-01 5.0300e-01 1.0610e+00 +GPX8 ENST00000503787 5.3068e-02 4.1102e-01 1.8600e-01 1.0610e+00 +RHOH ENST00000381799 1.4861e-01 3.3779e-01 1.3700e-01 1.0610e+00 +CDKN2AIPNL ENST00000458198 3.4205e-01 2.2545e-01 7.9000e-02 1.0620e+00 +DSN1 ENST00000426836 8.8514e-08 6.7904e-01 4.4700e-01 1.0620e+00 +CRYL1 ENST00000298248 3.7186e-06 6.4188e-01 4.0300e-01 1.0620e+00 +ARSB ENST00000264914 7.0009e-09 6.9899e-01 4.7200e-01 1.0620e+00 +SPATA16 ENST00000351008 1.4475e-10 7.2389e-01 5.0400e-01 1.0620e+00 +C2orf49 ENST00000258457 1.7223e-02 4.6435e-01 2.2800e-01 1.0620e+00 +SPTBN5 ENST00000320955 8.2224e-118 9.4077e-01 8.3400e-01 1.0620e+00 +PPM1K ENST00000608933 1.4736e-04 5.8874e-01 3.4500e-01 1.0620e+00 +FMO6P ENST00000236166 1.2788e-05 6.2625e-01 3.8500e-01 1.0620e+00 +ACY1 ENST00000404366 6.9169e-09 6.9967e-01 4.7300e-01 1.0630e+00 +TPGS2 ENST00000334295 1.4656e-04 5.8928e-01 3.4500e-01 1.0630e+00 +GPR108 ENST00000264080 1.8227e-13 7.5614e-01 5.4700e-01 1.0630e+00 +ACOX3 ENST00000356406 7.6016e-16 7.7503e-01 5.7300e-01 1.0630e+00 +DDRGK1 ENST00000354488 3.0689e-07 6.6857e-01 4.3400e-01 1.0630e+00 +ME2 ENST00000321341 3.0296e-15 7.7066e-01 5.6700e-01 1.0630e+00 +BTBD6 ENST00000392554 3.7117e-06 6.4203e-01 4.0300e-01 1.0630e+00 +CPN1 ENST00000370418 8.6973e-08 6.8018e-01 4.4800e-01 1.0630e+00 +SEC14L6 ENST00000402034 2.4606e-08 6.9040e-01 4.6100e-01 1.0630e+00 +CCDC38 ENST00000344280 1.8346e-13 7.5593e-01 5.4600e-01 1.0630e+00 +C2orf15 ENST00000512183 5.2798e-02 4.1175e-01 1.8700e-01 1.0630e+00 +MRPL30 ENST00000338148 5.2798e-02 4.1175e-01 1.8700e-01 1.0630e+00 +PIGZ ENST00000412723 1.2688e-05 6.2692e-01 3.8600e-01 1.0630e+00 +FCRL5 ENST00000361835 4.6105e-17 7.8355e-01 5.8500e-01 1.0630e+00 +PPP2R1B ENST00000311129 3.0047e-15 7.7090e-01 5.6700e-01 1.0630e+00 +PIGB ENST00000164305 3.8535e-11 7.3155e-01 5.1400e-01 1.0630e+00 +NOSIP ENST00000391853 1.2622e-05 6.2737e-01 3.8600e-01 1.0640e+00 +NOX1 ENST00000372966 8.6564e-08 6.8049e-01 4.4800e-01 1.0640e+00 +NEFH ENST00000310624 2.6684e-12 7.4510e-01 5.3100e-01 1.0640e+00 +GOLPH3L ENST00000271732 1.2615e-05 6.2742e-01 3.8600e-01 1.0640e+00 +NARFL ENST00000251588 1.8864e-09 7.0938e-01 4.8400e-01 1.0640e+00 +SST ENST00000287641 3.4128e-01 2.2587e-01 7.9000e-02 1.0640e+00 +GMFB ENST00000358056 5.3339e-03 5.0613e-01 2.6400e-01 1.0640e+00 +MYO15B ENST00000583560 4.9067e-04 5.6629e-01 3.2100e-01 1.0640e+00 +UGT1A6 ENST00000305139 3.0491e-07 6.6902e-01 4.3500e-01 1.0640e+00 +EVC ENST00000382674 3.4620e-25 8.2523e-01 6.4500e-01 1.0640e+00 +EVC2 ENST00000344408 1.0207e-34 8.5500e-01 6.9100e-01 1.0640e+00 +GPATCH2 ENST00000366935 1.0165e-11 7.3865e-01 5.2300e-01 1.0640e+00 +TCERG1L ENST00000368642 6.8376e-09 7.0032e-01 4.7300e-01 1.0640e+00 +DOC2B ENST00000343572 1.7055e-02 4.6564e-01 2.2800e-01 1.0650e+00 +APOBEC2 ENST00000244669 1.7070e-02 4.6552e-01 2.2800e-01 1.0650e+00 +PLD2 ENST00000263088 4.1429e-27 8.3321e-01 6.5700e-01 1.0650e+00 +SFT2D1 ENST00000361731 1.6186e-03 5.3971e-01 2.9500e-01 1.0650e+00 +AATF ENST00000225402 2.5958e-12 7.4612e-01 5.3200e-01 1.0650e+00 +ILDR1 ENST00000344209 2.6072e-12 7.4596e-01 5.3200e-01 1.0650e+00 +ATOX1 ENST00000524142 5.8645e-01 0.0000e+00 0.0000e+00 1.0650e+00 +RABAC1 ENST00000222008 5.2910e-03 5.0712e-01 2.6400e-01 1.0660e+00 +BBS2 ENST00000245157 1.0328e-17 7.8954e-01 5.9200e-01 1.0660e+00 +ADORA3 ENST00000369716 1.4410e-04 5.9095e-01 3.4600e-01 1.0660e+00 +VWA1 ENST00000476993 5.2878e-03 5.0719e-01 2.6400e-01 1.0660e+00 +CCDC42 ENST00000293845 3.6229e-06 6.4397e-01 4.0400e-01 1.0660e+00 +CPSF4L ENST00000344935 1.6119e-03 5.4018e-01 2.9500e-01 1.0660e+00 +ZNF577 ENST00000301399 4.2594e-05 6.1085e-01 3.6700e-01 1.0660e+00 +HOXD9 ENST00000249499 1.7004e-02 4.6603e-01 2.2900e-01 1.0660e+00 +HMGCLL1 ENST00000398661 2.9827e-07 6.7055e-01 4.3600e-01 1.0660e+00 +PCDHA6 ENST00000529310 3.6156e-11 7.3426e-01 5.1600e-01 1.0670e+00 +MFSD8 ENST00000296468 2.5375e-12 7.4697e-01 5.3300e-01 1.0670e+00 +KCTD6 ENST00000355076 1.6939e-02 4.6653e-01 2.2900e-01 1.0670e+00 +DLX4 ENST00000240306 1.6921e-02 4.6667e-01 2.2900e-01 1.0670e+00 +SLC5A11 ENST00000347898 1.6748e-13 7.5893e-01 5.4900e-01 1.0670e+00 +MIS12 ENST00000381165 1.4672e-01 3.3986e-01 1.3800e-01 1.0670e+00 +KRT8 ENST00000552150 2.3600e-08 6.9292e-01 4.6300e-01 1.0670e+00 +ABCA7 ENST00000263094 2.1111e-55 8.9526e-01 7.5400e-01 1.0670e+00 +MED7 ENST00000286317 1.6917e-02 4.6670e-01 2.2900e-01 1.0670e+00 +TCEAL1 ENST00000372625 5.8578e-01 0.0000e+00 0.0000e+00 1.0670e+00 +DYRK3 ENST00000367109 3.5842e-06 6.4483e-01 4.0500e-01 1.0670e+00 +LMBR1L ENST00000267102 6.6140e-13 7.5280e-01 5.4100e-01 1.0670e+00 +WDR93 ENST00000268130 4.0651e-17 7.8666e-01 5.8800e-01 1.0670e+00 +FSCN3 ENST00000265825 1.3467e-10 7.2718e-01 5.0600e-01 1.0670e+00 +NDUFAF3 ENST00000326925 5.2693e-03 5.0762e-01 2.6400e-01 1.0670e+00 +POLR3F ENST00000377603 1.0380e-06 6.5835e-01 4.2100e-01 1.0670e+00 +CCER1 ENST00000358859 4.1961e-05 6.1223e-01 3.6800e-01 1.0680e+00 +TRIM17 ENST00000366697 8.3141e-08 6.8311e-01 4.5000e-01 1.0680e+00 +ZNF548 ENST00000336128 3.3982e-01 2.2667e-01 7.9000e-02 1.0680e+00 +DNAAF2 ENST00000298292 6.4811e-09 7.0334e-01 4.7500e-01 1.0680e+00 +BATF2 ENST00000301887 5.8536e-01 0.0000e+00 0.0000e+00 1.0680e+00 +RGPD8 ENST00000302558 2.9332e-07 6.7172e-01 4.3600e-01 1.0680e+00 +SOCS1 ENST00000332029 5.8544e-01 0.0000e+00 0.0000e+00 1.0680e+00 +GALNT9 ENST00000397325 5.2407e-03 5.0828e-01 2.6500e-01 1.0680e+00 +SPATA5L1 ENST00000305560 3.5478e-11 7.3506e-01 5.1600e-01 1.0680e+00 +TRPM1 ENST00000542188 1.6009e-42 8.7528e-01 7.2100e-01 1.0680e+00 +IRX1 ENST00000302006 4.7650e-04 5.6939e-01 3.2300e-01 1.0690e+00 +FAM83C ENST00000374408 8.2423e-08 6.8367e-01 4.5100e-01 1.0690e+00 +C19orf59 ENST00000333598 1.4188e-04 5.9248e-01 3.4700e-01 1.0690e+00 +AIPL1 ENST00000381129 1.2220e-05 6.3016e-01 3.8800e-01 1.0690e+00 +GPN3 ENST00000543199 2.9029e-07 6.7244e-01 4.3700e-01 1.0690e+00 +GPA33 ENST00000367868 3.5516e-06 6.4557e-01 4.0500e-01 1.0690e+00 +ANKRA2 ENST00000296785 3.5443e-06 6.4573e-01 4.0500e-01 1.0690e+00 +TCEANC ENST00000314720 5.1926e-02 4.1414e-01 1.8800e-01 1.0690e+00 +RP11-371E8.4 ENST00000557574 1.6849e-02 4.6724e-01 2.2900e-01 1.0690e+00 +RP11-295D22.1 ENST00000565320 5.8464e-01 0.0000e+00 0.0000e+00 1.0700e+00 +CECR1 ENST00000399839 8.1396e-08 6.8448e-01 4.5100e-01 1.0700e+00 +SPRED2 ENST00000356388 2.8684e-07 6.7328e-01 4.3700e-01 1.0700e+00 +CD83 ENST00000379153 5.2136e-03 5.0891e-01 2.6500e-01 1.0700e+00 +ARHGEF37 ENST00000333677 6.1367e-13 7.5541e-01 5.4300e-01 1.0700e+00 +ABCA9 ENST00000340001 9.4911e-48 8.8630e-01 7.3700e-01 1.0700e+00 +FAM194B ENST00000298738 1.0046e-14 7.7126e-01 5.6400e-01 1.0700e+00 +SUMF1 ENST00000272902 2.2828e-08 6.9493e-01 4.6400e-01 1.0700e+00 +DNAJC25 ENST00000313525 1.2112e-05 6.3093e-01 3.8800e-01 1.0700e+00 +PMPCA ENST00000371717 3.4370e-11 7.3640e-01 5.1700e-01 1.0700e+00 +ADSL ENST00000216194 8.9207e-12 7.4383e-01 5.2700e-01 1.0710e+00 +TMEM147 ENST00000222284 1.4005e-04 5.9377e-01 3.4700e-01 1.0710e+00 +TTLL11 ENST00000321582 6.2403e-09 7.0546e-01 4.7700e-01 1.0710e+00 +MINA ENST00000333396 2.2584e-08 6.9558e-01 4.6400e-01 1.0710e+00 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1.0720e+00 +CPVL ENST00000409850 3.3502e-11 7.3748e-01 5.1800e-01 1.0720e+00 +OCIAD1 ENST00000381473 9.9492e-07 6.6152e-01 4.2300e-01 1.0720e+00 +ME3 ENST00000543262 1.5112e-13 7.6231e-01 5.5100e-01 1.0720e+00 +VAT1L ENST00000302536 9.9386e-07 6.6160e-01 4.2300e-01 1.0720e+00 +POLD4 ENST00000312419 1.4510e-01 3.4167e-01 1.3900e-01 1.0730e+00 +ABHD4 ENST00000428304 2.2197e-08 6.9662e-01 4.6500e-01 1.0730e+00 +TM4SF1 ENST00000305366 1.5619e-03 5.4378e-01 2.9700e-01 1.0730e+00 +CD7 ENST00000312648 5.1350e-02 4.1575e-01 1.8800e-01 1.0730e+00 +NPEPL1 ENST00000356091 9.8457e-07 6.6231e-01 4.2300e-01 1.0730e+00 +LPAR5 ENST00000329858 5.1408e-02 4.1559e-01 1.8800e-01 1.0730e+00 +SGPP1 ENST00000247225 1.3890e-04 5.9459e-01 3.4800e-01 1.0730e+00 +ERI1 ENST00000523898 1.1866e-05 6.3270e-01 3.8900e-01 1.0730e+00 +ACSM1 ENST00000307493 2.2841e-15 7.7860e-01 5.7300e-01 1.0740e+00 +RP11-644F5.10 ENST00000550412 5.1295e-02 4.1591e-01 1.8800e-01 1.0740e+00 +ITLN1 ENST00000326245 3.4119e-06 6.4879e-01 4.0700e-01 1.0740e+00 +ETNK2 ENST00000367202 9.8080e-07 6.6259e-01 4.2400e-01 1.0740e+00 +MICB ENST00000252229 4.0609e-05 6.1526e-01 3.7000e-01 1.0740e+00 +PRSS36 ENST00000268281 4.5100e-19 8.0336e-01 6.0800e-01 1.0740e+00 +SF3B5 ENST00000367569 5.8354e-01 0.0000e+00 0.0000e+00 1.0740e+00 +UAP1L1 ENST00000409858 3.4123e-06 6.4878e-01 4.0700e-01 1.0740e+00 +DPY19L4 ENST00000414645 1.4234e-21 8.1619e-01 6.2700e-01 1.0740e+00 +TCHHL1 ENST00000368806 5.8371e-01 0.0000e+00 0.0000e+00 1.0740e+00 +TTLL12 ENST00000216129 2.2425e-15 7.7911e-01 5.7300e-01 1.0740e+00 +GCA ENST00000437150 1.3787e-04 5.9533e-01 3.4800e-01 1.0740e+00 +WDR72 ENST00000396328 2.7330e-27 8.4018e-01 6.6200e-01 1.0740e+00 +MMP17 ENST00000360564 2.1964e-08 6.9726e-01 4.6600e-01 1.0740e+00 +TMEM185A ENST00000316916 1.6569e-02 4.6945e-01 2.3000e-01 1.0740e+00 +VRK3 ENST00000599538 3.2374e-11 7.3893e-01 5.1900e-01 1.0740e+00 +DDX58 ENST00000379883 1.7558e-23 8.2548e-01 6.4000e-01 1.0750e+00 +PRICKLE4 ENST00000458694 4.0289e-05 6.1600e-01 3.7000e-01 1.0750e+00 +CYB5RL ENST00000419823 3.3734e-06 6.4971e-01 4.0800e-01 1.0750e+00 +LGALS4 ENST00000307751 2.7538e-07 6.7612e-01 4.3900e-01 1.0750e+00 +PIGW ENST00000592983 1.1720e-05 6.3377e-01 3.9000e-01 1.0750e+00 +RAMP2 ENST00000253796 5.1127e-02 4.1638e-01 1.8900e-01 1.0750e+00 +BSPH1 ENST00000344839 1.6492e-02 4.7007e-01 2.3100e-01 1.0750e+00 +GINS4 ENST00000276533 1.3735e-04 5.9570e-01 3.4900e-01 1.0750e+00 +MAB21L3 ENST00000369500 9.6909e-07 6.6349e-01 4.2400e-01 1.0750e+00 +R3HDM4 ENST00000361574 4.6251e-04 5.7257e-01 3.2500e-01 1.0750e+00 +MBOAT1 ENST00000324607 2.1535e-12 7.5304e-01 5.3700e-01 1.0750e+00 +PTCRA ENST00000304672 1.4449e-01 3.4235e-01 1.3900e-01 1.0750e+00 +C5orf34 ENST00000306862 8.9961e-15 7.7451e-01 5.6700e-01 1.0750e+00 +FAM179A ENST00000379558 1.3100e-16 7.8867e-01 5.8600e-01 1.0750e+00 +LACC1 ENST00000441843 1.1655e-05 6.3424e-01 3.9000e-01 1.0760e+00 +AP1M2 ENST00000250244 2.1436e-08 6.9872e-01 4.6600e-01 1.0760e+00 +GPR82 ENST00000302548 1.4409e-01 3.4281e-01 1.3900e-01 1.0760e+00 +UQCRB ENST00000518406 1.6423e-02 4.7063e-01 2.3100e-01 1.0760e+00 +GRAMD1C ENST00000358160 5.6287e-21 8.1461e-01 6.2300e-01 1.0760e+00 +C16orf96 ENST00000444310 5.5816e-21 8.1478e-01 6.2400e-01 1.0760e+00 +MSTO1 ENST00000245564 1.6182e-09 7.1739e-01 4.9000e-01 1.0760e+00 +POPDC2 ENST00000264231 4.0063e-05 6.1652e-01 3.7100e-01 1.0760e+00 +SMYD4 ENST00000305513 8.7782e-15 7.7523e-01 5.6700e-01 1.0760e+00 +ZNF334 ENST00000347606 1.6122e-09 7.1759e-01 4.9000e-01 1.0760e+00 +LRRC38 ENST00000376085 1.4423e-01 3.4265e-01 1.3900e-01 1.0760e+00 +RP11-529K1.3 ENST00000567706 1.1648e-05 6.3430e-01 3.9000e-01 1.0760e+00 +ALDH16A1 ENST00000293350 2.3658e-20 8.1163e-01 6.1900e-01 1.0760e+00 +CXorf38 ENST00000327877 1.3652e-04 5.9631e-01 3.4900e-01 1.0760e+00 +MOB3B ENST00000262244 1.6386e-02 4.7093e-01 2.3100e-01 1.0770e+00 +ARPC4-TTLL3 ENST00000397256 1.3565e-13 7.6584e-01 5.5400e-01 1.0770e+00 +IDI1 ENST00000381344 3.9769e-05 6.1721e-01 3.7100e-01 1.0770e+00 +NTMT1 ENST00000372486 5.0783e-02 4.1737e-01 1.8900e-01 1.0770e+00 +TTLL6 ENST00000393382 9.7742e-20 8.0883e-01 6.1400e-01 1.0770e+00 +USHBP1 ENST00000252597 2.9968e-17 7.9421e-01 5.9300e-01 1.0770e+00 +PANX3 ENST00000284288 3.9672e-05 6.1743e-01 3.7100e-01 1.0770e+00 +ART5 ENST00000397068 4.5797e-04 5.7362e-01 3.2500e-01 1.0770e+00 +DRAM2 ENST00000286692 1.3570e-04 5.9691e-01 3.4900e-01 1.0770e+00 +PTGR2 ENST00000555661 2.7131e-07 6.7716e-01 4.4000e-01 1.0770e+00 +ADAP2 ENST00000330889 4.2394e-10 7.2727e-01 5.0200e-01 1.0780e+00 +C11orf21 ENST00000456145 1.6355e-02 4.7118e-01 2.3100e-01 1.0780e+00 +ANXA13 ENST00000262219 4.2441e-10 7.2722e-01 5.0200e-01 1.0780e+00 +TMEM232 ENST00000455884 7.9307e-12 7.4845e-01 5.3000e-01 1.0780e+00 +PCID2 ENST00000246505 5.2663e-13 7.6072e-01 5.4600e-01 1.0780e+00 +SLC17A4 ENST00000377905 1.5714e-09 7.1892e-01 4.9100e-01 1.0780e+00 +IDO1 ENST00000518237 3.3013e-06 6.5144e-01 4.0900e-01 1.0780e+00 +MITD1 ENST00000289359 1.1445e-05 6.3582e-01 3.9100e-01 1.0780e+00 +TJP3 ENST00000589378 6.7101e-23 8.2495e-01 6.3800e-01 1.0780e+00 +MAN2C1 ENST00000565683 2.7689e-29 8.4963e-01 6.7500e-01 1.0780e+00 +PNPLA7 ENST00000406427 5.3653e-37 8.7092e-01 7.0800e-01 1.0780e+00 +DPH6 ENST00000256538 1.1419e-05 6.3602e-01 3.9100e-01 1.0790e+00 +AP1S3 ENST00000396654 1.6298e-02 4.7165e-01 2.3100e-01 1.0790e+00 +TMEM136 ENST00000314475 5.0232e-03 5.1350e-01 2.6700e-01 1.0790e+00 +MMD ENST00000262065 1.3440e-04 5.9787e-01 3.5000e-01 1.0790e+00 +ZNF782 ENST00000481138 4.2150e-10 7.2755e-01 5.0200e-01 1.0790e+00 +FAM198B ENST00000393807 5.6948e-09 7.1059e-01 4.8000e-01 1.0790e+00 +CHRNA1 ENST00000261007 2.0681e-08 7.0088e-01 4.6800e-01 1.0790e+00 +FZD6 ENST00000358755 2.0034e-12 7.5570e-01 5.3900e-01 1.0790e+00 +FAM228A ENST00000295150 1.6302e-02 4.7162e-01 2.3100e-01 1.0790e+00 +SUOX ENST00000394109 9.3990e-07 6.6579e-01 4.2600e-01 1.0790e+00 +GUCY2C ENST00000261170 1.3919e-30 8.5428e-01 6.8100e-01 1.0790e+00 +SPATA5 ENST00000274008 9.0776e-20 8.1045e-01 6.1600e-01 1.0790e+00 +ATG16L2 ENST00000321297 4.6874e-16 7.8801e-01 5.8300e-01 1.0800e+00 +DMBT1 ENST00000368909 4.4760e-63 9.1532e-01 7.7800e-01 1.0800e+00 +PNMT ENST00000269582 5.0065e-03 5.1391e-01 2.6800e-01 1.0800e+00 +NPY ENST00000407573 1.4294e-01 3.4413e-01 1.4000e-01 1.0800e+00 +RBPJL ENST00000343694 2.9189e-11 7.4328e-01 5.2200e-01 1.0800e+00 +TRIM45 ENST00000256649 2.0610e-08 7.0109e-01 4.6800e-01 1.0800e+00 +TNNC2 ENST00000372555 1.6240e-02 4.7213e-01 2.3200e-01 1.0800e+00 +NGDN ENST00000408901 2.0427e-08 7.0163e-01 4.6800e-01 1.0800e+00 +SMUG1 ENST00000508394 4.5154e-04 5.7514e-01 3.2600e-01 1.0800e+00 +UGT1A1 ENST00000305208 3.2577e-06 6.5252e-01 4.1000e-01 1.0800e+00 +CEP55 ENST00000371485 1.9640e-12 7.5643e-01 5.3900e-01 1.0800e+00 +PEX11B ENST00000369306 1.3346e-04 5.9858e-01 3.5000e-01 1.0800e+00 +DFFB ENST00000378209 1.1349e-05 6.3655e-01 3.9200e-01 1.0800e+00 +SYNE3 ENST00000334258 1.7571e-25 8.3727e-01 6.5500e-01 1.0800e+00 +RLBP1 ENST00000268125 1.1303e-05 6.3691e-01 3.9200e-01 1.0800e+00 +ANKRD35 ENST00000355594 1.6568e-25 8.3833e-01 6.5600e-01 1.0810e+00 +NEIL3 ENST00000264596 1.5220e-09 7.2058e-01 4.9200e-01 1.0810e+00 +EEF2K ENST00000263026 8.3628e-20 8.1225e-01 6.1700e-01 1.0810e+00 +ABCB8 ENST00000358849 1.9164e-15 7.8352e-01 5.7700e-01 1.0810e+00 +PTCD3 ENST00000254630 2.4870e-22 8.2499e-01 6.3600e-01 1.0810e+00 +CYP27C1 ENST00000335247 9.2035e-07 6.6736e-01 4.2700e-01 1.0810e+00 +C5orf15 ENST00000231512 5.0281e-02 4.1882e-01 1.9000e-01 1.0810e+00 +ACE ENST00000290866 1.0344e-37 8.7460e-01 7.1200e-01 1.0810e+00 +MYH1 ENST00000226207 1.3645e-56 9.0838e-01 7.6600e-01 1.0810e+00 +CDK5RAP3 ENST00000338399 7.6348e-15 7.7934e-01 5.7000e-01 1.0810e+00 +PTTG1IP ENST00000330938 4.9827e-03 5.1450e-01 2.6800e-01 1.0810e+00 +TMEM208 ENST00000304800 1.5059e-03 5.4798e-01 2.9900e-01 1.0810e+00 +LOR ENST00000368742 3.3454e-01 2.2961e-01 8.1000e-02 1.0810e+00 +EXTL1 ENST00000374280 7.3142e-12 7.5162e-01 5.3200e-01 1.0820e+00 +NDOR1 ENST00000371521 4.8084e-13 7.6386e-01 5.4900e-01 1.0820e+00 +FBXO40 ENST00000338040 5.5318e-09 7.1221e-01 4.8100e-01 1.0820e+00 +CLDN19 ENST00000296387 4.9681e-03 5.1487e-01 2.6800e-01 1.0820e+00 +YAE1D1 ENST00000223273 1.4990e-03 5.4851e-01 2.9900e-01 1.0820e+00 +NHP2 ENST00000274606 5.0110e-02 4.1932e-01 1.9000e-01 1.0820e+00 +ALS2CL ENST00000318962 4.2970e-28 8.4880e-01 6.7100e-01 1.0820e+00 +OR11L1 ENST00000355784 5.0098e-02 4.1935e-01 1.9000e-01 1.0820e+00 +PTRF ENST00000357037 4.9657e-03 5.1493e-01 2.6800e-01 1.0820e+00 +ACOT11 ENST00000371316 1.0844e-16 7.9355e-01 5.9000e-01 1.0820e+00 +SLFNL1 ENST00000359345 3.8491e-05 6.2025e-01 3.7300e-01 1.0820e+00 +DPAGT1 ENST00000409993 1.1170e-05 6.3793e-01 3.9300e-01 1.0820e+00 +CDX1 ENST00000231656 1.4253e-01 3.4460e-01 1.4000e-01 1.0820e+00 +MOCS1 ENST00000373186 9.1165e-07 6.6808e-01 4.2700e-01 1.0820e+00 +QTRT1 ENST00000250237 2.5932e-07 6.8031e-01 4.4200e-01 1.0820e+00 +MZF1 ENST00000215057 1.0667e-10 7.3769e-01 5.1400e-01 1.0820e+00 +FCGR1A ENST00000369168 1.3116e-04 6.0032e-01 3.5100e-01 1.0830e+00 +CHCHD5 ENST00000324913 4.9956e-02 4.1977e-01 1.9000e-01 1.0830e+00 +ACTR6 ENST00000188312 5.4629e-09 7.1291e-01 4.8200e-01 1.0830e+00 +AIFM2 ENST00000307864 1.1064e-05 6.3876e-01 3.9300e-01 1.0830e+00 +RHO ENST00000296271 1.3108e-04 6.0038e-01 3.5100e-01 1.0830e+00 +GPC5 ENST00000377067 3.9864e-10 7.3024e-01 5.0400e-01 1.0830e+00 +LACTBL1 ENST00000426928 1.4956e-03 5.4877e-01 2.9900e-01 1.0830e+00 +AQP1 ENST00000509504 2.5697e-07 6.8094e-01 4.4200e-01 1.0830e+00 +CCDC62 ENST00000253079 4.3887e-16 7.8978e-01 5.8400e-01 1.0830e+00 +FRK ENST00000606080 1.8071e-12 7.5948e-01 5.4200e-01 1.0840e+00 +TRPV1 ENST00000571088 1.0103e-16 7.9538e-01 5.9100e-01 1.0840e+00 +ZNF559-ZNF177 ENST00000541595 4.4299e-04 5.7720e-01 3.2700e-01 1.0840e+00 +OSGEP ENST00000206542 7.0838e-08 6.9349e-01 4.5700e-01 1.0840e+00 +CCL15 ENST00000354059 3.3330e-01 2.3031e-01 8.1000e-02 1.0840e+00 +SHPK ENST00000572705 1.0103e-16 7.9538e-01 5.9100e-01 1.0840e+00 +RGS18 ENST00000367460 1.4903e-03 5.4918e-01 3.0000e-01 1.0840e+00 +SEPT1 ENST00000605106 1.9572e-08 7.0419e-01 4.7000e-01 1.0840e+00 +THY1 ENST00000284240 4.9895e-02 4.1995e-01 1.9000e-01 1.0840e+00 +FUT10 ENST00000327671 5.4119e-09 7.1343e-01 4.8200e-01 1.0840e+00 +LRRC6 ENST00000250173 1.0409e-10 7.3879e-01 5.1400e-01 1.0840e+00 +DOHH ENST00000427575 1.5986e-02 4.7424e-01 2.3300e-01 1.0840e+00 +ARSK ENST00000380009 3.9395e-10 7.3080e-01 5.0400e-01 1.0840e+00 +GC ENST00000504199 2.7301e-11 7.4607e-01 5.2400e-01 1.0840e+00 +XCR1 ENST00000309285 1.6001e-02 4.7411e-01 2.3300e-01 1.0840e+00 +IGSF6 ENST00000268389 1.4791e-03 5.5005e-01 3.0000e-01 1.0850e+00 +ACAD10 ENST00000455480 1.0177e-30 8.5923e-01 6.8500e-01 1.0850e+00 +PSMC3IP ENST00000393795 3.7819e-05 6.2189e-01 3.7400e-01 1.0850e+00 +TEKT1 ENST00000338694 8.9486e-07 6.6947e-01 4.2800e-01 1.0850e+00 +PIRT ENST00000580256 5.8020e-01 0.0000e+00 0.0000e+00 1.0850e+00 +SMPD1 ENST00000342245 3.8932e-10 7.3137e-01 5.0500e-01 1.0850e+00 +RFX8 ENST00000428343 5.3224e-09 7.1436e-01 4.8300e-01 1.0850e+00 +SLC35E4 ENST00000343605 1.5961e-02 4.7445e-01 2.3300e-01 1.0850e+00 +TAF13 ENST00000338366 1.5944e-02 4.7459e-01 2.3300e-01 1.0850e+00 +BTN1A1 ENST00000244513 1.9496e-08 7.0443e-01 4.7000e-01 1.0850e+00 +NIT1 ENST00000368009 8.9425e-07 6.6952e-01 4.2800e-01 1.0850e+00 +SPIDR ENST00000297423 2.3847e-17 7.9990e-01 5.9700e-01 1.0850e+00 +C5orf51 ENST00000381647 3.1090e-06 6.5629e-01 4.1200e-01 1.0860e+00 +ERCC2 ENST00000391945 7.0654e-20 8.1597e-01 6.2000e-01 1.0860e+00 +CD151 ENST00000397420 1.0841e-05 6.4053e-01 3.9400e-01 1.0860e+00 +MTMR11 ENST00000439741 4.7707e-23 8.3161e-01 6.4300e-01 1.0860e+00 +CDKL1 ENST00000395834 2.5004e-07 6.8285e-01 4.4400e-01 1.0860e+00 +CLIC2 ENST00000369449 4.9547e-02 4.2098e-01 1.9100e-01 1.0860e+00 +RWDD3 ENST00000370202 1.4761e-03 5.5029e-01 3.0000e-01 1.0860e+00 +RHOD ENST00000308831 1.5921e-02 4.7479e-01 2.3300e-01 1.0860e+00 +WDR64 ENST00000366552 4.9565e-32 8.6391e-01 6.9200e-01 1.0860e+00 +TBC1D26 ENST00000437605 1.0860e-05 6.4038e-01 3.9400e-01 1.0860e+00 +SLC37A3 ENST00000326232 1.1240e-13 7.7197e-01 5.5800e-01 1.0860e+00 +GRK4 ENST00000398052 1.6286e-15 7.8809e-01 5.8000e-01 1.0870e+00 +NHLH2 ENST00000369506 5.7964e-01 0.0000e+00 0.0000e+00 1.0870e+00 +CCDC172 ENST00000333254 3.7344e-05 6.2308e-01 3.7500e-01 1.0870e+00 +ACOT12 ENST00000307624 2.7282e-14 7.7806e-01 5.6600e-01 1.0870e+00 +AQP6 ENST00000315520 1.5875e-02 4.7518e-01 2.3300e-01 1.0870e+00 +NTSR2 ENST00000306928 4.8692e-03 5.1738e-01 2.6900e-01 1.0870e+00 +CCDC3 ENST00000378825 4.8709e-03 5.1734e-01 2.6900e-01 1.0870e+00 +USH1G ENST00000319642 3.7481e-05 6.2273e-01 3.7400e-01 1.0870e+00 +RPUSD2 ENST00000315616 8.8012e-07 6.7072e-01 4.2900e-01 1.0870e+00 +REXO4 ENST00000371942 8.7916e-07 6.7080e-01 4.2900e-01 1.0870e+00 +C6orf89 ENST00000355190 8.7766e-07 6.7093e-01 4.2900e-01 1.0870e+00 +RP11-58C22.1 ENST00000563764 5.7920e-01 0.0000e+00 0.0000e+00 1.0880e+00 +PDCL2 ENST00000295645 1.4645e-03 5.5121e-01 3.0100e-01 1.0880e+00 +SLC6A16 ENST00000335875 4.2922e-13 7.6778e-01 5.5100e-01 1.0880e+00 +CASP12 ENST00000422698 1.2749e-04 6.0318e-01 3.5300e-01 1.0880e+00 +EDEM1 ENST00000256497 1.0594e-13 7.7390e-01 5.6000e-01 1.0880e+00 +FGF4 ENST00000168712 1.4060e-01 3.4688e-01 1.4100e-01 1.0880e+00 +AACS ENST00000316519 9.1275e-17 7.9801e-01 5.9300e-01 1.0880e+00 +FAM161B ENST00000286544 1.0758e-13 7.7340e-01 5.5900e-01 1.0880e+00 +RPS21 ENST00000343986 1.4060e-01 3.4687e-01 1.4100e-01 1.0880e+00 +TACO1 ENST00000258975 1.4606e-03 5.5152e-01 3.0100e-01 1.0880e+00 +FRRS1L ENST00000561981 1.4611e-03 5.5148e-01 3.0100e-01 1.0880e+00 +CYP2A13 ENST00000330436 8.6461e-07 6.7205e-01 4.3000e-01 1.0890e+00 +CASP6 ENST00000265164 1.2665e-04 6.0384e-01 3.5300e-01 1.0890e+00 +LACTB2 ENST00000276590 3.6864e-05 6.2429e-01 3.7500e-01 1.0890e+00 +APPL2 ENST00000551662 1.1641e-18 8.1105e-01 6.1100e-01 1.0890e+00 +TRAF5 ENST00000261464 1.6736e-12 7.6229e-01 5.4400e-01 1.0890e+00 +ZNF627 ENST00000361113 3.3124e-01 2.3149e-01 8.1000e-02 1.0890e+00 +PTPN22 ENST00000359785 3.4921e-21 8.2460e-01 6.3100e-01 1.0890e+00 +EBNA1BP2 ENST00000431635 1.3668e-09 7.2613e-01 4.9600e-01 1.0890e+00 +HSD17B8 ENST00000374662 3.6923e-05 6.2414e-01 3.7500e-01 1.0890e+00 +FKBP2 ENST00000394540 4.9274e-02 4.2179e-01 1.9100e-01 1.0890e+00 +CEP19 ENST00000409690 1.5687e-02 4.7679e-01 2.3400e-01 1.0900e+00 +TMOD4 ENST00000295314 1.8344e-08 7.0808e-01 4.7300e-01 1.0900e+00 +DDX52 ENST00000349699 1.5121e-15 7.9018e-01 5.8100e-01 1.0900e+00 +DSG3 ENST00000257189 1.4584e-20 8.2201e-01 6.2700e-01 1.0900e+00 +SPDL1 ENST00000265295 8.5955e-17 7.9957e-01 5.9400e-01 1.0900e+00 +STXBP4 ENST00000376352 2.5154e-14 7.8056e-01 5.6800e-01 1.0900e+00 +NAALAD2 ENST00000534061 1.4282e-20 8.2247e-01 6.2700e-01 1.0900e+00 +SPATA18 ENST00000295213 1.0088e-13 7.7549e-01 5.6100e-01 1.0910e+00 +PXDNL ENST00000356297 2.2028e-35 8.7676e-01 7.0900e-01 1.0910e+00 +FAM168B ENST00000409185 1.5675e-02 4.7690e-01 2.3400e-01 1.0910e+00 +CUEDC1 ENST00000577830 6.6336e-08 6.9773e-01 4.6000e-01 1.0910e+00 +TTPA ENST00000260116 1.4409e-03 5.5311e-01 3.0200e-01 1.0910e+00 +HSD17B3 ENST00000375263 8.4911e-07 6.7341e-01 4.3100e-01 1.0910e+00 +SIGLEC7 ENST00000317643 2.3880e-07 6.8606e-01 4.4600e-01 1.0910e+00 +VILL ENST00000283713 3.9093e-23 8.3555e-01 6.4600e-01 1.0910e+00 +SLC34A2 ENST00000382051 9.3992e-11 7.4334e-01 5.1800e-01 1.0910e+00 +AP5M1 ENST00000261558 1.3325e-09 7.2744e-01 4.9700e-01 1.0910e+00 +PDCD2L ENST00000246535 8.4791e-07 6.7352e-01 4.3100e-01 1.0910e+00 +FANCG ENST00000378643 2.4859e-14 7.8093e-01 5.6800e-01 1.0910e+00 +CIB2 ENST00000258930 1.4456e-03 5.5272e-01 3.0200e-01 1.0910e+00 +ATF4 ENST00000337304 1.5659e-02 4.7704e-01 2.3400e-01 1.0910e+00 +DUSP11 ENST00000272444 8.4923e-07 6.7340e-01 4.3100e-01 1.0910e+00 +LYPLA1 ENST00000316963 3.6468e-05 6.2530e-01 3.7600e-01 1.0910e+00 +ZNF621 ENST00000339296 1.0463e-05 6.4362e-01 3.9600e-01 1.0920e+00 +ITIH2 ENST00000358415 3.8025e-23 8.3610e-01 6.4600e-01 1.0920e+00 +CABP5 ENST00000293255 4.7939e-03 5.1934e-01 2.7000e-01 1.0920e+00 +ZNF135 ENST00000401053 1.5569e-12 7.6493e-01 5.4600e-01 1.0920e+00 +GALK1 ENST00000588479 1.0420e-05 6.4398e-01 3.9600e-01 1.0920e+00 +KEL ENST00000355265 3.1154e-21 8.2701e-01 6.3300e-01 1.0920e+00 +CCDC71L ENST00000523505 5.7806e-01 0.0000e+00 0.0000e+00 1.0920e+00 +EXOSC7 ENST00000265564 1.0442e-05 6.4379e-01 3.9600e-01 1.0920e+00 +WIF1 ENST00000286574 1.3249e-09 7.2774e-01 4.9700e-01 1.0920e+00 +GMPPB ENST00000308375 8.4370e-07 6.7389e-01 4.3100e-01 1.0920e+00 +MED10 ENST00000255764 4.8839e-02 4.2311e-01 1.9200e-01 1.0920e+00 +PRRX2 ENST00000372469 1.3959e-01 3.4808e-01 1.4100e-01 1.0920e+00 +KRT27 ENST00000301656 1.7955e-08 7.0936e-01 4.7400e-01 1.0920e+00 +NINL ENST00000278886 2.6545e-39 8.8668e-01 7.2400e-01 1.0920e+00 +FAM217A ENST00000274673 4.8219e-09 7.1984e-01 4.8600e-01 1.0930e+00 +ADAMTSL4 ENST00000271643 2.6008e-28 8.5735e-01 6.7800e-01 1.0930e+00 +FMO1 ENST00000354841 9.1198e-11 7.4468e-01 5.1900e-01 1.0930e+00 +CA9 ENST00000378357 1.3027e-09 7.2860e-01 4.9800e-01 1.0930e+00 +C1QTNF1 ENST00000339142 4.2421e-04 5.8190e-01 3.3000e-01 1.0930e+00 +SPERT ENST00000310521 3.6118e-05 6.2621e-01 3.7600e-01 1.0930e+00 +SNX22 ENST00000325881 4.7609e-03 5.2021e-01 2.7100e-01 1.0930e+00 +HAUS3 ENST00000243706 1.2992e-09 7.2874e-01 4.9800e-01 1.0930e+00 +XRCC4 ENST00000511817 8.2774e-07 6.7533e-01 4.3200e-01 1.0940e+00 +CLDN12 ENST00000535571 4.8525e-02 4.2407e-01 1.9200e-01 1.0940e+00 +NOSTRIN ENST00000444448 3.2029e-16 7.9828e-01 5.9000e-01 1.0940e+00 +SAP30L ENST00000297109 1.4279e-03 5.5417e-01 3.0200e-01 1.0940e+00 +RFT1 ENST00000296292 3.7445e-13 7.7247e-01 5.5500e-01 1.0940e+00 +RD3L ENST00000557640 4.8594e-02 4.2386e-01 1.9200e-01 1.0940e+00 +C1QC ENST00000374639 4.8591e-02 4.2387e-01 1.9200e-01 1.0940e+00 +ATP8B4 ENST00000284509 3.6708e-34 8.7596e-01 7.0600e-01 1.0940e+00 +SH2D2A ENST00000392306 8.2695e-07 6.7540e-01 4.3200e-01 1.0940e+00 +SH2D5 ENST00000444387 6.4459e-08 6.9958e-01 4.6100e-01 1.0940e+00 +STON1-GTF2A1L ENST00000394754 1.5167e-22 8.3495e-01 6.4300e-01 1.0940e+00 +ALDH2 ENST00000261733 3.3959e-10 7.3792e-01 5.0900e-01 1.0940e+00 +PTPN7 ENST00000309017 9.4147e-14 7.7774e-01 5.6200e-01 1.0940e+00 +SEPP1 ENST00000514985 8.2884e-07 6.7523e-01 4.3200e-01 1.0940e+00 +NDUFB10 ENST00000268668 4.7516e-03 5.2046e-01 2.7100e-01 1.0940e+00 +TRMT112 ENST00000544844 1.3916e-01 3.4860e-01 1.4100e-01 1.0940e+00 +CCDC94 ENST00000262962 8.2518e-07 6.7556e-01 4.3200e-01 1.0950e+00 +RAD1 ENST00000382038 1.2252e-04 6.0719e-01 3.5500e-01 1.0950e+00 +C8orf34 ENST00000518698 1.4855e-12 7.6664e-01 5.4700e-01 1.0950e+00 +ULK4 ENST00000301831 4.4336e-38 8.8623e-01 7.2100e-01 1.0950e+00 +MID1IP1 ENST00000336949 5.7733e-01 0.0000e+00 0.0000e+00 1.0950e+00 +SNX31 ENST00000311812 3.6683e-13 7.7318e-01 5.5500e-01 1.0950e+00 +TUBA8 ENST00000330423 3.5702e-05 6.2730e-01 3.7700e-01 1.0950e+00 +RIOK1 ENST00000379834 2.2477e-14 7.8404e-01 5.7000e-01 1.0950e+00 +MSMP ENST00000436428 4.8387e-02 4.2449e-01 1.9200e-01 1.0950e+00 +ZNF620 ENST00000314529 4.1957e-04 5.8310e-01 3.3100e-01 1.0950e+00 +LPL ENST00000311322 1.2712e-09 7.2986e-01 4.9800e-01 1.0950e+00 +SCNM1 ENST00000368905 2.9187e-06 6.6141e-01 4.1500e-01 1.0950e+00 +KRT25 ENST00000312150 4.6459e-09 7.2190e-01 4.8800e-01 1.0960e+00 +PNCK ENST00000447676 1.0166e-05 6.4614e-01 3.9800e-01 1.0960e+00 +EXOSC2 ENST00000372358 2.8854e-06 6.6234e-01 4.1600e-01 1.0960e+00 +UCK1 ENST00000372211 1.0175e-05 6.4606e-01 3.9800e-01 1.0960e+00 +CLIC6 ENST00000349499 3.5342e-05 6.2826e-01 3.7800e-01 1.0960e+00 +MUC20 ENST00000447234 4.7211e-03 5.2127e-01 2.7100e-01 1.0960e+00 +GPIHBP1 ENST00000330824 1.3866e-01 3.4920e-01 1.4200e-01 1.0960e+00 +IFT57 ENST00000264538 3.3347e-10 7.3878e-01 5.1000e-01 1.0960e+00 +PPM1D ENST00000305921 2.2321e-11 7.5444e-01 5.3000e-01 1.0960e+00 +SUMO3 ENST00000332859 3.2841e-01 2.3313e-01 8.2000e-02 1.0960e+00 +CTC-435M10.3 ENST00000540732 3.3296e-10 7.3886e-01 5.1000e-01 1.0960e+00 +FOLR3 ENST00000456237 1.5409e-02 4.7923e-01 2.3500e-01 1.0960e+00 +TMPRSS7 ENST00000419127 3.9482e-18 8.1269e-01 6.1000e-01 1.0970e+00 +ARL3 ENST00000260746 1.4071e-03 5.5590e-01 3.0300e-01 1.0970e+00 +ARMC10 ENST00000323716 1.2123e-04 6.0827e-01 3.5600e-01 1.0970e+00 +QPRT ENST00000395384 4.6997e-03 5.2185e-01 2.7200e-01 1.0970e+00 +GALNT14 ENST00000324589 7.0648e-17 8.0467e-01 5.9800e-01 1.0970e+00 +BAIAP2L2 ENST00000381669 1.2298e-09 7.3156e-01 5.0000e-01 1.0970e+00 +ACOXL ENST00000439055 5.2479e-15 7.9037e-01 5.7800e-01 1.0970e+00 +NDUFA10 ENST00000252711 6.2418e-08 7.0166e-01 4.6200e-01 1.0970e+00 +CCDC33 ENST00000398814 4.9566e-20 8.2387e-01 6.2600e-01 1.0970e+00 +BDKRB1 ENST00000216629 4.6897e-03 5.2212e-01 2.7200e-01 1.0970e+00 +CYP4B1 ENST00000371923 3.2777e-10 7.3960e-01 5.1000e-01 1.0970e+00 +BCL2L15 ENST00000393316 4.8246e-02 4.2493e-01 1.9300e-01 1.0970e+00 +ARHGAP19 ENST00000358531 1.4213e-12 7.6824e-01 5.4800e-01 1.0970e+00 +C1orf74 ENST00000294811 1.5314e-02 4.8008e-01 2.3500e-01 1.0980e+00 +SLC2A8 ENST00000373371 8.0241e-07 6.7767e-01 4.3300e-01 1.0980e+00 +RPL39 ENST00000361575 5.7637e-01 0.0000e+00 0.0000e+00 1.0980e+00 +GGT5 ENST00000398292 2.1567e-11 7.5586e-01 5.3100e-01 1.0980e+00 +MED8 ENST00000290663 2.8440e-06 6.6351e-01 4.1700e-01 1.0980e+00 +SCCPDH ENST00000366510 4.5839e-09 7.2264e-01 4.8800e-01 1.0980e+00 +ZNF324B ENST00000336614 3.4989e-05 6.2920e-01 3.7800e-01 1.0980e+00 +SMG9 ENST00000270066 3.4628e-13 7.7516e-01 5.5700e-01 1.0980e+00 +HTR1F ENST00000319595 4.6656e-03 5.2277e-01 2.7200e-01 1.0990e+00 +ROM1 ENST00000278833 4.1221e-04 5.8503e-01 3.3200e-01 1.0990e+00 +CYP2W1 ENST00000308919 2.2124e-07 6.9138e-01 4.4900e-01 1.0990e+00 +CCL25 ENST00000390669 1.5241e-02 4.8073e-01 2.3600e-01 1.0990e+00 +MRPL38 ENST00000309352 4.5080e-09 7.2357e-01 4.8900e-01 1.0990e+00 +PRR3 ENST00000376560 1.3939e-03 5.5701e-01 3.0400e-01 1.0990e+00 +TRPM4 ENST00000252826 5.6531e-33 8.7633e-01 7.0300e-01 1.0990e+00 +DEPDC7 ENST00000241051 8.3246e-11 7.4873e-01 5.2100e-01 1.0990e+00 +VSIG2 ENST00000326621 1.2031e-04 6.0904e-01 3.5600e-01 1.0990e+00 +ASPA ENST00000263080 4.1128e-04 5.8528e-01 3.3200e-01 1.0990e+00 +RRAS ENST00000246792 4.6630e-03 5.2284e-01 2.7200e-01 1.0990e+00 +PTGIS ENST00000244043 1.1970e-09 7.3294e-01 5.0100e-01 1.0990e+00 +AFMID ENST00000327898 4.4977e-09 7.2369e-01 4.8900e-01 1.0990e+00 +CCDC90B ENST00000529689 9.9297e-06 6.4820e-01 3.9900e-01 1.0990e+00 +ALDOB ENST00000374855 7.8786e-07 6.7904e-01 4.3400e-01 1.1000e+00 +FAP ENST00000188790 1.9009e-28 8.6277e-01 6.8200e-01 1.1000e+00 +CLEC12B ENST00000338896 9.9015e-06 6.4845e-01 3.9900e-01 1.1000e+00 +SLC9A4 ENST00000295269 8.2860e-14 7.8189e-01 5.6500e-01 1.1000e+00 +SWI5 ENST00000320188 1.3862e-03 5.5766e-01 3.0400e-01 1.1000e+00 +KLK15 ENST00000598239 1.5191e-02 4.8118e-01 2.3600e-01 1.1000e+00 +ADORA1 ENST00000367236 1.5215e-02 4.8097e-01 2.3600e-01 1.1000e+00 +CDADC1 ENST00000251108 3.1468e-10 7.4154e-01 5.1200e-01 1.1000e+00 +MIPOL1 ENST00000327441 2.0845e-11 7.5726e-01 5.3200e-01 1.1000e+00 +PIDD ENST00000347755 6.4350e-17 8.0711e-01 6.0000e-01 1.1000e+00 +ZNF677 ENST00000333952 1.6591e-08 7.1408e-01 4.7700e-01 1.1000e+00 +PRODH ENST00000357068 5.3577e-12 7.6372e-01 5.4100e-01 1.1000e+00 +P2RX6 ENST00000413302 4.4680e-09 7.2406e-01 4.8900e-01 1.1000e+00 +RPUSD3 ENST00000383820 2.2032e-07 6.9167e-01 4.4900e-01 1.1000e+00 +NRL ENST00000561028 4.7637e-02 4.2684e-01 1.9300e-01 1.1010e+00 +YIF1B ENST00000339413 3.4314e-05 6.3104e-01 3.7900e-01 1.1010e+00 +ZNF630 ENST00000409324 1.1900e-04 6.1016e-01 3.5700e-01 1.1010e+00 +HLTF ENST00000310053 1.8724e-28 8.6303e-01 6.8200e-01 1.1010e+00 +TTC38 ENST00000381031 3.2628e-13 7.7719e-01 5.5800e-01 1.1010e+00 +MARCKS ENST00000368635 3.2648e-01 2.3428e-01 8.2000e-02 1.1010e+00 +KRT34 ENST00000394001 5.9309e-08 7.0495e-01 4.6500e-01 1.1020e+00 +SMIM20 ENST00000506197 5.7531e-01 0.0000e+00 0.0000e+00 1.1020e+00 +OLFM4 ENST00000219022 2.7754e-06 6.6549e-01 4.1800e-01 1.1020e+00 +CCDC83 ENST00000280245 1.1628e-09 7.3443e-01 5.0200e-01 1.1020e+00 +CDC20B ENST00000381375 5.1167e-12 7.6550e-01 5.4200e-01 1.1020e+00 +MAL2 ENST00000276681 1.3691e-01 3.5135e-01 1.4300e-01 1.1020e+00 +MTERFD2 ENST00000391980 3.4049e-05 6.3178e-01 3.8000e-01 1.1020e+00 +CCM2L ENST00000262659 7.7785e-07 6.8000e-01 4.3500e-01 1.1020e+00 +DHX58 ENST00000251642 3.2013e-13 7.7785e-01 5.5900e-01 1.1020e+00 +MRI1 ENST00000040663 4.0621e-04 5.8664e-01 3.3300e-01 1.1020e+00 +COLQ ENST00000383788 7.9356e-14 7.8329e-01 5.6600e-01 1.1020e+00 +GPR149 ENST00000389740 4.3654e-09 7.2534e-01 4.9000e-01 1.1020e+00 +C1orf52 ENST00000471115 4.7382e-02 4.2765e-01 1.9400e-01 1.1030e+00 +ZNF560 ENST00000301480 9.6685e-06 6.5053e-01 4.0000e-01 1.1030e+00 +PLCD1 ENST00000463876 1.7370e-19 8.2513e-01 6.2400e-01 1.1030e+00 +RBM18 ENST00000417201 4.0287e-04 5.8755e-01 3.3300e-01 1.1030e+00 +AARD ENST00000378279 3.2580e-01 2.3468e-01 8.2000e-02 1.1030e+00 +MRPS30 ENST00000507110 1.5937e-08 7.1648e-01 4.7800e-01 1.1030e+00 +BCKDHB ENST00000320393 4.3112e-09 7.2603e-01 4.9100e-01 1.1030e+00 +NTAN1 ENST00000287706 2.7337e-06 6.6672e-01 4.1900e-01 1.1040e+00 +PNOC ENST00000301908 1.5028e-02 4.8267e-01 2.3700e-01 1.1040e+00 +POLM ENST00000242248 7.6227e-11 7.5262e-01 5.2400e-01 1.1040e+00 +CCDC53 ENST00000240079 4.5705e-03 5.2540e-01 2.7400e-01 1.1040e+00 +CENPM ENST00000215980 1.5010e-02 4.8284e-01 2.3700e-01 1.1040e+00 +LINC00692 ENST00000451284 3.2549e-01 2.3486e-01 8.2000e-02 1.1040e+00 +HIST1H1B ENST00000331442 5.7467e-01 0.0000e+00 0.0000e+00 1.1040e+00 +TGIF2 ENST00000373874 1.3641e-01 3.5197e-01 1.4300e-01 1.1040e+00 +RFX5 ENST00000290524 1.9605e-11 7.5979e-01 5.3400e-01 1.1040e+00 +KIF6 ENST00000287152 3.0905e-27 8.6163e-01 6.7800e-01 1.1050e+00 +ANKRD27 ENST00000306065 3.8647e-31 8.7490e-01 6.9800e-01 1.1050e+00 +KIAA0753 ENST00000361413 1.5545e-28 8.6629e-01 6.8500e-01 1.1050e+00 +PNPLA3 ENST00000216180 5.7409e-08 7.0705e-01 4.6600e-01 1.1050e+00 +STX2 ENST00000392373 2.1087e-07 6.9472e-01 4.5100e-01 1.1050e+00 +FAM92A1 ENST00000518322 5.7880e-08 7.0652e-01 4.6600e-01 1.1050e+00 +CDH15 ENST00000289746 1.7656e-14 7.9150e-01 5.7600e-01 1.1050e+00 +KCNK18 ENST00000334549 1.3568e-03 5.6020e-01 3.0600e-01 1.1050e+00 +PMFBP1 ENST00000237353 9.3390e-34 8.8283e-01 7.1000e-01 1.1050e+00 +RGS11 ENST00000397770 7.3266e-14 7.8588e-01 5.6800e-01 1.1050e+00 +DAP3 ENST00000368336 1.1143e-09 7.3660e-01 5.0300e-01 1.1050e+00 +FBXL6 ENST00000331890 4.2187e-09 7.2722e-01 4.9100e-01 1.1050e+00 +ODF3B ENST00000329363 4.5516e-03 5.2593e-01 2.7400e-01 1.1050e+00 +AGPAT9 ENST00000395226 4.8042e-12 7.6793e-01 5.4400e-01 1.1060e+00 +TXLNB ENST00000358430 4.8053e-12 7.6792e-01 5.4400e-01 1.1060e+00 +ZFP69 ENST00000372706 1.5454e-08 7.1831e-01 4.8000e-01 1.1060e+00 +MYOM3 ENST00000374434 1.4264e-47 9.1409e-01 7.5900e-01 1.1060e+00 +WDR88 ENST00000355868 1.5429e-08 7.1840e-01 4.8000e-01 1.1060e+00 +C2orf71 ENST00000331664 3.0058e-18 8.1938e-01 6.1500e-01 1.1060e+00 +SLC26A2 ENST00000286298 7.4963e-07 6.8278e-01 4.3700e-01 1.1060e+00 +KLK13 ENST00000595793 4.5435e-03 5.2615e-01 2.7400e-01 1.1060e+00 +FABP5 ENST00000297258 4.7008e-02 4.2885e-01 1.9400e-01 1.1060e+00 +SLC35F6 ENST00000344420 1.1541e-04 6.1328e-01 3.5900e-01 1.1060e+00 +GLDC ENST00000321612 6.5777e-28 8.6494e-01 6.8200e-01 1.1060e+00 +BCL2L14 ENST00000308721 3.3304e-05 6.3387e-01 3.8100e-01 1.1060e+00 +IFRD2 ENST00000429673 1.0980e-09 7.3736e-01 5.0400e-01 1.1060e+00 +CPNE1 ENST00000317677 1.7292e-14 7.9214e-01 5.7600e-01 1.1060e+00 +TMEM138 ENST00000278826 4.7034e-02 4.2876e-01 1.9400e-01 1.1060e+00 +TSPAN13 ENST00000262067 1.1554e-04 6.1317e-01 3.5900e-01 1.1060e+00 +TDP1 ENST00000335725 1.2652e-17 8.1587e-01 6.0900e-01 1.1070e+00 +RMND1 ENST00000367303 1.0863e-09 7.3790e-01 5.0400e-01 1.1070e+00 +S1PR3 ENST00000375846 4.6945e-02 4.2905e-01 1.9400e-01 1.1070e+00 +SLC25A38 ENST00000273158 9.4313e-06 6.5272e-01 4.0200e-01 1.1070e+00 +SUSD2 ENST00000358321 1.8144e-21 8.3861e-01 6.4200e-01 1.1070e+00 +ZNF438 ENST00000436087 2.6656e-06 6.6878e-01 4.2000e-01 1.1070e+00 +ZNF446 ENST00000594369 5.6695e-08 7.0785e-01 4.6700e-01 1.1070e+00 +GPR180 ENST00000376958 4.0903e-09 7.2893e-01 4.9200e-01 1.1070e+00 +TPO ENST00000345913 1.8182e-21 8.3857e-01 6.4200e-01 1.1070e+00 +CYP4X1 ENST00000371901 4.7167e-12 7.6864e-01 5.4400e-01 1.1070e+00 +LHFPL1 ENST00000371968 1.3548e-01 3.5313e-01 1.4300e-01 1.1070e+00 +ADPRM ENST00000379774 3.9545e-04 5.8960e-01 3.3400e-01 1.1070e+00 +ATG9B ENST00000377974 1.2544e-17 8.1609e-01 6.1000e-01 1.1070e+00 +RP4-559A3.7 ENST00000432920 7.4364e-07 6.8339e-01 4.3700e-01 1.1070e+00 +MTFR2 ENST00000420702 2.6584e-06 6.6900e-01 4.2000e-01 1.1070e+00 +XPNPEP2 ENST00000371106 2.8670e-13 7.8163e-01 5.6100e-01 1.1070e+00 +ADCK4 ENST00000324464 2.8159e-13 7.8224e-01 5.6200e-01 1.1080e+00 +FAM129C ENST00000335393 2.2418e-16 8.0797e-01 5.9800e-01 1.1080e+00 +RETSAT ENST00000295802 6.8328e-14 7.8815e-01 5.7000e-01 1.1080e+00 +CTC-360G5.8 ENST00000599996 6.6002e-19 8.2453e-01 6.2100e-01 1.1080e+00 +HSF4 ENST00000264009 1.0632e-09 7.3900e-01 5.0500e-01 1.1080e+00 +TRIM6 ENST00000380097 1.1425e-12 7.7617e-01 5.5400e-01 1.1080e+00 +AARSD1 ENST00000427569 4.0653e-09 7.2926e-01 4.9300e-01 1.1080e+00 +ESYT3 ENST00000389567 2.3108e-25 8.5716e-01 6.6900e-01 1.1090e+00 +CLEC4G ENST00000328853 9.3088e-06 6.5387e-01 4.0200e-01 1.1090e+00 +GDPD4 ENST00000315938 2.7987e-13 7.8245e-01 5.6200e-01 1.1090e+00 +C15orf60 ENST00000331090 3.2736e-05 6.3550e-01 3.8200e-01 1.1090e+00 +C16orf87 ENST00000285697 4.4861e-03 5.2779e-01 2.7500e-01 1.1090e+00 +ZFYVE27 ENST00000356257 1.0613e-09 7.3909e-01 5.0500e-01 1.1090e+00 +AQP10 ENST00000324978 1.3339e-03 5.6223e-01 3.0700e-01 1.1090e+00 +SNX11 ENST00000393405 7.3043e-07 6.8474e-01 4.3800e-01 1.1090e+00 +AMBN ENST00000322937 1.0497e-09 7.3965e-01 5.0500e-01 1.1090e+00 +C2orf74 ENST00000432605 1.3499e-01 3.5376e-01 1.4400e-01 1.1090e+00 +RAD52 ENST00000358495 7.1128e-11 7.5567e-01 5.2600e-01 1.1090e+00 +SNRNP25 ENST00000383018 1.3382e-03 5.6184e-01 3.0700e-01 1.1090e+00 +FRAT1 ENST00000371021 3.2349e-01 2.3606e-01 8.3000e-02 1.1090e+00 +FAM45A ENST00000361432 5.4591e-08 7.1028e-01 4.6800e-01 1.1100e+00 +EXOSC9 ENST00000379663 1.7871e-11 7.6360e-01 5.3600e-01 1.1100e+00 +B4GALT7 ENST00000029410 1.1304e-04 6.1542e-01 3.6000e-01 1.1100e+00 +CDK18 ENST00000506784 6.9526e-11 7.5667e-01 5.2700e-01 1.1100e+00 +METAP1D ENST00000315796 2.5794e-06 6.7145e-01 4.2200e-01 1.1110e+00 +C19orf44 ENST00000221671 3.8831e-09 7.3178e-01 4.9400e-01 1.1110e+00 +WDR41 ENST00000296679 6.4998e-14 7.8977e-01 5.7100e-01 1.1110e+00 +RPE65 ENST00000262340 6.4889e-14 7.8983e-01 5.7100e-01 1.1110e+00 +XXYLT1 ENST00000310380 1.3246e-03 5.6306e-01 3.0700e-01 1.1110e+00 +ZCCHC12 ENST00000310164 4.6470e-02 4.3060e-01 1.9500e-01 1.1110e+00 +SSC5D ENST00000389623 8.1581e-23 8.4775e-01 6.5300e-01 1.1110e+00 +FAM189A2 ENST00000257515 1.0131e-09 7.4145e-01 5.0600e-01 1.1120e+00 +RPP30 ENST00000413330 5.3582e-08 7.1148e-01 4.6900e-01 1.1120e+00 +CYP3A43 ENST00000222382 1.7165e-11 7.6526e-01 5.3700e-01 1.1120e+00 +LY9 ENST00000263285 2.6039e-13 7.8492e-01 5.6400e-01 1.1120e+00 +RND2 ENST00000587250 3.8579e-04 5.9234e-01 3.3600e-01 1.1120e+00 +UGT1A9 ENST00000354728 5.3634e-08 7.1142e-01 4.6900e-01 1.1120e+00 +VMA21 ENST00000330374 5.7236e-01 0.0000e+00 0.0000e+00 1.1120e+00 +CELA2B ENST00000375910 2.5651e-06 6.7191e-01 4.2200e-01 1.1120e+00 +EMC9 ENST00000419198 1.3199e-03 5.6348e-01 3.0800e-01 1.1120e+00 +CRISP3 ENST00000433368 2.5650e-06 6.7191e-01 4.2200e-01 1.1120e+00 +SPO11 ENST00000371263 1.4473e-08 7.2220e-01 4.8200e-01 1.1120e+00 +WDR65 ENST00000528956 1.0541e-12 7.7909e-01 5.5600e-01 1.1120e+00 +AP3M2 ENST00000518421 1.9720e-07 6.9938e-01 4.5400e-01 1.1120e+00 +TRPM2 ENST00000397928 8.9633e-44 9.1133e-01 7.5100e-01 1.1120e+00 +LRRC70 ENST00000334994 1.9724e-07 6.9937e-01 4.5400e-01 1.1120e+00 +HMGCL ENST00000374490 2.5638e-06 6.7195e-01 4.2200e-01 1.1120e+00 +SH3YL1 ENST00000356150 5.3675e-08 7.1137e-01 4.6900e-01 1.1120e+00 +MAPK13 ENST00000211287 6.7197e-11 7.5817e-01 5.2800e-01 1.1120e+00 +CAPN14 ENST00000403897 1.5664e-21 8.4181e-01 6.4400e-01 1.1120e+00 +HS3ST1 ENST00000002596 4.4305e-03 5.2940e-01 2.7600e-01 1.1130e+00 +TLCD1 ENST00000292090 4.4281e-03 5.2947e-01 2.7600e-01 1.1130e+00 +METTL11B ENST00000439373 4.4204e-03 5.2969e-01 2.7600e-01 1.1130e+00 +DCST1 ENST00000295542 1.2681e-19 8.3249e-01 6.3000e-01 1.1130e+00 +KRBA1 ENST00000255992 8.2344e-16 8.0737e-01 5.9400e-01 1.1130e+00 +CMBL ENST00000296658 1.1148e-04 6.1685e-01 3.6100e-01 1.1130e+00 +TTC1 ENST00000231238 2.5494e-06 6.7240e-01 4.2200e-01 1.1130e+00 +HMCES ENST00000383463 1.9468e-07 7.0027e-01 4.5500e-01 1.1130e+00 +PAFAH2 ENST00000374282 3.8282e-09 7.3256e-01 4.9500e-01 1.1130e+00 +CAPNS1 ENST00000246533 7.1100e-07 6.8677e-01 4.3900e-01 1.1130e+00 +SLC4A9 ENST00000230993 3.2089e-22 8.4717e-01 6.5100e-01 1.1140e+00 +TALDO1 ENST00000319006 2.5234e-06 6.7324e-01 4.2300e-01 1.1140e+00 +TUBB3 ENST00000556922 2.5676e-10 7.5117e-01 5.1800e-01 1.1140e+00 +TIMP4 ENST00000287814 3.8342e-04 5.9303e-01 3.3600e-01 1.1140e+00 +CCDC151 ENST00000356392 3.4684e-15 8.0261e-01 5.8700e-01 1.1140e+00 +DUS4L ENST00000265720 3.1791e-05 6.3829e-01 3.8400e-01 1.1140e+00 +TRIM10 ENST00000449742 3.7432e-09 7.3379e-01 4.9600e-01 1.1140e+00 +RHPN1 ENST00000289013 1.0250e-12 7.8010e-01 5.5600e-01 1.1140e+00 +ZNF707 ENST00000532205 1.3100e-03 5.6439e-01 3.0800e-01 1.1140e+00 +TM2D1 ENST00000371180 1.0999e-04 6.1823e-01 3.6200e-01 1.1150e+00 +AIRE ENST00000291582 4.0468e-12 7.7454e-01 5.4800e-01 1.1150e+00 +DUSP27 ENST00000361200 5.2331e-19 8.3013e-01 6.2600e-01 1.1150e+00 +DYX1C1 ENST00000321149 9.7181e-10 7.4356e-01 5.0800e-01 1.1150e+00 +LRRC57 ENST00000323443 1.3041e-03 5.6493e-01 3.0800e-01 1.1150e+00 +IL10RB ENST00000290200 2.5103e-06 6.7366e-01 4.2300e-01 1.1150e+00 +SERPINB6 ENST00000380520 1.1009e-04 6.1814e-01 3.6200e-01 1.1150e+00 +PUS3 ENST00000227474 1.4003e-08 7.2416e-01 4.8400e-01 1.1150e+00 +MAPKAPK3 ENST00000446044 3.7216e-09 7.3411e-01 4.9600e-01 1.1150e+00 +TRIM38 ENST00000357085 1.3947e-08 7.2440e-01 4.8400e-01 1.1150e+00 +ACMSD ENST00000356140 1.3920e-08 7.2451e-01 4.8400e-01 1.1160e+00 +CLCNKA ENST00000331433 4.2296e-17 8.1818e-01 6.0800e-01 1.1160e+00 +MRPL37 ENST00000360840 1.3929e-08 7.2447e-01 4.8400e-01 1.1160e+00 +MORN1 ENST00000378531 1.6137e-11 7.6779e-01 5.3900e-01 1.1160e+00 +TTC19 ENST00000261647 1.3788e-08 7.2508e-01 4.8400e-01 1.1160e+00 +ZXDA ENST00000358697 4.3723e-03 5.3111e-01 2.7700e-01 1.1160e+00 +ZNF558 ENST00000601372 8.8874e-06 6.5795e-01 4.0500e-01 1.1160e+00 +ROS1 ENST00000368508 1.6184e-72 9.5484e-01 8.1900e-01 1.1160e+00 +LY6E ENST00000520466 3.2110e-01 2.3751e-01 8.3000e-02 1.1160e+00 +SERPINE3 ENST00000521255 2.4978e-06 6.7407e-01 4.2300e-01 1.1160e+00 +WDR4 ENST00000398208 1.3806e-08 7.2500e-01 4.8400e-01 1.1160e+00 +CLEC11A ENST00000250340 3.8003e-04 5.9401e-01 3.3700e-01 1.1160e+00 +FAM229B ENST00000368656 5.7066e-01 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6.1100e-01 1.1330e+00 +APOL5 ENST00000249044 6.0075e-07 6.9946e-01 4.4700e-01 1.1330e+00 +NCF1 ENST00000289473 2.8311e-05 6.4941e-01 3.9000e-01 1.1330e+00 +CLN6 ENST00000249806 1.0025e-04 6.2786e-01 3.6700e-01 1.1330e+00 +SPINK1 ENST00000296695 3.1476e-01 2.4148e-01 8.5000e-02 1.1330e+00 +AC007040.11 ENST00000606025 4.1170e-03 5.3900e-01 2.8100e-01 1.1330e+00 +ZBTB25 ENST00000608382 2.1949e-06 6.8464e-01 4.3000e-01 1.1330e+00 +HBG1 ENST00000330597 5.6611e-01 0.0000e+00 0.0000e+00 1.1330e+00 +LRRC20 ENST00000355790 4.3870e-02 4.3951e-01 1.9900e-01 1.1330e+00 +SLC47A2 ENST00000325411 9.2836e-15 8.1149e-01 5.9000e-01 1.1330e+00 +RNASEL ENST00000367559 1.9513e-10 7.6405e-01 5.2700e-01 1.1330e+00 +PDSS2 ENST00000369037 4.3743e-08 7.2448e-01 4.7700e-01 1.1330e+00 +OPA3 ENST00000323060 5.6570e-01 0.0000e+00 0.0000e+00 1.1340e+00 +UGT1A4 ENST00000373409 5.9807e-07 6.9980e-01 4.4700e-01 1.1340e+00 +TDP2 ENST00000378198 1.1340e-08 7.3661e-01 4.9200e-01 1.1340e+00 +SHQ1 ENST00000325599 4.7806e-11 7.7306e-01 5.3800e-01 1.1340e+00 +COG8 ENST00000306875 2.9725e-09 7.4637e-01 5.0400e-01 1.1340e+00 +GLT8D1 ENST00000407584 1.1343e-08 7.3660e-01 4.9200e-01 1.1340e+00 +C17orf66 ENST00000311880 4.8498e-16 8.2258e-01 6.0500e-01 1.1340e+00 +PDZD7 ENST00000370215 7.6433e-10 7.5570e-01 5.1600e-01 1.1340e+00 +CXCL11 ENST00000306621 3.1408e-01 2.4192e-01 8.5000e-02 1.1350e+00 +SH3BP2 ENST00000503393 1.1560e-11 7.8142e-01 5.4900e-01 1.1350e+00 +TFEC ENST00000265440 4.2824e-08 7.2583e-01 4.7800e-01 1.1350e+00 +MRFAP1 ENST00000320912 3.1404e-01 2.4194e-01 8.5000e-02 1.1350e+00 +BRMS1 ENST00000425825 1.5790e-07 7.1481e-01 4.6400e-01 1.1360e+00 +CLEC10A ENST00000254868 7.7599e-06 6.6998e-01 4.1200e-01 1.1360e+00 +PADI1 ENST00000375471 2.0388e-15 8.1849e-01 5.9900e-01 1.1360e+00 +PADI4 ENST00000375448 4.6001e-16 8.2412e-01 6.0600e-01 1.1360e+00 +TMEM30C ENST00000429523 5.6514e-01 0.0000e+00 0.0000e+00 1.1360e+00 +PVRIG ENST00000317271 4.0685e-03 5.4057e-01 2.8100e-01 1.1360e+00 +HOXC11 ENST00000546378 4.0590e-03 5.4088e-01 2.8200e-01 1.1360e+00 +KRT28 ENST00000306658 7.4212e-10 7.5718e-01 5.1700e-01 1.1360e+00 +CHRNA5 ENST00000299565 2.1488e-06 6.8638e-01 4.3100e-01 1.1360e+00 +RIC3 ENST00000309737 2.1447e-06 6.8653e-01 4.3100e-01 1.1360e+00 +COMMD3 ENST00000376836 2.7760e-05 6.5131e-01 3.9200e-01 1.1360e+00 +OR10K1 ENST00000289451 3.1356e-01 2.4225e-01 8.5000e-02 1.1360e+00 +PIK3C2G ENST00000433979 9.5013e-40 9.2110e-01 7.5100e-01 1.1360e+00 +HS3ST3A1 ENST00000284110 1.3565e-02 4.9713e-01 2.4400e-01 1.1360e+00 +PINK1 ENST00000321556 1.8749e-10 7.6592e-01 5.2800e-01 1.1360e+00 +ACTL9 ENST00000324436 4.0543e-03 5.4104e-01 2.8200e-01 1.1370e+00 +CCDC58 ENST00000291458 4.0567e-03 5.4096e-01 2.8200e-01 1.1370e+00 +GUF1 ENST00000281543 5.3495e-18 8.3818e-01 6.2600e-01 1.1370e+00 +B4GALT4 ENST00000483209 5.8287e-07 7.0174e-01 4.4900e-01 1.1370e+00 +C9orf24 ENST00000297623 2.1359e-06 6.8687e-01 4.3100e-01 1.1370e+00 +NPL ENST00000367553 1.5688e-07 7.1526e-01 4.6500e-01 1.1370e+00 +FUT4 ENST00000358752 7.7294e-06 6.7033e-01 4.1300e-01 1.1370e+00 +CCDC85B ENST00000312579 3.1331e-01 2.4241e-01 8.5000e-02 1.1370e+00 +OVOL3 ENST00000262637 1.1868e-03 5.7639e-01 3.1500e-01 1.1370e+00 +PNKD ENST00000273077 4.1392e-08 7.2800e-01 4.8000e-01 1.1380e+00 +POF1B ENST00000262753 4.5070e-11 7.7562e-01 5.4000e-01 1.1380e+00 +LMOD3 ENST00000420581 1.5519e-07 7.1602e-01 4.6500e-01 1.1380e+00 +SPR ENST00000234454 4.3400e-02 4.4121e-01 2.0000e-01 1.1380e+00 +ASTE1 ENST00000264992 7.2103e-10 7.5863e-01 5.1800e-01 1.1380e+00 +WFIKKN1 ENST00000319070 7.7014e-06 6.7065e-01 4.1300e-01 1.1380e+00 +ALDH9A1 ENST00000354775 1.0995e-11 7.8347e-01 5.5000e-01 1.1380e+00 +ZNF502 ENST00000296091 4.1603e-08 7.2768e-01 4.8000e-01 1.1380e+00 +NOX4 ENST00000263317 5.7555e-20 8.5143e-01 6.4400e-01 1.1380e+00 +IL17RB ENST00000288167 4.4601e-11 7.7608e-01 5.4000e-01 1.1390e+00 +ITGB1BP1 ENST00000360635 9.6972e-05 6.3134e-01 3.7000e-01 1.1390e+00 +CENPH ENST00000283006 1.5465e-07 7.1625e-01 4.6500e-01 1.1390e+00 +RAD51L3-RFFL ENST00000593039 2.0968e-06 6.8838e-01 4.3200e-01 1.1390e+00 +HSD17B13 ENST00000328546 2.7371e-05 6.5268e-01 3.9200e-01 1.1390e+00 +CTC-512J12.6 ENST00000588212 1.2761e-01 3.6357e-01 1.4800e-01 1.1390e+00 +C6ORF165 ENST00000369562 8.0894e-15 8.1582e-01 5.9400e-01 1.1390e+00 +NEBL ENST00000377122 1.7679e-36 9.1507e-01 7.4000e-01 1.1390e+00 +ZNF185 ENST00000535861 6.3026e-13 7.9773e-01 5.6900e-01 1.1390e+00 +FAM177A1 ENST00000280987 1.1791e-03 5.7719e-01 3.1500e-01 1.1390e+00 +TRMT10C ENST00000309922 9.7105e-05 6.3120e-01 3.6900e-01 1.1390e+00 +FBXO44 ENST00000376770 2.1091e-06 6.8790e-01 4.3200e-01 1.1390e+00 +FAM81B ENST00000283357 1.0816e-11 7.8414e-01 5.5100e-01 1.1390e+00 +HEXDC ENST00000337014 4.3406e-11 7.7726e-01 5.4100e-01 1.1400e+00 +ASPG ENST00000551177 6.1787e-13 7.9845e-01 5.7000e-01 1.1400e+00 +EXOSC5 ENST00000221233 4.0091e-03 5.4253e-01 2.8300e-01 1.1400e+00 +LZIC ENST00000377223 1.1711e-03 5.7804e-01 3.1500e-01 1.1400e+00 +CAPN9 ENST00000271971 1.3256e-22 8.6656e-01 6.6600e-01 1.1400e+00 +HSPB8 ENST00000281938 4.3128e-02 4.4220e-01 2.0000e-01 1.1400e+00 +HSPBAP1 ENST00000306103 4.4074e-11 7.7660e-01 5.4100e-01 1.1400e+00 +RDH8 ENST00000591589 1.1708e-03 5.7806e-01 3.1600e-01 1.1400e+00 +C14orf164 ENST00000399910 1.0617e-08 7.4049e-01 4.9400e-01 1.1400e+00 +CALR3 ENST00000269881 6.9788e-10 7.6027e-01 5.1900e-01 1.1400e+00 +CTD-2260A17.2 ENST00000504056 5.6415e-01 0.0000e+00 0.0000e+00 1.1400e+00 +OSCP1 ENST00000235532 7.0317e-10 7.5989e-01 5.1900e-01 1.1400e+00 +TMA16 ENST00000358572 9.6522e-05 6.3183e-01 3.7000e-01 1.1400e+00 +FAM64A ENST00000250056 1.1659e-03 5.7859e-01 3.1600e-01 1.1410e+00 +NAGS ENST00000293404 4.0325e-08 7.2967e-01 4.8100e-01 1.1410e+00 +ANO6 ENST00000423947 7.3158e-32 9.0322e-01 7.2000e-01 1.1410e+00 +PCDHGB2 ENST00000522605 2.5408e-12 7.9241e-01 5.6100e-01 1.1410e+00 +C11orf70 ENST00000434758 2.0691e-06 6.8947e-01 4.3300e-01 1.1410e+00 +HTR3A ENST00000355556 1.7499e-10 7.6914e-01 5.3100e-01 1.1410e+00 +COX7C ENST00000509578 5.6366e-01 0.0000e+00 0.0000e+00 1.1410e+00 +HAAO ENST00000294973 1.0561e-08 7.4080e-01 4.9500e-01 1.1410e+00 +PAPLN ENST00000340738 7.4895e-38 9.1991e-01 7.4600e-01 1.1410e+00 +IL17A ENST00000340057 4.3049e-02 4.4249e-01 2.0000e-01 1.1410e+00 +SKA3 ENST00000314759 1.5109e-07 7.1787e-01 4.6600e-01 1.1410e+00 +STOM ENST00000286713 2.7047e-05 6.5383e-01 3.9300e-01 1.1410e+00 +SAMD12 ENST00000314727 1.1661e-03 5.7856e-01 3.1600e-01 1.1410e+00 +SLC2A9 ENST00000264784 6.9451e-10 7.6051e-01 5.1900e-01 1.1410e+00 +C15orf52 ENST00000559313 1.4050e-13 8.0612e-01 5.7900e-01 1.1420e+00 +UBXN11 ENST00000374222 1.3973e-13 8.0631e-01 5.7900e-01 1.1420e+00 +PPP1R36 ENST00000298705 1.7114e-10 7.7017e-01 5.3100e-01 1.1420e+00 +KCNJ5 ENST00000529694 3.3577e-04 6.0797e-01 3.4500e-01 1.1420e+00 +AGBL1 ENST00000441037 1.4377e-30 9.0035e-01 7.1500e-01 1.1420e+00 +CCDC37 ENST00000352312 4.6757e-18 8.4174e-01 6.2900e-01 1.1420e+00 +CBLC ENST00000270279 4.2394e-11 7.7829e-01 5.4200e-01 1.1420e+00 +GRAMD3 ENST00000513040 2.5212e-12 7.9270e-01 5.6100e-01 1.1420e+00 +ZFYVE19 ENST00000355341 3.2046e-14 8.1290e-01 5.8800e-01 1.1430e+00 +KIF9 ENST00000335044 5.4841e-22 8.6532e-01 6.6200e-01 1.1430e+00 +CDCA5 ENST00000275517 1.1583e-03 5.7939e-01 3.1600e-01 1.1430e+00 +DMP1 ENST00000339673 1.4881e-07 7.1892e-01 4.6700e-01 1.1430e+00 +ENPEP ENST00000265162 1.3878e-28 8.9366e-01 7.0500e-01 1.1430e+00 +RBFA ENST00000306735 9.5095e-05 6.3340e-01 3.7100e-01 1.1430e+00 +SARM1 ENST00000457710 1.7007e-10 7.7047e-01 5.3200e-01 1.1430e+00 +TERF2IP ENST00000300086 2.6683e-05 6.5514e-01 3.9400e-01 1.1430e+00 +DALRD3 ENST00000341949 1.6886e-10 7.7080e-01 5.3200e-01 1.1430e+00 +CCER2 ENST00000571838 3.9706e-03 5.4382e-01 2.8300e-01 1.1430e+00 +PPP1R14A ENST00000301242 1.2672e-01 3.6482e-01 1.4800e-01 1.1430e+00 +PRG3 ENST00000287143 3.3439e-04 6.0844e-01 3.4500e-01 1.1430e+00 +C2orf61 ENST00000445927 9.5142e-05 6.3334e-01 3.7100e-01 1.1430e+00 +SCRN3 ENST00000272732 1.4833e-07 7.1915e-01 4.6700e-01 1.1430e+00 +ACAT2 ENST00000367048 5.5303e-07 7.0570e-01 4.5100e-01 1.1430e+00 +GPR113 ENST00000311519 1.1879e-22 8.6902e-01 6.6700e-01 1.1430e+00 +DQX1 ENST00000404568 5.0034e-20 8.5487e-01 6.4700e-01 1.1430e+00 +HDHD1 ENST00000424830 1.2667e-01 3.6489e-01 1.4800e-01 1.1430e+00 +SCTR ENST00000019103 2.4257e-12 7.9419e-01 5.6200e-01 1.1440e+00 +ADAD2 ENST00000268624 2.3904e-12 7.9475e-01 5.6300e-01 1.1440e+00 +TSEN2 ENST00000284995 1.0092e-11 7.8696e-01 5.5300e-01 1.1440e+00 +C3orf20 ENST00000253697 2.3810e-21 8.6288e-01 6.5800e-01 1.1440e+00 +CSRP1 ENST00000367306 3.3280e-04 6.0899e-01 3.4500e-01 1.1440e+00 +LRRC2 ENST00000395905 5.5017e-07 7.0609e-01 4.5100e-01 1.1440e+00 +SNAI3 ENST00000332281 1.3249e-02 5.0055e-01 2.4600e-01 1.1440e+00 +RP11-385D13.1 ENST00000455584 5.7998e-26 8.8462e-01 6.9000e-01 1.1440e+00 +TRIT1 ENST00000316891 4.0895e-11 7.7986e-01 5.4300e-01 1.1440e+00 +HYKK ENST00000388988 7.3257e-06 6.7511e-01 4.1500e-01 1.1450e+00 +KRT84 ENST00000257951 6.5597e-10 7.6338e-01 5.2100e-01 1.1450e+00 +MPO ENST00000225275 7.1050e-15 8.1992e-01 5.9700e-01 1.1450e+00 +SLC22A8 ENST00000336232 2.6004e-09 7.5363e-01 5.0900e-01 1.1450e+00 +VAMP1 ENST00000396308 3.9396e-03 5.4487e-01 2.8400e-01 1.1450e+00 +HAO1 ENST00000378789 1.4578e-07 7.2035e-01 4.6800e-01 1.1450e+00 +ZNF786 ENST00000491431 2.3543e-12 7.9534e-01 5.6300e-01 1.1450e+00 +TATDN3 ENST00000532324 5.4402e-07 7.0694e-01 4.5200e-01 1.1450e+00 +CES3 ENST00000303334 2.3374e-12 7.9561e-01 5.6300e-01 1.1460e+00 +CSNK1A1L ENST00000379800 1.3174e-02 5.0138e-01 2.4600e-01 1.1460e+00 +IQCK ENST00000320394 2.0032e-06 6.9213e-01 4.3500e-01 1.1460e+00 +GPR112 ENST00000394143 1.2147e-34 9.1575e-01 7.3600e-01 1.1460e+00 +MASP2 ENST00000400897 3.0428e-14 8.1461e-01 5.8900e-01 1.1460e+00 +TIMM21 ENST00000169551 9.3324e-05 6.3538e-01 3.7200e-01 1.1460e+00 +SLC13A2 ENST00000444914 1.2919e-13 8.0902e-01 5.8100e-01 1.1460e+00 +CSH2 ENST00000392886 1.3182e-02 5.0129e-01 2.4600e-01 1.1460e+00 +TRPV3 ENST00000301365 4.6013e-20 8.5694e-01 6.4800e-01 1.1460e+00 +ESD ENST00000378720 5.3945e-07 7.0757e-01 4.5200e-01 1.1460e+00 +MRPS24 ENST00000317534 3.9242e-03 5.4540e-01 2.8400e-01 1.1460e+00 +ANKRD61 ENST00000409061 3.9262e-03 5.4533e-01 2.8400e-01 1.1460e+00 +TTC16 ENST00000373289 4.1102e-18 8.4518e-01 6.3100e-01 1.1460e+00 +TRIM69 ENST00000559390 2.5727e-09 7.5421e-01 5.1000e-01 1.1460e+00 +ZNF432 ENST00000594154 3.0049e-14 8.1502e-01 5.8900e-01 1.1460e+00 +TSR3 ENST00000007390 1.1406e-03 5.8130e-01 3.1700e-01 1.1470e+00 +NBPF1 ENST00000430580 2.3773e-25 8.8416e-01 6.8800e-01 1.1470e+00 +HMGN5 ENST00000358130 3.0957e-01 2.4484e-01 8.6000e-02 1.1470e+00 +MRPL2 ENST00000388752 1.4285e-07 7.2175e-01 4.6900e-01 1.1470e+00 +SH3RF2 ENST00000511217 1.2714e-13 8.0957e-01 5.8200e-01 1.1470e+00 +ARSG ENST00000448504 6.3682e-10 7.6486e-01 5.2200e-01 1.1470e+00 +CIB1 ENST00000328649 3.2612e-04 6.1131e-01 3.4700e-01 1.1480e+00 +KIR2DL4 ENST00000345540 4.2308e-02 4.4526e-01 2.0200e-01 1.1480e+00 +ATP5J2-PTCD1 ENST00000413834 2.9087e-14 8.1610e-01 5.9000e-01 1.1480e+00 +TGDS ENST00000261296 2.4826e-09 7.5614e-01 5.1100e-01 1.1480e+00 +PTCD1 ENST00000555673 2.9087e-14 8.1610e-01 5.9000e-01 1.1480e+00 +CDKL3 ENST00000265334 2.2569e-12 7.9696e-01 5.6400e-01 1.1480e+00 +CHRNA3 ENST00000326828 1.4197e-07 7.2218e-01 4.6900e-01 1.1480e+00 +RILPL2 ENST00000280571 3.8900e-03 5.4658e-01 2.8500e-01 1.1480e+00 +SPATA7 ENST00000393545 5.1769e-13 8.0488e-01 5.7400e-01 1.1490e+00 +SCPEP1 ENST00000262288 1.2284e-13 8.1076e-01 5.8200e-01 1.1490e+00 +FAM195B ENST00000576730 4.2217e-02 4.4561e-01 2.0200e-01 1.1490e+00 +CA4 ENST00000300900 7.1318e-06 6.7751e-01 4.1700e-01 1.1490e+00 +DFNB59 ENST00000409117 3.7194e-08 7.3482e-01 4.8400e-01 1.1490e+00 +PLK5 ENST00000334770 9.1971e-05 6.3692e-01 3.7300e-01 1.1490e+00 +GCKR ENST00000264717 8.5354e-19 8.5129e-01 6.3900e-01 1.1490e+00 +SH2D1B ENST00000367929 1.3037e-02 5.0290e-01 2.4700e-01 1.1490e+00 +CD276 ENST00000318443 2.4699e-09 7.5642e-01 5.1100e-01 1.1490e+00 +IQCF1 ENST00000310914 1.1241e-03 5.8312e-01 3.1800e-01 1.1500e+00 +ZNF195 ENST00000399602 3.8677e-03 5.4736e-01 2.8500e-01 1.1500e+00 +HOXC9 ENST00000303450 1.2993e-02 5.0340e-01 2.4700e-01 1.1500e+00 +ZNF738 ENST00000311015 4.2023e-02 4.4634e-01 2.0200e-01 1.1500e+00 +FUNDC1 ENST00000378045 4.2053e-02 4.4623e-01 2.0200e-01 1.1500e+00 +TIFA ENST00000361717 1.2501e-01 3.6726e-01 1.4900e-01 1.1500e+00 +TPMT ENST00000309983 7.1064e-06 6.7783e-01 4.1700e-01 1.1500e+00 +VWA8 ENST00000379310 8.4114e-70 9.7917e-01 8.3600e-01 1.1500e+00 +CWF19L1 ENST00000354105 1.4404e-15 8.2904e-01 6.0700e-01 1.1500e+00 +TSSK2 ENST00000399635 3.8610e-03 5.4759e-01 2.8500e-01 1.1500e+00 +LPO ENST00000262290 7.4989e-17 8.3849e-01 6.2000e-01 1.1500e+00 +ADAMTSL5 ENST00000330475 3.7025e-11 7.8418e-01 5.4600e-01 1.1510e+00 +OTOP3 ENST00000328801 3.6938e-11 7.8428e-01 5.4600e-01 1.1510e+00 +CAPN11 ENST00000398776 4.4077e-24 8.8100e-01 6.8100e-01 1.1510e+00 +NBPF3 ENST00000318249 8.0766e-19 8.5274e-01 6.4000e-01 1.1510e+00 +ZSCAN31 ENST00000414429 3.6470e-08 7.3607e-01 4.8500e-01 1.1510e+00 +CCDC154 ENST00000389176 7.2485e-17 8.3946e-01 6.2100e-01 1.1510e+00 +TMC2 ENST00000358864 2.0830e-27 8.9547e-01 7.0200e-01 1.1510e+00 +ARHGEF19 ENST00000270747 3.9492e-20 8.6073e-01 6.5100e-01 1.1510e+00 +MFAP3 ENST00000436816 1.1201e-03 5.8356e-01 3.1900e-01 1.1510e+00 +RPTN ENST00000316073 2.5475e-05 6.5964e-01 3.9700e-01 1.1510e+00 +TLL2 ENST00000357947 2.1374e-31 9.0932e-01 7.2400e-01 1.1510e+00 +GCSAML ENST00000366488 1.2474e-01 3.6765e-01 1.4900e-01 1.1510e+00 +TMPRSS15 ENST00000284885 4.5847e-32 9.1150e-01 7.2700e-01 1.1510e+00 +BAG2 ENST00000370693 4.2000e-02 4.4643e-01 2.0200e-01 1.1510e+00 +PRCP ENST00000393399 8.7577e-12 7.9275e-01 5.5700e-01 1.1520e+00 +EXOC3L1 ENST00000314586 1.7404e-19 8.5751e-01 6.4600e-01 1.1520e+00 +PNP ENST00000361505 6.9987e-06 6.7919e-01 4.1800e-01 1.1520e+00 +COMMD4 ENST00000267935 3.2013e-04 6.1344e-01 3.4800e-01 1.1520e+00 +FARS2 ENST00000324331 9.2964e-09 7.4828e-01 5.0000e-01 1.1520e+00 +PDPN ENST00000294489 3.2048e-04 6.1331e-01 3.4800e-01 1.1520e+00 +MUL1 ENST00000264198 1.9108e-06 6.9601e-01 4.3700e-01 1.1520e+00 +SERPINB13 ENST00000344731 7.0156e-06 6.7898e-01 4.1800e-01 1.1520e+00 +MBOAT4 ENST00000320542 1.3575e-07 7.2528e-01 4.7100e-01 1.1530e+00 +EDARADD ENST00000334232 3.1820e-04 6.1413e-01 3.4800e-01 1.1530e+00 +C1QA ENST00000374642 3.8204e-03 5.4902e-01 2.8600e-01 1.1530e+00 +PFKP ENST00000381125 8.8342e-25 8.8579e-01 6.8700e-01 1.1530e+00 +ACADM ENST00000420607 2.0548e-12 8.0057e-01 5.6700e-01 1.1530e+00 +PLA2G3 ENST00000215885 3.5604e-11 7.8588e-01 5.4700e-01 1.1530e+00 +CNGB1 ENST00000251102 1.8369e-37 9.2835e-01 7.5200e-01 1.1530e+00 +SCLY ENST00000254663 2.3341e-09 7.5947e-01 5.1300e-01 1.1530e+00 +CHRNA6 ENST00000276410 3.5719e-08 7.3739e-01 4.8600e-01 1.1530e+00 +PLSCR4 ENST00000354952 1.8979e-06 6.9656e-01 4.3700e-01 1.1530e+00 +SLC35A5 ENST00000492406 1.8916e-06 6.9684e-01 4.3800e-01 1.1530e+00 +WHAMM ENST00000286760 4.8122e-13 8.0755e-01 5.7600e-01 1.1530e+00 +ARMC4 ENST00000305242 1.9031e-25 8.8885e-01 6.9100e-01 1.1530e+00 +RNF141 ENST00000265981 9.0192e-05 6.3899e-01 3.7400e-01 1.1530e+00 +CNTN6 ENST00000446702 9.0232e-31 9.0890e-01 7.2200e-01 1.1530e+00 +ZNF623 ENST00000501748 6.9313e-06 6.8006e-01 4.1900e-01 1.1530e+00 +MOCOS ENST00000261326 1.6193e-19 8.5936e-01 6.4800e-01 1.1540e+00 +YPEL3 ENST00000398841 4.1612e-02 4.4793e-01 2.0300e-01 1.1540e+00 +SLC22A2 ENST00000366953 2.0202e-12 8.0122e-01 5.6700e-01 1.1540e+00 +SPRY3 ENST00000302805 3.8066e-03 5.4951e-01 2.8600e-01 1.1540e+00 +TWIST2 ENST00000448943 5.6004e-01 0.0000e+00 0.0000e+00 1.1540e+00 +NR1I3 ENST00000367980 3.5259e-08 7.3822e-01 4.8700e-01 1.1540e+00 +FAM183A ENST00000335282 4.1627e-02 4.4787e-01 2.0300e-01 1.1540e+00 +TMEM127 ENST00000258439 1.2865e-02 5.0485e-01 2.4800e-01 1.1540e+00 +FIGF ENST00000297904 2.4980e-05 6.6156e-01 3.9800e-01 1.1540e+00 +FASTKD3 ENST00000264669 5.8599e-10 7.6903e-01 5.2500e-01 1.1540e+00 +ZNF165 ENST00000377325 9.1110e-09 7.4946e-01 5.0000e-01 1.1540e+00 +OFCC1 ENST00000460363 1.8876e-06 6.9701e-01 4.3800e-01 1.1540e+00 +NEK4 ENST00000233027 8.6883e-27 8.9493e-01 7.0000e-01 1.1540e+00 +LEPREL1 ENST00000319332 7.7878e-21 8.6717e-01 6.5900e-01 1.1550e+00 +MTHFD2L ENST00000395759 6.8566e-06 6.8103e-01 4.1900e-01 1.1550e+00 +C18orf54 ENST00000300091 1.8657e-06 6.9797e-01 4.3800e-01 1.1550e+00 +C1RL ENST00000266542 3.4642e-08 7.3934e-01 4.8700e-01 1.1560e+00 +HLA-DRB1 ENST00000360004 1.0997e-03 5.8586e-01 3.2000e-01 1.1560e+00 +HRH1 ENST00000397056 1.8580e-06 6.9831e-01 4.3900e-01 1.1560e+00 +NCR3LG1 ENST00000338965 8.8569e-05 6.4092e-01 3.7500e-01 1.1560e+00 +C9orf117 ENST00000373295 8.2434e-12 7.9522e-01 5.5900e-01 1.1560e+00 +DIRC2 ENST00000261038 2.2526e-09 7.6139e-01 5.1400e-01 1.1560e+00 +OXSM ENST00000280701 2.4742e-05 6.6249e-01 3.9800e-01 1.1560e+00 +OIT3 ENST00000334011 3.3920e-11 7.8799e-01 5.4900e-01 1.1560e+00 +IZUMO2 ENST00000293405 2.4749e-05 6.6246e-01 3.9800e-01 1.1560e+00 +DCDC2 ENST00000378454 5.6611e-10 7.7076e-01 5.2600e-01 1.1560e+00 +DCSTAMP ENST00000297581 1.8609e-06 6.9818e-01 4.3800e-01 1.1560e+00 +ISCU ENST00000311893 4.1463e-02 4.4851e-01 2.0300e-01 1.1560e+00 +PCDHA13 ENST00000289272 2.4469e-14 8.2183e-01 5.9400e-01 1.1560e+00 +LRRC9 ENST00000445360 1.5993e-33 9.2048e-01 7.3700e-01 1.1570e+00 +TACR2 ENST00000373306 8.8349e-05 6.4118e-01 3.7500e-01 1.1570e+00 +XKRX ENST00000372956 3.1303e-04 6.1603e-01 3.4900e-01 1.1570e+00 +KHDC3L ENST00000370367 1.2327e-01 3.6981e-01 1.5000e-01 1.1570e+00 +C16orf97 ENST00000562818 4.1330e-02 4.4903e-01 2.0300e-01 1.1570e+00 +MSRB3 ENST00000355192 3.7660e-03 5.5097e-01 2.8700e-01 1.1570e+00 +OR8D4 ENST00000321355 1.2338e-01 3.6964e-01 1.5000e-01 1.1570e+00 +NDUFS4 ENST00000296684 3.1196e-04 6.1642e-01 3.5000e-01 1.1570e+00 +TRPA1 ENST00000262209 7.2309e-35 9.2451e-01 7.4300e-01 1.1570e+00 +SLC9A3R1 ENST00000262613 8.8416e-05 6.4110e-01 3.7500e-01 1.1570e+00 +C11orf88 ENST00000332814 3.1184e-04 6.1646e-01 3.5000e-01 1.1580e+00 +ABCC2 ENST00000370449 5.2025e-47 9.5304e-01 7.8800e-01 1.1580e+00 +PTPMT1 ENST00000326674 1.2681e-02 5.0698e-01 2.4900e-01 1.1580e+00 +ORMDL1 ENST00000325795 1.2321e-01 3.6989e-01 1.5000e-01 1.1580e+00 +TFAP2E ENST00000373235 2.4455e-05 6.6363e-01 3.9900e-01 1.1580e+00 +MSH3 ENST00000265081 7.4413e-31 9.1248e-01 7.2500e-01 1.1580e+00 +SBSPON ENST00000297354 6.7083e-06 6.8299e-01 4.2000e-01 1.1580e+00 +EFCAB6 ENST00000262726 1.1933e-45 9.5015e-01 7.8400e-01 1.1580e+00 +STX4 ENST00000313843 1.3021e-07 7.2817e-01 4.7300e-01 1.1580e+00 +H3F3A ENST00000366813 1.2310e-01 3.7005e-01 1.5000e-01 1.1580e+00 +SIAE ENST00000263593 7.7865e-12 7.9755e-01 5.6000e-01 1.1590e+00 +EPCAM ENST00000263735 1.2844e-07 7.2911e-01 4.7400e-01 1.1590e+00 +CLIC4 ENST00000374379 1.0866e-03 5.8737e-01 3.2100e-01 1.1590e+00 +ZNF226 ENST00000590089 5.2389e-15 8.2961e-01 6.0400e-01 1.1590e+00 +SLC12A9 ENST00000354161 1.1806e-15 8.3515e-01 6.1100e-01 1.1590e+00 +ZNF595 ENST00000526473 3.0550e-01 2.4756e-01 8.7000e-02 1.1590e+00 +MLNR ENST00000218721 1.2661e-02 5.0722e-01 2.4900e-01 1.1590e+00 +EIF4EBP2 ENST00000373218 3.0552e-01 2.4755e-01 8.7000e-02 1.1590e+00 +HPSE ENST00000405413 2.2660e-14 8.2439e-01 5.9600e-01 1.1590e+00 +BAG5 ENST00000337322 1.8100e-06 7.0046e-01 4.4000e-01 1.1590e+00 +SLC25A10 ENST00000331531 4.8646e-07 7.1537e-01 4.5700e-01 1.1590e+00 +SLC25A29 ENST00000359232 1.0861e-03 5.8742e-01 3.2100e-01 1.1590e+00 +FAM153A ENST00000440605 6.6975e-06 6.8314e-01 4.2000e-01 1.1590e+00 +CEP44 ENST00000457424 1.2728e-07 7.2974e-01 4.7400e-01 1.1600e+00 +CMTR2 ENST00000338099 5.3475e-10 7.7361e-01 5.2800e-01 1.1600e+00 +HSD17B7 ENST00000254521 6.6475e-06 6.8381e-01 4.2100e-01 1.1600e+00 +FAM169B ENST00000558256 1.2612e-02 5.0779e-01 2.4900e-01 1.1600e+00 +TPBG ENST00000369750 1.2627e-02 5.0761e-01 2.4900e-01 1.1600e+00 +MRO ENST00000436348 1.7975e-06 7.0104e-01 4.4000e-01 1.1600e+00 +GYPA ENST00000360771 1.0811e-03 5.8800e-01 3.2100e-01 1.1600e+00 +SLX1A ENST00000251303 1.2268e-01 3.7068e-01 1.5000e-01 1.1600e+00 +ZNF675 ENST00000359788 1.2265e-01 3.7072e-01 1.5000e-01 1.1600e+00 +ZNF200 ENST00000431561 1.7956e-06 7.0112e-01 4.4000e-01 1.1600e+00 +CHTF18 ENST00000262315 3.0747e-28 9.0560e-01 7.1200e-01 1.1610e+00 +ZNHIT6 ENST00000370574 7.5337e-12 7.9890e-01 5.6100e-01 1.1610e+00 +GCNT2 ENST00000379597 2.4065e-05 6.6520e-01 4.0000e-01 1.1610e+00 +DFFA ENST00000377038 8.6585e-05 6.4333e-01 3.7700e-01 1.1610e+00 +RHOB ENST00000272233 1.2253e-01 3.7091e-01 1.5100e-01 1.1610e+00 +AC006547.14 ENST00000439765 4.7950e-07 7.1646e-01 4.5800e-01 1.1610e+00 +TMED6 ENST00000288025 8.6323e-05 6.4365e-01 3.7700e-01 1.1610e+00 +RPUSD4 ENST00000298317 4.7321e-07 7.1745e-01 4.5900e-01 1.1620e+00 +ANKK1 ENST00000303941 7.4008e-12 7.9963e-01 5.6200e-01 1.1620e+00 +PCDHA11 ENST00000398640 5.4635e-17 8.4759e-01 6.2700e-01 1.1620e+00 +ADAM28 ENST00000265769 2.9634e-24 8.8978e-01 6.8800e-01 1.1620e+00 +MCAT ENST00000290429 3.0611e-04 6.1861e-01 3.5100e-01 1.1620e+00 +PLEKHF1 ENST00000436066 1.2523e-02 5.0884e-01 2.5000e-01 1.1620e+00 +GDAP1 ENST00000220822 3.2448e-08 7.4349e-01 4.9000e-01 1.1620e+00 +SYNM ENST00000336292 3.0339e-24 8.8926e-01 6.8800e-01 1.1620e+00 +TULP2 ENST00000221399 2.4676e-16 8.4247e-01 6.2000e-01 1.1620e+00 +PIGX ENST00000296333 2.3843e-05 6.6611e-01 4.0100e-01 1.1620e+00 +OCEL1 ENST00000215061 3.0592e-04 6.1869e-01 3.5100e-01 1.1620e+00 +ADM ENST00000528655 4.0831e-02 4.5100e-01 2.0400e-01 1.1620e+00 +SERPINB11 ENST00000544088 4.7328e-07 7.1744e-01 4.5900e-01 1.1620e+00 +GNE ENST00000396594 2.4844e-16 8.4227e-01 6.2000e-01 1.1620e+00 +MLC1 ENST00000311597 3.2425e-08 7.4354e-01 4.9000e-01 1.1620e+00 +ACADL ENST00000233710 1.7430e-12 8.0692e-01 5.7100e-01 1.1620e+00 +LDLRAP1 ENST00000374338 6.5037e-06 6.8577e-01 4.2200e-01 1.1630e+00 +C2orf62 ENST00000289388 2.0831e-09 7.6562e-01 5.1700e-01 1.1630e+00 +ELL3 ENST00000319359 1.6997e-12 8.0789e-01 5.7200e-01 1.1630e+00 +PPAN ENST00000556468 1.7244e-12 8.0733e-01 5.7200e-01 1.1630e+00 +PPAN-P2RY11 ENST00000393796 1.7244e-12 8.0733e-01 5.7200e-01 1.1630e+00 +CA13 ENST00000321764 1.7599e-06 7.0277e-01 4.4100e-01 1.1630e+00 +BAG1 ENST00000472232 6.5264e-06 6.8546e-01 4.2200e-01 1.1630e+00 +FUT11 ENST00000372841 1.7598e-06 7.0278e-01 4.4100e-01 1.1630e+00 +SLC24A5 ENST00000341459 5.1503e-10 7.7548e-01 5.3000e-01 1.1630e+00 +SLC19A1 ENST00000311124 6.4655e-06 6.8630e-01 4.2200e-01 1.1640e+00 +NPSR1 ENST00000359791 2.0518e-09 7.6643e-01 5.1800e-01 1.1640e+00 +MEGT1 ENST00000503322 1.2340e-07 7.3189e-01 4.7600e-01 1.1640e+00 +TRIM62 ENST00000291416 3.1787e-08 7.4480e-01 4.9100e-01 1.1640e+00 +TIGD1 ENST00000408957 3.6808e-03 5.5410e-01 2.8900e-01 1.1640e+00 +LTF ENST00000231751 1.2665e-21 8.7797e-01 6.7000e-01 1.1640e+00 +SLC22A18 ENST00000380574 6.4580e-06 6.8641e-01 4.2200e-01 1.1640e+00 +TPD52 ENST00000379097 8.4929e-05 6.4539e-01 3.7800e-01 1.1640e+00 +SAMD15 ENST00000216471 1.2383e-10 7.8524e-01 5.4200e-01 1.1640e+00 +C19orf55 ENST00000544099 5.0594e-10 7.7637e-01 5.3000e-01 1.1650e+00 +LGALS9B ENST00000324290 8.4381e-05 6.4608e-01 3.7800e-01 1.1650e+00 +TSPAN2 ENST00000369516 2.3496e-05 6.6755e-01 4.0100e-01 1.1650e+00 +CRTAM ENST00000227348 8.0626e-09 7.5661e-01 5.0500e-01 1.1650e+00 +ZC3HAV1L ENST00000275766 1.0577e-03 5.9076e-01 3.2200e-01 1.1650e+00 +GTF2IRD2 ENST00000405086 3.1521e-08 7.4533e-01 4.9100e-01 1.1650e+00 +CBLN2 ENST00000269503 1.2162e-01 3.7226e-01 1.5100e-01 1.1650e+00 +NOD1 ENST00000222823 2.4602e-18 8.5909e-01 6.4200e-01 1.1650e+00 +GRHPR ENST00000318158 4.6393e-07 7.1895e-01 4.6000e-01 1.1650e+00 +POLR3GL ENST00000369314 2.3404e-05 6.6793e-01 4.0200e-01 1.1650e+00 +PCDHB17 ENST00000539533 2.3485e-05 6.6759e-01 4.0100e-01 1.1650e+00 +CYP2E1 ENST00000463117 8.0688e-09 7.5656e-01 5.0500e-01 1.1650e+00 +CRYZL1 ENST00000381554 2.0125e-09 7.6747e-01 5.1900e-01 1.1660e+00 +FAM83D ENST00000217429 3.1280e-08 7.4582e-01 4.9200e-01 1.1660e+00 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1.0081e-23 8.9371e-01 6.8900e-01 1.1710e+00 +FAM153B ENST00000515817 2.9703e-08 7.4910e-01 4.9400e-01 1.1710e+00 +SNRNP48 ENST00000342415 7.5727e-09 7.6027e-01 5.0800e-01 1.1710e+00 +TMEM41A ENST00000421852 2.9269e-04 6.2384e-01 3.5400e-01 1.1710e+00 +DBF4B ENST00000315005 2.6770e-11 7.9830e-01 5.5600e-01 1.1710e+00 +PMM1 ENST00000216259 1.6587e-06 7.0765e-01 4.4400e-01 1.1710e+00 +FAM227A ENST00000406767 1.9662e-16 8.4931e-01 6.2500e-01 1.1710e+00 +CPT2 ENST00000371486 4.5980e-10 7.8115e-01 5.3400e-01 1.1720e+00 +ABRA ENST00000311955 6.1508e-06 6.9079e-01 4.2500e-01 1.1720e+00 +DMRT3 ENST00000190165 6.1531e-06 6.9076e-01 4.2500e-01 1.1720e+00 +HELB ENST00000247815 9.5899e-26 9.0360e-01 7.0300e-01 1.1720e+00 +LTB4R ENST00000396789 1.1994e-01 3.7485e-01 1.5200e-01 1.1720e+00 +ACADSB ENST00000358776 2.6565e-11 7.9863e-01 5.5600e-01 1.1720e+00 +GSTM3 ENST00000540225 4.3638e-07 7.2357e-01 4.6300e-01 1.1720e+00 +TKTL2 ENST00000280605 1.1378e-07 7.3749e-01 4.7900e-01 1.1720e+00 +OR10T2 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1.0389e-07 7.4378e-01 4.8300e-01 1.1820e+00 +FAM71F1 ENST00000315184 1.0457e-07 7.4333e-01 4.8300e-01 1.1820e+00 +PCDHGA7 ENST00000518325 1.2273e-12 8.2054e-01 5.8100e-01 1.1820e+00 +IL13RA2 ENST00000371936 4.0210e-07 7.2974e-01 4.6700e-01 1.1820e+00 +LURAP1 ENST00000371980 1.1822e-02 5.1752e-01 2.5400e-01 1.1820e+00 +EFCC1 ENST00000480450 1.0453e-07 7.4335e-01 4.8300e-01 1.1820e+00 +SSUH2 ENST00000544814 3.9939e-10 7.8819e-01 5.3800e-01 1.1820e+00 +EIF1AY ENST00000361365 5.5208e-01 0.0000e+00 0.0000e+00 1.1820e+00 +SEL1L2 ENST00000378072 7.3382e-20 8.8010e-01 6.6300e-01 1.1820e+00 +TMEM179B ENST00000333449 9.8906e-04 5.9933e-01 3.2700e-01 1.1820e+00 +TXNDC17 ENST00000250101 3.8897e-02 4.5902e-01 2.0800e-01 1.1820e+00 +EFCAB1 ENST00000262103 2.7724e-04 6.3022e-01 3.5700e-01 1.1830e+00 +PNLIPRP2 ENST00000537242 3.9766e-10 7.8841e-01 5.3900e-01 1.1830e+00 +C6orf10 ENST00000447241 1.4756e-16 8.5806e-01 6.3100e-01 1.1830e+00 +FARP2 ENST00000264042 4.6425e-36 9.4703e-01 7.6300e-01 1.1830e+00 +TAPBP ENST00000426633 6.6044e-09 7.6825e-01 5.1300e-01 1.1830e+00 +KLRG1 ENST00000356986 3.4459e-03 5.6325e-01 2.9300e-01 1.1830e+00 +OR6A2 ENST00000332601 1.1773e-01 3.7832e-01 1.5400e-01 1.1830e+00 +SRCRB4D ENST00000275560 5.1832e-12 8.1425e-01 5.7200e-01 1.1830e+00 +CALY ENST00000252939 3.8696e-02 4.5989e-01 2.0800e-01 1.1840e+00 +IFIT3 ENST00000371818 1.1732e-01 3.7897e-01 1.5400e-01 1.1840e+00 +PCDHGA4 ENST00000571252 2.1897e-11 8.0707e-01 5.6200e-01 1.1840e+00 +BBS4 ENST00000268057 1.4549e-16 8.5849e-01 6.3200e-01 1.1840e+00 +ALOX15B ENST00000380183 1.4819e-18 8.7321e-01 6.5200e-01 1.1840e+00 +METTL6 ENST00000443029 2.1044e-05 6.7841e-01 4.0800e-01 1.1840e+00 +NINJ1 ENST00000375446 1.1745e-01 3.7876e-01 1.5400e-01 1.1840e+00 +RASD1 ENST00000225688 3.8736e-02 4.5971e-01 2.0800e-01 1.1840e+00 +TRMT10A ENST00000273962 3.8911e-10 7.8950e-01 5.3900e-01 1.1840e+00 +C8A ENST00000361249 6.5536e-16 8.5358e-01 6.2500e-01 1.1840e+00 +C2orf48 ENST00000381786 2.9640e-01 2.5392e-01 8.9000e-02 1.1850e+00 +PNLIPRP3 ENST00000369230 2.1705e-11 8.0746e-01 5.6200e-01 1.1850e+00 +EID2 ENST00000390658 2.9648e-01 2.5387e-01 8.9000e-02 1.1850e+00 +LMAN1L ENST00000309664 2.6071e-13 8.3013e-01 5.9200e-01 1.1850e+00 +TGM2 ENST00000361475 6.8118e-18 8.6874e-01 6.4600e-01 1.1850e+00 +SPINK4 ENST00000379721 2.9634e-01 2.5396e-01 8.9000e-02 1.1860e+00 +MPC1 ENST00000360961 3.8495e-02 4.6076e-01 2.0900e-01 1.1860e+00 +STYK1 ENST00000075503 9.1009e-11 7.9959e-01 5.5200e-01 1.1860e+00 +ARMCX6 ENST00000539247 1.1709e-01 3.7934e-01 1.5400e-01 1.1860e+00 +TK2 ENST00000451102 3.9054e-07 7.3195e-01 4.6800e-01 1.1860e+00 +HFE ENST00000357618 2.5587e-08 7.5856e-01 5.0000e-01 1.1860e+00 +EIF1AD ENST00000312234 3.4032e-03 5.6500e-01 2.9400e-01 1.1860e+00 +SGCZ ENST00000382080 6.4001e-09 7.7008e-01 5.1400e-01 1.1860e+00 +CYP2R1 ENST00000334636 3.7930e-10 7.9077e-01 5.4000e-01 1.1860e+00 +RAP2C ENST00000342983 2.9631e-01 2.5399e-01 8.9000e-02 1.1860e+00 +GPR157 ENST00000377411 9.7453e-04 6.0123e-01 3.2800e-01 1.1860e+00 +HIBCH ENST00000359678 2.5766e-13 8.3057e-01 5.9200e-01 1.1860e+00 +ABCA8 ENST00000269080 1.6090e-52 9.8450e-01 8.2100e-01 1.1860e+00 +ACD ENST00000393919 1.1148e-12 8.2430e-01 5.8400e-01 1.1870e+00 +PDE6B ENST00000496514 2.6155e-27 9.2018e-01 7.2000e-01 1.1870e+00 +TAC3 ENST00000458521 1.1650e-02 5.1977e-01 2.5500e-01 1.1870e+00 +THUMPD2 ENST00000505747 1.5442e-09 7.8175e-01 5.2800e-01 1.1870e+00 +C11orf48 ENST00000532208 2.0614e-05 6.8045e-01 4.0900e-01 1.1870e+00 +WDR31 ENST00000374193 1.5482e-09 7.8161e-01 5.2800e-01 1.1870e+00 +ADAT1 ENST00000307921 2.5388e-13 8.3113e-01 5.9300e-01 1.1870e+00 +C1orf35 ENST00000272139 7.5680e-05 6.5780e-01 3.8500e-01 1.1870e+00 +CNTLN ENST00000380647 3.9521e-49 9.7974e-01 8.1200e-01 1.1870e+00 +C7orf73 ENST00000507606 5.5075e-01 0.0000e+00 0.0000e+00 1.1870e+00 +OR2B6 ENST00000244623 3.4004e-03 5.6512e-01 2.9400e-01 1.1870e+00 +CAPZA3 ENST00000317658 9.7097e-04 6.0171e-01 3.2800e-01 1.1870e+00 +PSPH ENST00000395471 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ENST00000228820 6.1763e-09 7.7215e-01 5.1600e-01 1.1890e+00 +SLC25A30 ENST00000519676 6.1722e-09 7.7219e-01 5.1600e-01 1.1890e+00 +PRF1 ENST00000441259 5.4875e-06 7.0110e-01 4.3200e-01 1.1890e+00 +YEATS4 ENST00000247843 7.4640e-05 6.5930e-01 3.8600e-01 1.1890e+00 +PCDHA12 ENST00000398631 2.4185e-13 8.3294e-01 5.9400e-01 1.1890e+00 +CD109 ENST00000287097 2.2707e-44 9.7153e-01 7.9800e-01 1.1890e+00 +TMEM40 ENST00000314124 2.4842e-08 7.6043e-01 5.0100e-01 1.1890e+00 +PRODH2 ENST00000301175 2.4520e-13 8.3242e-01 5.9400e-01 1.1890e+00 +ATP6V0E2 ENST00000421974 2.9517e-01 2.5481e-01 8.9000e-02 1.1890e+00 +WDR89 ENST00000394942 7.4832e-05 6.5902e-01 3.8600e-01 1.1890e+00 +CTD-2410N18.5 ENST00000519718 1.1635e-01 3.8055e-01 1.5400e-01 1.1890e+00 +PPIH ENST00000304979 7.4626e-05 6.5932e-01 3.8600e-01 1.1890e+00 +ABHD16B ENST00000369916 7.4371e-05 6.5970e-01 3.8600e-01 1.1900e+00 +AK8 ENST00000298545 2.0053e-11 8.1093e-01 5.6500e-01 1.1900e+00 +ACBD7 ENST00000356189 1.1605e-01 3.8103e-01 1.5500e-01 1.1900e+00 +PRKAG3 ENST00000529249 4.6180e-12 8.1902e-01 5.7500e-01 1.1900e+00 +CLDN22 ENST00000323319 3.8131e-02 4.6237e-01 2.1000e-01 1.1900e+00 +CMTM7 ENST00000334983 3.8169e-02 4.6220e-01 2.0900e-01 1.1900e+00 +CENPA ENST00000335756 1.1536e-02 5.2128e-01 2.5600e-01 1.1900e+00 +IQCF5 ENST00000446461 1.1551e-02 5.2108e-01 2.5600e-01 1.1900e+00 +APOA4 ENST00000357780 5.4536e-06 7.0167e-01 4.3200e-01 1.1900e+00 +HDDC2 ENST00000398153 2.0302e-05 6.8196e-01 4.1000e-01 1.1900e+00 +GANC ENST00000318010 7.5457e-35 9.4933e-01 7.6200e-01 1.1910e+00 +SLC2A5 ENST00000377424 3.5691e-10 7.9382e-01 5.4200e-01 1.1910e+00 +TRDMT1 ENST00000377799 3.5589e-10 7.9396e-01 5.4200e-01 1.1910e+00 +PLA2G12B ENST00000373032 9.5391e-04 6.0400e-01 3.3000e-01 1.1910e+00 +SFXN3 ENST00000224807 2.4372e-08 7.6164e-01 5.0200e-01 1.1910e+00 +MUTYH ENST00000372098 1.2619e-18 8.7777e-01 6.5600e-01 1.1910e+00 +ZKSCAN3 ENST00000377255 1.9697e-11 8.1171e-01 5.6500e-01 1.1910e+00 +CYP26A1 ENST00000224356 8.4269e-11 8.0318e-01 5.5400e-01 1.1910e+00 +PGLYRP3 ENST00000290722 9.6075e-08 7.4918e-01 4.8700e-01 1.1910e+00 +EPPIN ENST00000555685 7.4025e-05 6.6020e-01 3.8600e-01 1.1910e+00 +EPPIN-WFDC6 ENST00000504988 7.4025e-05 6.6020e-01 3.8600e-01 1.1910e+00 +ERAP2 ENST00000437043 1.0028e-28 9.2859e-01 7.3000e-01 1.1910e+00 +DDX49 ENST00000247003 5.2505e-14 8.4068e-01 6.0400e-01 1.1910e+00 +APOM ENST00000375916 9.5567e-04 6.0376e-01 3.3000e-01 1.1910e+00 +RNF39 ENST00000244360 2.0207e-05 6.8243e-01 4.1000e-01 1.1910e+00 +DGUOK ENST00000264093 3.7122e-07 7.3578e-01 4.7000e-01 1.1920e+00 +MAP9 ENST00000311277 2.5444e-15 8.5315e-01 6.2100e-01 1.1920e+00 +RPF1 ENST00000370654 2.3931e-08 7.6280e-01 5.0300e-01 1.1920e+00 +EFCAB7 ENST00000371088 2.6115e-17 8.6941e-01 6.4300e-01 1.1920e+00 +EFNA2 ENST00000215368 3.8008e-02 4.6291e-01 2.1000e-01 1.1920e+00 +AWAT1 ENST00000374521 2.6614e-04 6.3506e-01 3.6000e-01 1.1920e+00 +OPRD1 ENST00000234961 3.3233e-03 5.6836e-01 2.9600e-01 1.1930e+00 +BTN3A1 ENST00000289361 5.8712e-09 7.7511e-01 5.1800e-01 1.1930e+00 +IGFBP1 ENST00000275525 9.4677e-04 6.0498e-01 3.3000e-01 1.1930e+00 +STARD6 ENST00000581310 2.6527e-04 6.3545e-01 3.6000e-01 1.1930e+00 +TSTD2 ENST00000341170 1.8987e-11 8.1332e-01 5.6600e-01 1.1930e+00 +ANGPTL6 ENST00000253109 2.3705e-08 7.6340e-01 5.0300e-01 1.1930e+00 +TRAPPC12 ENST00000324266 5.3624e-16 8.5999e-01 6.2900e-01 1.1930e+00 +SH2D7 ENST00000328828 2.3722e-08 7.6335e-01 5.0300e-01 1.1930e+00 +FAM163A ENST00000341785 1.1550e-01 3.8193e-01 1.5500e-01 1.1930e+00 +RUFY4 ENST00000374155 5.0653e-14 8.4197e-01 6.0500e-01 1.1930e+00 +SLAMF8 ENST00000289707 5.3410e-06 7.0356e-01 4.3300e-01 1.1930e+00 +ANKRD9 ENST00000286918 2.9363e-01 2.5594e-01 9.0000e-02 1.1940e+00 +C3orf30 ENST00000295622 5.8545e-09 7.7527e-01 5.1800e-01 1.1940e+00 +CCDC171 ENST00000380701 3.0350e-47 9.8160e-01 8.1100e-01 1.1940e+00 +CD68 ENST00000250092 1.4063e-06 7.2129e-01 4.5300e-01 1.1940e+00 +CALHM3 ENST00000369783 3.3060e-03 5.6910e-01 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1.5324e-15 8.7023e-01 6.3300e-01 1.2150e+00 +CCDC66 ENST00000394672 5.6053e-36 9.7030e-01 7.8000e-01 1.2150e+00 +FSHR ENST00000406846 1.3689e-11 8.2778e-01 5.7600e-01 1.2150e+00 +RNH1 ENST00000534797 2.5541e-10 8.1061e-01 5.5400e-01 1.2160e+00 +TDRD6 ENST00000316081 5.4437e-45 9.9379e-01 8.1600e-01 1.2160e+00 +BEX1 ENST00000372728 5.4273e-01 0.0000e+00 0.0000e+00 1.2160e+00 +GOLGA8N ENST00000448387 2.8645e-01 2.6135e-01 9.2000e-02 1.2160e+00 +FOXL1 ENST00000320241 3.5865e-02 4.7289e-01 2.1400e-01 1.2160e+00 +NAGK ENST00000455662 4.5517e-09 7.8996e-01 5.2800e-01 1.2160e+00 +OR10Z1 ENST00000361284 1.1093e-01 3.8973e-01 1.5800e-01 1.2160e+00 +CHMP2B ENST00000263780 4.6203e-06 7.1675e-01 4.4100e-01 1.2160e+00 +AIMP1 ENST00000394701 3.0411e-07 7.5086e-01 4.8000e-01 1.2160e+00 +ZNF829 ENST00000520965 5.8965e-11 8.1995e-01 5.6600e-01 1.2160e+00 +GRAP ENST00000284154 1.1064e-01 3.9024e-01 1.5800e-01 1.2170e+00 +PLSCR2 ENST00000497985 1.1863e-06 7.3540e-01 4.6200e-01 1.2170e+00 +HS1BP3 ENST00000304031 1.1873e-06 7.3533e-01 4.6200e-01 1.2170e+00 +CEACAM6 ENST00000199764 1.1884e-06 7.3525e-01 4.6200e-01 1.2170e+00 +PDLIM3 ENST00000284770 3.0320e-07 7.5109e-01 4.8000e-01 1.2170e+00 +DPH7 ENST00000277540 1.8603e-08 7.7876e-01 5.1300e-01 1.2170e+00 +PPFIBP2 ENST00000299492 6.0040e-34 9.6569e-01 7.7200e-01 1.2170e+00 +IRG1 ENST00000377462 4.5659e-06 7.1784e-01 4.4200e-01 1.2170e+00 +STRA13 ENST00000392359 1.1069e-01 3.9016e-01 1.5800e-01 1.2170e+00 +GNG3 ENST00000294117 5.4217e-01 0.0000e+00 0.0000e+00 1.2180e+00 +RP11-433C9.2 ENST00000419960 3.5697e-02 4.7372e-01 2.1500e-01 1.2180e+00 +RP11-477N12.3 ENST00000399363 2.3666e-04 6.4917e-01 3.6800e-01 1.2180e+00 +DGAT1 ENST00000332324 1.4082e-17 8.8841e-01 6.5700e-01 1.2180e+00 +TMEM244 ENST00000438392 1.0646e-02 5.3385e-01 2.6200e-01 1.2180e+00 +PLA2G2C ENST00000429261 3.5718e-02 4.7361e-01 2.1500e-01 1.2180e+00 +ASB2 ENST00000555019 6.7740e-15 8.6589e-01 6.2600e-01 1.2180e+00 +C1QL2 ENST00000272520 3.5707e-02 4.7367e-01 2.1500e-01 1.2180e+00 +RAD51D ENST00000590016 1.0631e-09 8.0189e-01 5.4200e-01 1.2180e+00 +LRRC23 ENST00000007969 1.8429e-08 7.7936e-01 5.1400e-01 1.2180e+00 +CCDC81 ENST00000445632 5.0855e-23 9.2346e-01 7.0700e-01 1.2190e+00 +MAP6D1 ENST00000318631 1.1028e-01 3.9089e-01 1.5900e-01 1.2190e+00 +CD3G ENST00000532917 1.7120e-05 6.9900e-01 4.2000e-01 1.2190e+00 +EFS ENST00000216733 1.8222e-08 7.8007e-01 5.1400e-01 1.2190e+00 +MLF1 ENST00000392822 4.3955e-09 7.9200e-01 5.2900e-01 1.2190e+00 +ZNF71 ENST00000328070 1.8350e-08 7.7963e-01 5.1400e-01 1.2190e+00 +PGAM5 ENST00000498926 6.4116e-05 6.7596e-01 3.9600e-01 1.2190e+00 +TMPPE ENST00000342462 8.5170e-04 6.1891e-01 3.3800e-01 1.2200e+00 +LRRIQ3 ENST00000354431 1.3740e-13 8.5439e-01 6.0900e-01 1.2200e+00 +LTK ENST00000263800 9.2860e-26 9.3716e-01 7.2700e-01 1.2200e+00 +RP11-162P23.2 ENST00000546840 4.4737e-06 7.1970e-01 4.4300e-01 1.2200e+00 +SPRY1 ENST00000394339 3.0398e-03 5.8118e-01 3.0300e-01 1.2200e+00 +ZNF480 ENST00000595962 3.5570e-02 4.7434e-01 2.1500e-01 1.2200e+00 +UGT2B4 ENST00000305107 4.3777e-09 7.9224e-01 5.2900e-01 1.2200e+00 +ZNF692 ENST00000451251 1.2582e-11 8.3153e-01 5.7900e-01 1.2200e+00 +SKA1 ENST00000285116 1.7022e-05 6.9958e-01 4.2100e-01 1.2200e+00 +BCAT2 ENST00000316273 2.8260e-12 8.3956e-01 5.9000e-01 1.2200e+00 +PCOLCE2 ENST00000295992 5.4571e-11 8.2361e-01 5.6800e-01 1.2210e+00 +HEMGN ENST00000259456 1.0292e-09 8.0365e-01 5.4300e-01 1.2210e+00 +MRPL53 ENST00000258105 2.8485e-01 2.6259e-01 9.2000e-02 1.2210e+00 +ADRA2B ENST00000409345 4.4533e-06 7.2012e-01 4.4300e-01 1.2210e+00 +LDHD ENST00000300051 1.3494e-13 8.5508e-01 6.1000e-01 1.2210e+00 +CD300A ENST00000360141 1.1537e-06 7.3772e-01 4.6300e-01 1.2210e+00 +KLHL30 ENST00000409223 5.4481e-11 8.2368e-01 5.6800e-01 1.2210e+00 +ZNF789 ENST00000331410 2.9215e-07 7.5390e-01 4.8200e-01 1.2210e+00 +UPK3B ENST00000419923 2.3426e-04 6.5041e-01 3.6900e-01 1.2210e+00 +KRT39 ENST00000355612 6.2024e-13 8.4758e-01 6.0000e-01 1.2210e+00 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9.0112e-01 6.7300e-01 1.2220e+00 +ACTA1 ENST00000366684 1.1385e-06 7.3882e-01 4.6400e-01 1.2230e+00 +OVCH1 ENST00000318184 3.9432e-36 9.7695e-01 7.8600e-01 1.2230e+00 +CHRFAM7A ENST00000299847 2.3228e-04 6.5144e-01 3.6900e-01 1.2230e+00 +C12orf40 ENST00000324616 1.2906e-13 8.5680e-01 6.1100e-01 1.2230e+00 +MFRP ENST00000555262 1.3093e-15 8.7564e-01 6.3700e-01 1.2230e+00 +TFPI2 ENST00000222543 8.4274e-04 6.2032e-01 3.3900e-01 1.2230e+00 +CEP89 ENST00000305768 8.3504e-26 9.3973e-01 7.2900e-01 1.2230e+00 +NFAM1 ENST00000329021 6.2864e-05 6.7815e-01 3.9700e-01 1.2230e+00 +SPAG6 ENST00000376624 1.2980e-13 8.5658e-01 6.1100e-01 1.2230e+00 +SCG5 ENST00000300175 6.2865e-05 6.7814e-01 3.9700e-01 1.2230e+00 +EFCAB11 ENST00000316738 2.3166e-04 6.5177e-01 3.7000e-01 1.2230e+00 +AK2 ENST00000354858 6.2706e-05 6.7842e-01 3.9700e-01 1.2230e+00 +CTC-454I21.3 ENST00000588873 1.0952e-01 3.9225e-01 1.5900e-01 1.2230e+00 +GKN2 ENST00000328895 2.3223e-04 6.5147e-01 3.6900e-01 1.2230e+00 +TMEM79 ENST00000405535 4.3888e-06 7.2145e-01 4.4400e-01 1.2230e+00 +C12orf45 ENST00000552951 1.0456e-02 5.3673e-01 2.6300e-01 1.2240e+00 +CATSPER2 ENST00000321596 5.8613e-17 8.8723e-01 6.5300e-01 1.2240e+00 +CLDN10 ENST00000299339 8.3876e-04 6.2095e-01 3.3900e-01 1.2240e+00 +PIWIL3 ENST00000332271 5.3547e-32 9.6436e-01 7.6600e-01 1.2240e+00 +SLC13A1 ENST00000194130 1.2291e-17 8.9269e-01 6.6000e-01 1.2240e+00 +SEC22C ENST00000264454 2.8553e-07 7.5564e-01 4.8300e-01 1.2240e+00 +GTPBP3 ENST00000358792 4.1886e-09 7.9482e-01 5.3100e-01 1.2240e+00 +PRSS38 ENST00000366757 6.2675e-05 6.7848e-01 3.9700e-01 1.2240e+00 +KCNA10 ENST00000369771 8.3822e-04 6.2104e-01 3.3900e-01 1.2240e+00 +TAPBPL ENST00000266556 2.3058e-10 8.1577e-01 5.5700e-01 1.2240e+00 +PLEKHG4B ENST00000283426 1.0827e-32 9.6690e-01 7.7000e-01 1.2240e+00 +NEK11 ENST00000383366 1.0374e-21 9.1930e-01 6.9800e-01 1.2240e+00 +GPR115 ENST00000283303 2.7656e-14 8.6406e-01 6.2100e-01 1.2240e+00 +OBFC1 ENST00000224950 2.2950e-10 8.1601e-01 5.5700e-01 1.2240e+00 +HAND1 ENST00000231121 1.0914e-01 3.9294e-01 1.5900e-01 1.2250e+00 +DUSP26 ENST00000256261 2.3011e-04 6.5259e-01 3.7000e-01 1.2250e+00 +GBP1 ENST00000370473 1.2564e-15 8.7707e-01 6.3800e-01 1.2250e+00 +C1QTNF2 ENST00000393975 8.3478e-04 6.2159e-01 3.3900e-01 1.2250e+00 +SLC12A8 ENST00000393469 5.3107e-19 9.0310e-01 6.7500e-01 1.2250e+00 +MCUR1 ENST00000379170 1.1206e-06 7.4015e-01 4.6500e-01 1.2250e+00 +SLC7A4 ENST00000382932 2.8317e-07 7.5626e-01 4.8400e-01 1.2250e+00 +FAXDC2 ENST00000326080 1.7164e-08 7.8387e-01 5.1700e-01 1.2250e+00 +SBDS ENST00000246868 6.2076e-05 6.7954e-01 3.9800e-01 1.2250e+00 +GJC2 ENST00000366714 1.0438e-02 5.3701e-01 2.6300e-01 1.2250e+00 +SGOL1 ENST00000263753 2.5902e-12 8.4325e-01 5.9200e-01 1.2250e+00 +CLN5 ENST00000377453 1.7111e-08 7.8407e-01 5.1700e-01 1.2260e+00 +EPX ENST00000225371 2.2664e-20 9.1266e-01 6.8800e-01 1.2260e+00 +LEPRE1 ENST00000236040 2.2869e-20 9.1241e-01 6.8800e-01 1.2260e+00 +MYF5 ENST00000228644 2.2918e-04 6.5308e-01 3.7000e-01 1.2260e+00 +PLB1 ENST00000327757 1.7315e-72 1.0440e+00 8.9200e-01 1.2260e+00 +ZNF154 ENST00000512439 2.8224e-07 7.5651e-01 4.8400e-01 1.2260e+00 +NAA11 ENST00000286794 1.0415e-02 5.3736e-01 2.6400e-01 1.2260e+00 +SYTL3 ENST00000297239 2.2377e-20 9.1303e-01 6.8800e-01 1.2260e+00 +STARD5 ENST00000302824 6.1762e-05 6.8011e-01 3.9800e-01 1.2260e+00 +ZNF19 ENST00000288177 4.3113e-06 7.2309e-01 4.4500e-01 1.2260e+00 +CCDC153 ENST00000503566 1.6504e-05 7.0270e-01 4.2300e-01 1.2260e+00 +PTPRCAP ENST00000326294 5.4001e-01 0.0000e+00 0.0000e+00 1.2260e+00 +TTLL3 ENST00000426895 1.0765e-19 9.0858e-01 6.8200e-01 1.2260e+00 +WDR49 ENST00000308378 1.0465e-19 9.0941e-01 6.8200e-01 1.2270e+00 +GPR110 ENST00000371253 2.0011e-22 9.2513e-01 7.0600e-01 1.2270e+00 +AANAT ENST00000250615 2.9690e-03 5.8463e-01 3.0400e-01 1.2270e+00 +TTC23L ENST00000505624 5.0245e-11 8.2752e-01 5.7100e-01 1.2270e+00 +SLC27A1 ENST00000252595 2.5752e-16 8.8411e-01 6.4700e-01 1.2270e+00 +ANKRD7 ENST00000265224 4.2975e-06 7.2338e-01 4.4500e-01 1.2270e+00 +HOXA5 ENST00000222726 2.9693e-03 5.8462e-01 3.0400e-01 1.2270e+00 +IQCC ENST00000537469 4.0474e-09 7.9683e-01 5.3200e-01 1.2270e+00 +SAMSN1 ENST00000285670 5.0417e-11 8.2736e-01 5.7100e-01 1.2270e+00 +SIGLEC12 ENST00000291707 1.2163e-13 8.5910e-01 6.1300e-01 1.2270e+00 +RP11-723O4.6 ENST00000508239 2.1637e-10 8.1899e-01 5.5900e-01 1.2280e+00 +DPT ENST00000367817 4.2743e-06 7.2388e-01 4.4600e-01 1.2280e+00 +MFAP2 ENST00000375535 4.2671e-06 7.2403e-01 4.4600e-01 1.2280e+00 +POLR3K ENST00000293860 1.0849e-01 3.9412e-01 1.6000e-01 1.2280e+00 +ZNF275 ENST00000370251 2.2666e-04 6.5443e-01 3.7100e-01 1.2280e+00 +CHCHD7 ENST00000303759 3.4885e-02 4.7777e-01 2.1600e-01 1.2280e+00 +FTCD ENST00000291670 5.5230e-15 8.7319e-01 6.3100e-01 1.2280e+00 +KXD1 ENST00000602094 3.4926e-02 4.7756e-01 2.1600e-01 1.2280e+00 +TNFAIP6 ENST00000243347 1.0939e-06 7.4215e-01 4.6600e-01 1.2280e+00 +ANKRD42 ENST00000393392 2.1439e-10 8.1946e-01 5.6000e-01 1.2290e+00 +ATP6V1E2 ENST00000306448 2.9486e-03 5.8564e-01 3.0500e-01 1.2290e+00 +ARL10 ENST00000310389 8.2222e-04 6.2362e-01 3.4000e-01 1.2290e+00 +KRT38 ENST00000246646 3.9395e-09 7.9841e-01 5.3300e-01 1.2290e+00 +C15orf62 ENST00000344320 3.4814e-02 4.7813e-01 2.1700e-01 1.2290e+00 +MRPS36 ENST00000256441 1.0812e-01 3.9482e-01 1.6000e-01 1.2300e+00 +EME1 ENST00000393271 2.4963e-14 8.6788e-01 6.2300e-01 1.2300e+00 +APOF ENST00000398189 1.0295e-02 5.3924e-01 2.6500e-01 1.2300e+00 +MEDAG ENST00000380482 1.6145e-05 7.0491e-01 4.2400e-01 1.2300e+00 +LANCL1 ENST00000443314 1.0827e-11 8.3825e-01 5.8400e-01 1.2300e+00 +ARL14EPL ENST00000601302 3.4771e-02 4.7835e-01 2.1700e-01 1.2300e+00 +ITIH1 ENST00000273283 2.0755e-31 9.6691e-01 7.6600e-01 1.2300e+00 +SIGLEC1 ENST00000344754 5.3298e-46 1.0069e+00 8.2800e-01 1.2300e+00 +XRCC6BP1 ENST00000300145 1.6095e-05 7.0523e-01 4.2400e-01 1.2300e+00 +KIAA1407 ENST00000295878 4.1656e-32 9.6962e-01 7.7000e-01 1.2300e+00 +ADRA2A ENST00000280155 8.1816e-04 6.2429e-01 3.4100e-01 1.2310e+00 +GJE1 ENST00000450456 1.0802e-01 3.9500e-01 1.6000e-01 1.2310e+00 +GRSF1 ENST00000254799 1.0660e-11 8.3895e-01 5.8400e-01 1.2310e+00 +AKNAD1 ENST00000370001 3.6153e-23 9.3243e-01 7.1400e-01 1.2310e+00 +LCTL ENST00000341509 9.6021e-20 9.1195e-01 6.8400e-01 1.2310e+00 +NAAA ENST00000286733 2.0742e-10 8.2113e-01 5.6100e-01 1.2320e+00 +LRRC29 ENST00000409037 2.2334e-04 6.5623e-01 3.7200e-01 1.2320e+00 +NFU1 ENST00000410022 4.1487e-06 7.2661e-01 4.4700e-01 1.2320e+00 +CORIN ENST00000273857 6.5072e-35 9.8032e-01 7.8500e-01 1.2320e+00 +ZNF260 ENST00000523638 6.0163e-05 6.8303e-01 4.0000e-01 1.2320e+00 +SPEF1 ENST00000379756 1.5956e-05 7.0611e-01 4.2500e-01 1.2320e+00 +ENTPD8 ENST00000371506 1.0421e-11 8.3997e-01 5.8500e-01 1.2320e+00 +MUT ENST00000274813 1.7087e-22 9.2939e-01 7.0900e-01 1.2320e+00 +KRT3 ENST00000417996 8.9951e-10 8.1096e-01 5.4800e-01 1.2320e+00 +TCTN1 ENST00000397659 1.0708e-15 8.8263e-01 6.4200e-01 1.2330e+00 +CHST5 ENST00000336257 2.2148e-04 6.5726e-01 3.7300e-01 1.2330e+00 +ECI2 ENST00000380118 6.5525e-08 7.7565e-01 5.0400e-01 1.2330e+00 +GOLGA6L2 ENST00000567107 1.0579e-06 7.4494e-01 4.6800e-01 1.2330e+00 +PNLIPRP1 ENST00000528052 1.0944e-13 8.6321e-01 6.1600e-01 1.2330e+00 +KBTBD12 ENST00000405109 2.3384e-14 8.7033e-01 6.2500e-01 1.2330e+00 +GPR75 ENST00000394705 1.5813e-05 7.0702e-01 4.2500e-01 1.2330e+00 +TNFAIP8L1 ENST00000536716 5.3790e-01 0.0000e+00 0.0000e+00 1.2330e+00 +OLFML1 ENST00000329293 1.5857e-08 7.8890e-01 5.2000e-01 1.2330e+00 +HTRA3 ENST00000307358 6.5843e-08 7.7532e-01 5.0400e-01 1.2330e+00 +CD1C ENST00000368170 1.5963e-08 7.8848e-01 5.2000e-01 1.2330e+00 +HSPA1L ENST00000375654 1.0570e-06 7.4502e-01 4.6800e-01 1.2330e+00 +C9orf156 ENST00000375119 6.4724e-08 7.7651e-01 5.0500e-01 1.2340e+00 +ATP6V1G3 ENST00000281087 1.0745e-01 3.9606e-01 1.6100e-01 1.2340e+00 +AP1G2 ENST00000308724 5.0978e-28 9.5695e-01 7.4900e-01 1.2340e+00 +PTMA ENST00000341369 3.4451e-02 4.8000e-01 2.1700e-01 1.2340e+00 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1.0127e-02 5.4189e-01 2.6600e-01 1.2360e+00 +BCS1L ENST00000431802 4.6972e-13 8.5886e-01 6.0800e-01 1.2370e+00 +PLA1A ENST00000273371 4.3709e-11 8.3416e-01 5.7600e-01 1.2370e+00 +CWH43 ENST00000226432 7.2561e-22 9.2918e-01 7.0600e-01 1.2370e+00 +CHIA ENST00000369740 1.0115e-13 8.6629e-01 6.1800e-01 1.2370e+00 +PCNXL4 ENST00000317623 1.5173e-22 9.3263e-01 7.1100e-01 1.2370e+00 +HESX1 ENST00000295934 7.9734e-04 6.2777e-01 3.4300e-01 1.2370e+00 +DDO ENST00000368924 8.3982e-10 8.1469e-01 5.5100e-01 1.2370e+00 +C1QTNF1-AS1 ENST00000581579 5.3681e-01 0.0000e+00 0.0000e+00 1.2370e+00 +C9orf64 ENST00000376344 1.0255e-06 7.4754e-01 4.7000e-01 1.2370e+00 +CDH26 ENST00000348616 5.3761e-26 9.5053e-01 7.3700e-01 1.2370e+00 +GCAT ENST00000323205 1.5281e-08 7.9126e-01 5.2200e-01 1.2370e+00 +CPA6 ENST00000297770 4.3984e-17 8.9664e-01 6.6000e-01 1.2370e+00 +CYP2B6 ENST00000324071 1.9303e-10 8.2479e-01 5.6300e-01 1.2370e+00 +SLC25A13 ENST00000416240 1.2833e-24 9.4400e-01 7.2800e-01 1.2370e+00 +MS4A18 ENST00000398983 1.0223e-06 7.4780e-01 4.7000e-01 1.2380e+00 +SLC8B1 ENST00000552014 2.0302e-16 8.9217e-01 6.5300e-01 1.2380e+00 +TEX101 ENST00000602198 7.9525e-04 6.2812e-01 3.4300e-01 1.2380e+00 +PAXIP1-AS2 ENST00000397551 2.7949e-01 2.6687e-01 9.4000e-02 1.2380e+00 +ATP6V1G2 ENST00000303892 2.8604e-03 5.9013e-01 3.0700e-01 1.2380e+00 +PIGV ENST00000374145 1.5131e-08 7.9188e-01 5.2200e-01 1.2380e+00 +GPR83 ENST00000243673 1.0181e-06 7.4814e-01 4.7000e-01 1.2380e+00 +C1D ENST00000355848 3.4110e-02 4.8178e-01 2.1800e-01 1.2380e+00 +C17orf96 ENST00000325814 2.7965e-01 2.6674e-01 9.4000e-02 1.2380e+00 +IGSF10 ENST00000282466 5.8027e-49 1.0187e+00 8.4200e-01 1.2380e+00 +FAM43B ENST00000332947 1.0664e-01 3.9757e-01 1.6100e-01 1.2380e+00 +CLCNKB ENST00000375679 1.4025e-22 9.3478e-01 7.1300e-01 1.2390e+00 +AP5B1 ENST00000532090 4.2746e-11 8.3523e-01 5.7600e-01 1.2390e+00 +DUSP19 ENST00000354221 1.0044e-02 5.4324e-01 2.6600e-01 1.2390e+00 +APBA3 ENST00000316757 2.0716e-12 8.5279e-01 5.9900e-01 1.2390e+00 +NUDT10 ENST00000376006 1.0650e-01 3.9784e-01 1.6100e-01 1.2390e+00 +MLKL ENST00000308807 2.0931e-14 8.7450e-01 6.2800e-01 1.2390e+00 +EFHB ENST00000295824 5.7973e-24 9.4257e-01 7.2400e-01 1.2400e+00 +FIG4 ENST00000230124 2.3423e-34 9.8458e-01 7.8700e-01 1.2400e+00 +GPR89B ENST00000314163 2.1519e-04 6.6081e-01 3.7500e-01 1.2400e+00 +CCDC116 ENST00000292779 3.9339e-06 7.3150e-01 4.5000e-01 1.2400e+00 +KRAS ENST00000256078 7.8803e-04 6.2936e-01 3.4400e-01 1.2400e+00 +ZMAT5 ENST00000397781 1.5247e-05 7.1071e-01 4.2700e-01 1.2400e+00 +GBP4 ENST00000355754 9.1784e-16 8.8806e-01 6.4600e-01 1.2400e+00 +ANXA10 ENST00000359299 9.5506e-14 8.6855e-01 6.2000e-01 1.2400e+00 +HAPLN3 ENST00000359595 1.0068e-06 7.4907e-01 4.7100e-01 1.2400e+00 +ALDH7A1 ENST00000409134 1.3923e-22 9.3498e-01 7.1300e-01 1.2400e+00 +PRSS12 ENST00000296498 8.3820e-29 9.6474e-01 7.5700e-01 1.2400e+00 +SPAM1 ENST00000340011 1.8621e-10 8.2662e-01 5.6500e-01 1.2400e+00 +FAM105A ENST00000274217 3.4462e-09 8.0626e-01 5.3800e-01 1.2410e+00 +IGJ ENST00000254801 3.3839e-02 4.8321e-01 2.1900e-01 1.2410e+00 +TMEM200C ENST00000581347 1.0617e-01 3.9847e-01 1.6200e-01 1.2410e+00 +PDK4 ENST00000005178 9.1420e-12 8.4588e-01 5.8900e-01 1.2410e+00 +ADH1B ENST00000305046 9.9340e-07 7.5019e-01 4.7100e-01 1.2410e+00 +ANKRD2 ENST00000307518 1.4714e-08 7.9367e-01 5.2300e-01 1.2410e+00 +BAMBI ENST00000375533 2.1381e-04 6.6160e-01 3.7500e-01 1.2410e+00 +ARMC6 ENST00000535612 1.8352e-10 8.2736e-01 5.6500e-01 1.2410e+00 +LDLRAD2 ENST00000344642 2.1385e-04 6.6158e-01 3.7500e-01 1.2410e+00 +WFDC5 ENST00000372789 3.3893e-02 4.8293e-01 2.1900e-01 1.2410e+00 +CYP2F1 ENST00000331105 3.4078e-09 8.0692e-01 5.3900e-01 1.2420e+00 +PARP3 ENST00000398755 1.9738e-14 8.7673e-01 6.3000e-01 1.2420e+00 +OR2B2 ENST00000303324 9.9618e-03 5.4458e-01 2.6700e-01 1.2420e+00 +DCPS ENST00000263579 2.4654e-07 7.6678e-01 4.9000e-01 1.2420e+00 +FAM186B ENST00000257894 5.5062e-24 9.4393e-01 7.2500e-01 1.2420e+00 +CGNL1 ENST00000281282 4.6860e-42 1.0069e+00 8.2100e-01 1.2420e+00 +WDR16 ENST00000352665 8.1211e-18 9.0597e-01 6.7000e-01 1.2420e+00 +MBD4 ENST00000249910 1.9706e-14 8.7679e-01 6.3000e-01 1.2420e+00 +SLC28A3 ENST00000376238 2.6549e-23 9.4070e-01 7.2000e-01 1.2420e+00 +GUCA1B ENST00000230361 2.1337e-04 6.6186e-01 3.7500e-01 1.2420e+00 +C11orf87 ENST00000327419 2.7816e-01 2.6795e-01 9.4000e-02 1.2420e+00 +CNBD2 ENST00000349339 3.8389e-17 9.0117e-01 6.6300e-01 1.2430e+00 +NGRN ENST00000379095 7.7946e-04 6.3084e-01 3.4400e-01 1.2430e+00 +GPATCH4 ENST00000438976 5.6931e-05 6.8920e-01 4.0300e-01 1.2430e+00 +SAMD9 ENST00000379958 1.0521e-33 9.8440e-01 7.8500e-01 1.2430e+00 +PRR15 ENST00000319694 5.3532e-01 0.0000e+00 0.0000e+00 1.2430e+00 +NLRC3 ENST00000448023 2.2317e-25 9.5147e-01 7.3600e-01 1.2430e+00 +FAM129A ENST00000367511 7.1694e-20 9.2067e-01 6.9100e-01 1.2430e+00 +ZNF333 ENST00000292530 7.7896e-18 9.0732e-01 6.7100e-01 1.2440e+00 +ANKS4B ENST00000311620 1.4867e-05 7.1328e-01 4.2900e-01 1.2440e+00 +GPR97 ENST00000333493 8.9433e-14 8.7114e-01 6.2100e-01 1.2440e+00 +TPD52L1 ENST00000534000 1.4908e-05 7.1299e-01 4.2900e-01 1.2440e+00 +PACRG ENST00000337019 2.4288e-07 7.6792e-01 4.9100e-01 1.2440e+00 +PYHIN1 ENST00000368140 7.7771e-10 8.1889e-01 5.5300e-01 1.2440e+00 +PDZD9 ENST00000537222 2.8043e-03 5.9309e-01 3.0900e-01 1.2440e+00 +IL17B ENST00000261796 3.3631e-02 4.8432e-01 2.1900e-01 1.2440e+00 +CCBL1 ENST00000302586 1.8743e-12 8.5710e-01 6.0200e-01 1.2450e+00 +RASSF9 ENST00000361228 1.4029e-08 7.9670e-01 5.2500e-01 1.2450e+00 +C22orf15 ENST00000402217 2.7949e-03 5.9359e-01 3.0900e-01 1.2450e+00 +PCDHA3 ENST00000522353 8.3984e-16 8.9121e-01 6.4800e-01 1.2450e+00 +MMP25 ENST00000336577 8.7309e-14 8.7209e-01 6.2200e-01 1.2450e+00 +KLHL38 ENST00000325995 1.4099e-08 7.9639e-01 5.2500e-01 1.2450e+00 +BNIP1 ENST00000231668 9.6780e-07 7.5238e-01 4.7300e-01 1.2450e+00 +INHBC ENST00000309668 5.6341e-05 6.9037e-01 4.0400e-01 1.2450e+00 +LRRC56 ENST00000270115 7.6752e-10 8.1961e-01 5.5400e-01 1.2450e+00 +TMEM88 ENST00000301599 2.7743e-01 2.6856e-01 9.4000e-02 1.2450e+00 +CDC25C ENST00000323760 4.1014e-13 8.6444e-01 6.1200e-01 1.2450e+00 +BTBD16 ENST00000260723 3.5604e-17 9.0369e-01 6.6500e-01 1.2460e+00 +SPRYD7 ENST00000361840 2.0923e-04 6.6428e-01 3.7700e-01 1.2460e+00 +HES3 ENST00000377898 2.7711e-01 2.6882e-01 9.4000e-02 1.2460e+00 +PRAME ENST00000543184 2.3940e-07 7.6902e-01 4.9200e-01 1.2460e+00 +KIF25 ENST00000443060 9.6357e-07 7.5274e-01 4.7300e-01 1.2460e+00 +POLR3D ENST00000397802 3.8286e-11 8.4051e-01 5.8000e-01 1.2460e+00 +SPATC1 ENST00000377470 3.2793e-09 8.0918e-01 5.4000e-01 1.2460e+00 +TMEM100 ENST00000575734 5.3437e-01 0.0000e+00 0.0000e+00 1.2460e+00 +TRUB2 ENST00000372890 3.7900e-06 7.3494e-01 4.5200e-01 1.2460e+00 +CCDC169 ENST00000503173 3.7927e-06 7.3487e-01 4.5200e-01 1.2460e+00 +TMEM237 ENST00000409883 1.8704e-12 8.5719e-01 6.0200e-01 1.2460e+00 +KNOP1 ENST00000219837 2.3895e-07 7.6916e-01 4.9200e-01 1.2460e+00 +KRTAP10-12 ENST00000400365 9.8403e-03 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ENST00000362032 7.6877e-04 6.3272e-01 3.4500e-01 1.2470e+00 +LY6G6F ENST00000375832 9.5579e-07 7.5342e-01 4.7300e-01 1.2470e+00 +RNASEH2B ENST00000336617 3.2569e-09 8.0959e-01 5.4100e-01 1.2470e+00 +AMIGO3 ENST00000535833 2.0785e-04 6.6510e-01 3.7700e-01 1.2480e+00 +PENK ENST00000314922 2.0770e-04 6.6519e-01 3.7700e-01 1.2480e+00 +KCNK15 ENST00000372861 3.3356e-02 4.8581e-01 2.2000e-01 1.2480e+00 +SERINC2 ENST00000373710 3.9153e-13 8.6636e-01 6.1300e-01 1.2480e+00 +PKD2L1 ENST00000318222 1.5748e-27 9.6514e-01 7.5300e-01 1.2480e+00 +ATIC ENST00000236959 3.0109e-19 9.2046e-01 6.8800e-01 1.2480e+00 +RAB36 ENST00000263116 1.6531e-10 8.3270e-01 5.6900e-01 1.2490e+00 +FAM181A ENST00000267594 7.6374e-04 6.3362e-01 3.4600e-01 1.2490e+00 +C17orf72 ENST00000425164 9.7713e-03 5.4775e-01 2.6900e-01 1.2490e+00 +THUMPD3 ENST00000345094 8.1727e-14 8.7471e-01 6.2400e-01 1.2490e+00 +ZNF580 ENST00000543039 5.3362e-01 0.0000e+00 0.0000e+00 1.2490e+00 +MATN3 ENST00000407540 1.3500e-08 7.9916e-01 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5.5748e-08 7.8688e-01 5.1100e-01 1.2510e+00 +RHNO1 ENST00000489288 2.7455e-03 5.9626e-01 3.1100e-01 1.2510e+00 +KRT40 ENST00000377755 7.0984e-10 8.2388e-01 5.5700e-01 1.2510e+00 +CLEC14A ENST00000342213 1.4324e-05 7.1707e-01 4.3100e-01 1.2510e+00 +CHAC1 ENST00000446533 2.0552e-04 6.6650e-01 3.7800e-01 1.2510e+00 +SPNS3 ENST00000355530 1.7173e-12 8.6090e-01 6.0500e-01 1.2510e+00 +BPIFB3 ENST00000375494 3.6763e-13 8.6897e-01 6.1500e-01 1.2510e+00 +CTSV ENST00000259470 2.3031e-07 7.7197e-01 4.9400e-01 1.2510e+00 +GALK2 ENST00000560031 7.8958e-14 8.7608e-01 6.2500e-01 1.2510e+00 +PGLS ENST00000252603 7.5276e-04 6.3560e-01 3.4700e-01 1.2520e+00 +BPI ENST00000262865 1.6514e-14 8.8354e-01 6.3500e-01 1.2520e+00 +SLC28A1 ENST00000394573 5.7370e-20 9.2744e-01 6.9600e-01 1.2520e+00 +REG4 ENST00000354219 7.5276e-04 6.3560e-01 3.4700e-01 1.2520e+00 +NT5C ENST00000245552 2.7292e-03 5.9716e-01 3.1100e-01 1.2520e+00 +STX8 ENST00000306357 1.3184e-08 8.0067e-01 5.2800e-01 1.2520e+00 +SFTPC 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8.0293e-01 5.2900e-01 1.2550e+00 +GATS ENST00000436886 9.6067e-03 5.5056e-01 2.7000e-01 1.2550e+00 +ARV1 ENST00000310256 3.5867e-06 7.4003e-01 4.5600e-01 1.2550e+00 +IRAK2 ENST00000256458 2.6055e-19 9.2499e-01 6.9100e-01 1.2550e+00 +MELK ENST00000298048 4.5055e-22 9.4268e-01 7.1600e-01 1.2550e+00 +LEPREL4 ENST00000355468 1.5029e-10 8.3759e-01 5.7200e-01 1.2560e+00 +UPB1 ENST00000326010 7.3647e-12 8.5574e-01 5.9600e-01 1.2560e+00 +OPTN ENST00000378748 5.9100e-18 9.1640e-01 6.7800e-01 1.2560e+00 +CARD6 ENST00000254691 3.3903e-13 8.7234e-01 6.1800e-01 1.2560e+00 +SDHC ENST00000367975 2.0065e-04 6.6948e-01 3.8000e-01 1.2560e+00 +SPATS1 ENST00000288390 8.9551e-07 7.5888e-01 4.7700e-01 1.2560e+00 +TIGD4 ENST00000304337 5.3397e-08 7.8988e-01 5.1300e-01 1.2560e+00 +MRPL51 ENST00000229238 3.2765e-02 4.8907e-01 2.2200e-01 1.2560e+00 +KRT73 ENST00000305748 7.1972e-12 8.5679e-01 5.9700e-01 1.2570e+00 +PYCR1 ENST00000329875 1.9947e-04 6.7022e-01 3.8000e-01 1.2570e+00 +NUDT11 ENST00000375992 1.0316e-01 4.0433e-01 1.6400e-01 1.2570e+00 +INIP ENST00000374242 3.2654e-02 4.8970e-01 2.2200e-01 1.2570e+00 +SOWAHD ENST00000343905 5.3135e-01 0.0000e+00 0.0000e+00 1.2570e+00 +HIGD1A ENST00000452906 3.2658e-02 4.8967e-01 2.2200e-01 1.2570e+00 +SRFBP1 ENST00000339397 7.1253e-12 8.5726e-01 5.9700e-01 1.2580e+00 +HOXB6 ENST00000484302 7.3817e-04 6.3829e-01 3.4800e-01 1.2580e+00 +ACSM5 ENST00000331849 1.1745e-18 9.2261e-01 6.8600e-01 1.2580e+00 +GFRAL ENST00000340465 6.5227e-10 8.2853e-01 5.6000e-01 1.2580e+00 +AP001468.1 ENST00000594486 1.0302e-01 4.0463e-01 1.6400e-01 1.2580e+00 +PEPD ENST00000244137 1.4633e-14 8.8821e-01 6.3800e-01 1.2580e+00 +LY6G6D ENST00000375825 3.2554e-02 4.9026e-01 2.2200e-01 1.2580e+00 +PRAMEF12 ENST00000357726 5.2721e-05 6.9785e-01 4.0900e-01 1.2580e+00 +SUPT3H ENST00000371460 3.2442e-11 8.4851e-01 5.8600e-01 1.2580e+00 +CHRNA2 ENST00000407991 6.4532e-10 8.2912e-01 5.6000e-01 1.2590e+00 +KLHL17 ENST00000338591 1.3052e-16 9.0749e-01 6.6400e-01 1.2590e+00 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3.8400e-01 1.2690e+00 +FBXW8 ENST00000309909 5.2356e-16 9.0830e-01 6.6100e-01 1.2690e+00 +DPH5 ENST00000370109 8.1083e-07 7.6723e-01 4.8200e-01 1.2690e+00 +NDUFC1 ENST00000544855 1.0105e-01 4.0863e-01 1.6600e-01 1.2690e+00 +GBP6 ENST00000370456 5.2330e-16 9.0832e-01 6.6100e-01 1.2690e+00 +FAM150B ENST00000403610 3.1797e-02 4.9461e-01 2.2400e-01 1.2690e+00 +FSBP ENST00000481490 7.0681e-04 6.4430e-01 3.5200e-01 1.2690e+00 +LMF1 ENST00000262301 5.1419e-16 9.0896e-01 6.6100e-01 1.2690e+00 +FAM221B ENST00000423537 1.1077e-08 8.1183e-01 5.3500e-01 1.2690e+00 +CCDC176 ENST00000394009 1.0672e-16 9.1463e-01 6.6900e-01 1.2690e+00 +VAMP3 ENST00000054666 2.5882e-03 6.0522e-01 3.1500e-01 1.2690e+00 +GTF2A1L ENST00000403751 2.7752e-11 8.5613e-01 5.9100e-01 1.2690e+00 +STAMBPL1 ENST00000371926 1.1971e-14 8.9604e-01 6.4400e-01 1.2690e+00 +ACAD8 ENST00000281182 5.6389e-14 8.8967e-01 6.3500e-01 1.2700e+00 +OAS3 ENST00000228928 1.9653e-33 1.0032e+00 7.9900e-01 1.2700e+00 +SLITRK6 ENST00000400286 5.6989e-14 8.8923e-01 6.3400e-01 1.2700e+00 +DUOX2 ENST00000603300 4.5032e-56 1.0568e+00 8.8300e-01 1.2700e+00 +SULT1E1 ENST00000226444 1.9701e-07 7.8390e-01 5.0100e-01 1.2700e+00 +PPP1R32 ENST00000338608 2.4447e-15 9.0333e-01 6.5300e-01 1.2700e+00 +BATF3 ENST00000243440 3.1710e-02 4.9513e-01 2.2400e-01 1.2700e+00 +KIAA0226L ENST00000429979 4.3599e-18 9.2659e-01 6.8600e-01 1.2700e+00 +SLCO1A2 ENST00000307378 1.0581e-16 9.1494e-01 6.7000e-01 1.2700e+00 +FSD2 ENST00000334574 1.5277e-21 9.4957e-01 7.1900e-01 1.2700e+00 +ADH4 ENST00000265512 8.0684e-07 7.6764e-01 4.8200e-01 1.2700e+00 +TNFRSF13C ENST00000291232 2.6993e-01 2.7494e-01 9.6000e-02 1.2700e+00 +PNPLA4 ENST00000381042 2.5724e-03 6.0616e-01 3.1600e-01 1.2710e+00 +FAM101B ENST00000329099 2.6962e-01 2.7522e-01 9.6000e-02 1.2710e+00 +ZFR2 ENST00000262961 9.7623e-26 9.7302e-01 7.5200e-01 1.2710e+00 +FGF11 ENST00000293829 1.8767e-04 6.7787e-01 3.8400e-01 1.2710e+00 +PXMP2 ENST00000317479 9.1780e-03 5.5821e-01 2.7400e-01 1.2710e+00 +NUTM2G ENST00000372322 5.6293e-10 8.3667e-01 5.6500e-01 1.2710e+00 +BEX2 ENST00000536889 1.0078e-01 4.0920e-01 1.6600e-01 1.2710e+00 +RHBDD3 ENST00000216085 4.9464e-05 7.0509e-01 4.1300e-01 1.2710e+00 +UTS2 ENST00000054668 3.1612e-02 4.9570e-01 2.2500e-01 1.2710e+00 +PLLP ENST00000219207 9.1916e-03 5.5796e-01 2.7400e-01 1.2710e+00 +ZNF44 ENST00000356109 2.5686e-03 6.0639e-01 3.1600e-01 1.2710e+00 +YJEFN3 ENST00000514277 1.2695e-05 7.2944e-01 4.3900e-01 1.2720e+00 +AC008271.1 ENST00000436967 1.0066e-01 4.0946e-01 1.6600e-01 1.2720e+00 +CCDC84 ENST00000334418 5.4698e-14 8.9091e-01 6.3600e-01 1.2720e+00 +RRP8 ENST00000254605 1.2303e-10 8.4794e-01 5.7900e-01 1.2720e+00 +VWA5B1 ENST00000375079 9.1392e-33 1.0027e+00 7.9600e-01 1.2720e+00 +PGLYRP2 ENST00000340880 2.6765e-11 8.5790e-01 5.9200e-01 1.2720e+00 +KRT6B ENST00000252252 5.5245e-10 8.3771e-01 5.6600e-01 1.2720e+00 +CPA1 ENST00000011292 2.6567e-11 8.5827e-01 5.9200e-01 1.2730e+00 +ANGPTL1 ENST00000234816 1.2103e-10 8.4880e-01 5.8000e-01 1.2730e+00 +GLUD2 ENST00000328078 3.1520e-02 4.9625e-01 2.2500e-01 1.2730e+00 +CDHR3 ENST00000317716 2.3071e-24 9.6752e-01 7.4300e-01 1.2730e+00 +GLDN ENST00000335449 2.5809e-13 8.8385e-01 6.2600e-01 1.2730e+00 +OC90 ENST00000254627 5.6811e-12 8.6774e-01 6.0400e-01 1.2730e+00 +OC90 ENST00000603859 5.6811e-12 8.6774e-01 6.0400e-01 1.2730e+00 +FLJ27365 ENST00000360737 1.0042e-01 4.0994e-01 1.6600e-01 1.2730e+00 +CLCA2 ENST00000370565 1.4744e-28 9.8686e-01 7.7200e-01 1.2730e+00 +REEP5 ENST00000379638 6.9737e-04 6.4617e-01 3.5300e-01 1.2730e+00 +CD55 ENST00000314754 5.6753e-12 8.6779e-01 6.0400e-01 1.2730e+00 +PSAT1 ENST00000376588 1.0621e-08 8.1454e-01 5.3700e-01 1.2730e+00 +INPP1 ENST00000392329 7.8980e-07 7.6944e-01 4.8300e-01 1.2730e+00 +KIF4B ENST00000435029 4.6327e-25 9.7099e-01 7.4800e-01 1.2730e+00 +CLDN18 ENST00000183605 1.8650e-04 6.7866e-01 3.8500e-01 1.2730e+00 +TRIM74 ENST00000285805 9.1423e-03 5.5887e-01 2.7400e-01 1.2730e+00 +APEX1 ENST00000216714 1.9191e-07 7.8591e-01 5.0300e-01 1.2730e+00 +TMEM206 ENST00000535273 5.4081e-10 8.3889e-01 5.6700e-01 1.2740e+00 +RP11-383H13.1 ENST00000537896 6.9491e-04 6.4666e-01 3.5300e-01 1.2740e+00 +ABCC12 ENST00000311303 4.5659e-49 1.0474e+00 8.6500e-01 1.2740e+00 +MARC1 ENST00000366910 4.5163e-08 8.0158e-01 5.2100e-01 1.2740e+00 +SERGEF ENST00000265965 5.2893e-14 8.9228e-01 6.3700e-01 1.2740e+00 +SMPDL3B ENST00000373894 2.4146e-09 8.2731e-01 5.5300e-01 1.2740e+00 +ZADH2 ENST00000322342 2.5430e-03 6.0793e-01 3.1700e-01 1.2740e+00 +EFHD2 ENST00000375980 9.0981e-03 5.5969e-01 2.7500e-01 1.2750e+00 +URM1 ENST00000452446 3.1327e-02 4.9740e-01 2.2500e-01 1.2750e+00 +MCFD2 ENST00000409105 1.0011e-01 4.1060e-01 1.6700e-01 1.2750e+00 +RPS27L ENST00000330964 1.0011e-01 4.1061e-01 1.6700e-01 1.2750e+00 +HTR6 ENST00000289753 1.8524e-04 6.7952e-01 3.8500e-01 1.2750e+00 +PPA2 ENST00000341695 1.1789e-10 8.5016e-01 5.8100e-01 1.2750e+00 +RP11-176H8.1 ENST00000547378 1.0001e-01 4.1081e-01 1.6700e-01 1.2750e+00 +C3orf22 ENST00000318225 1.0010e-01 4.1062e-01 1.6700e-01 1.2750e+00 +SORD ENST00000267814 4.4938e-08 8.0193e-01 5.2100e-01 1.2750e+00 +TMEM43 ENST00000306077 1.1608e-12 8.7814e-01 6.1700e-01 1.2760e+00 +OMD ENST00000375550 1.2430e-05 7.3161e-01 4.4000e-01 1.2760e+00 +SH3TC1 ENST00000245105 6.0939e-35 1.0129e+00 8.1000e-01 1.2760e+00 +TMEM160 ENST00000253047 9.9858e-02 4.1114e-01 1.6700e-01 1.2760e+00 +DHRS12 ENST00000444610 1.0374e-08 8.1605e-01 5.3800e-01 1.2760e+00 +MED31 ENST00000225728 6.8836e-04 6.4799e-01 3.5400e-01 1.2760e+00 +KRBA2 ENST00000331336 1.8795e-07 7.8750e-01 5.0400e-01 1.2760e+00 +MTERFD1 ENST00000287025 1.0306e-08 8.1647e-01 5.3800e-01 1.2760e+00 +GMPR2 ENST00000420554 1.0324e-08 8.1636e-01 5.3800e-01 1.2760e+00 +DPEP3 ENST00000268793 5.2742e-10 8.4028e-01 5.6800e-01 1.2760e+00 +PTGES2 ENST00000338961 2.3610e-09 8.2865e-01 5.5300e-01 1.2760e+00 +FAM63A ENST00000361738 4.5522e-16 9.1347e-01 6.6500e-01 1.2760e+00 +SLC25A18 ENST00000327451 1.8732e-07 7.8776e-01 5.0400e-01 1.2760e+00 +GINS1 ENST00000262460 7.7028e-07 7.7155e-01 4.8500e-01 1.2770e+00 +FAM228B ENST00000420135 1.8573e-07 7.8842e-01 5.0400e-01 1.2770e+00 +BCO2 ENST00000357685 3.7829e-18 9.3143e-01 6.8900e-01 1.2770e+00 +FAM132B ENST00000546354 2.5225e-03 6.0918e-01 3.1700e-01 1.2770e+00 +BMP15 ENST00000252677 1.8320e-04 6.8092e-01 3.8600e-01 1.2770e+00 +STEAP1B ENST00000404369 1.2368e-05 7.3212e-01 4.4000e-01 1.2770e+00 +FADD ENST00000301838 5.2595e-01 0.0000e+00 0.0000e+00 1.2770e+00 +CDHR5 ENST00000358353 7.7447e-19 9.3630e-01 6.9600e-01 1.2770e+00 +MESP2 ENST00000341735 3.1138e-06 7.5315e-01 4.6400e-01 1.2770e+00 +ARHGEF39 ENST00000378387 1.1334e-10 8.5222e-01 5.8200e-01 1.2780e+00 +DDIT4 ENST00000307365 6.8309e-04 6.4906e-01 3.5400e-01 1.2780e+00 +TSPYL4 ENST00000420283 1.2306e-05 7.3264e-01 4.4100e-01 1.2780e+00 +GPX4 ENST00000354171 4.7865e-05 7.0884e-01 4.1500e-01 1.2780e+00 +SLAMF9 ENST00000368093 1.2303e-05 7.3267e-01 4.4100e-01 1.2780e+00 +PHF11 ENST00000378319 4.3505e-08 8.0420e-01 5.2300e-01 1.2780e+00 +NTPCR ENST00000366628 2.5124e-03 6.0980e-01 3.1800e-01 1.2780e+00 +FEN1 ENST00000305885 4.7743e-05 7.0913e-01 4.1500e-01 1.2780e+00 +PARVB ENST00000406477 2.3813e-13 8.8729e-01 6.2800e-01 1.2780e+00 +ZNF488 ENST00000395702 3.0911e-06 7.5383e-01 4.6400e-01 1.2780e+00 +GOT1L1 ENST00000307599 5.1791e-10 8.4130e-01 5.6900e-01 1.2780e+00 +SSX3 ENST00000298396 9.0260e-03 5.6104e-01 2.7500e-01 1.2780e+00 +TMEM177 ENST00000424086 8.9914e-03 5.6170e-01 2.7600e-01 1.2790e+00 +YIPF2 ENST00000586748 4.3157e-08 8.0476e-01 5.2300e-01 1.2790e+00 +FCRL3 ENST00000368184 5.9739e-21 9.5254e-01 7.1800e-01 1.2790e+00 +TTC32 ENST00000333610 3.1091e-02 4.9882e-01 2.2600e-01 1.2790e+00 +GALNT15 ENST00000339732 3.6481e-18 9.3267e-01 6.9000e-01 1.2790e+00 +MEP1B ENST00000269202 1.9369e-24 9.7240e-01 7.4700e-01 1.2790e+00 +MCM7 ENST00000303887 1.9396e-24 9.7236e-01 7.4700e-01 1.2790e+00 +CTD-3105H18.16 ENST00000595562 9.9394e-02 4.1212e-01 1.6700e-01 1.2790e+00 +EFCAB10 ENST00000485614 8.9932e-03 5.6166e-01 2.7600e-01 1.2790e+00 +HN1 ENST00000356033 2.5050e-03 6.1025e-01 3.1800e-01 1.2790e+00 +SUMF2 ENST00000342190 9.9738e-09 8.1859e-01 5.4000e-01 1.2790e+00 +MCHR1 ENST00000249016 4.7359e-05 7.1005e-01 4.1600e-01 1.2800e+00 +C4orf29 ENST00000398965 1.0881e-12 8.8103e-01 6.1900e-01 1.2800e+00 +DAPK2 ENST00000261891 5.0088e-10 8.4316e-01 5.7000e-01 1.2800e+00 +CRHR2 ENST00000348438 8.5473e-17 9.2263e-01 6.7500e-01 1.2800e+00 +GM2A ENST00000357164 3.1030e-02 4.9919e-01 2.2600e-01 1.2800e+00 +SLC16A8 ENST00000320521 8.9726e-03 5.6205e-01 2.7600e-01 1.2800e+00 +KRCC1 ENST00000347055 6.7915e-04 6.4987e-01 3.5500e-01 1.2800e+00 +SAMD11 ENST00000342066 4.7681e-14 8.9656e-01 6.4000e-01 1.2800e+00 +C1QTNF3 ENST00000382065 1.8089e-07 7.9044e-01 5.0600e-01 1.2800e+00 +LIM2 ENST00000221973 6.7834e-04 6.5004e-01 3.5500e-01 1.2800e+00 +FGF23 ENST00000237837 3.1014e-02 4.9929e-01 2.2600e-01 1.2800e+00 +FPGT ENST00000609362 1.0949e-10 8.5403e-01 5.8300e-01 1.2810e+00 +NAA40 ENST00000377793 9.7852e-09 8.1982e-01 5.4000e-01 1.2810e+00 +CDH16 ENST00000299752 3.6527e-25 9.7751e-01 7.5300e-01 1.2810e+00 +ENTHD2 ENST00000300714 9.8236e-09 8.1957e-01 5.4000e-01 1.2810e+00 +TRABD2A ENST00000335459 2.2361e-09 8.3189e-01 5.5600e-01 1.2810e+00 +hsa-mir-1199 ENST00000269720 6.7712e-04 6.5029e-01 3.5500e-01 1.2810e+00 +MYBPH ENST00000255416 2.2535e-13 8.8966e-01 6.3000e-01 1.2810e+00 +C2orf47 ENST00000295079 3.0232e-06 7.5591e-01 4.6500e-01 1.2810e+00 +PRELP ENST00000343110 4.7067e-05 7.1076e-01 4.1600e-01 1.2810e+00 +PDCD1LG2 ENST00000397747 1.2030e-05 7.3498e-01 4.4200e-01 1.2820e+00 +NIF3L1 ENST00000409020 9.7207e-09 8.2025e-01 5.4100e-01 1.2820e+00 +EIF2S3L ENST00000322446 1.7977e-04 6.8332e-01 3.8800e-01 1.2820e+00 +C6orf57 ENST00000370474 9.8879e-02 4.1323e-01 1.6800e-01 1.2820e+00 +CNKSR1 ENST00000361530 4.2890e-30 9.9999e-01 7.8700e-01 1.2820e+00 +EXOSC6 ENST00000435634 5.2473e-01 0.0000e+00 0.0000e+00 1.2820e+00 +PRDX5 ENST00000265462 1.7921e-04 6.8371e-01 3.8800e-01 1.2820e+00 +OXLD1 ENST00000374741 2.6634e-01 2.7814e-01 9.7000e-02 1.2820e+00 +P2RX4 ENST00000359949 4.9835e-12 8.7388e-01 6.0900e-01 1.2820e+00 +RERG ENST00000256953 1.2001e-05 7.3524e-01 4.4200e-01 1.2820e+00 +ARRDC2 ENST00000222250 2.1977e-09 8.3293e-01 5.5600e-01 1.2820e+00 +CHST12 ENST00000258711 4.6561e-05 7.1200e-01 4.1700e-01 1.2830e+00 +RP11-455G16.1 ENST00000503243 3.0803e-02 5.0058e-01 2.2700e-01 1.2830e+00 +ADPRH ENST00000478399 2.9910e-06 7.5691e-01 4.6600e-01 1.2830e+00 +NME5 ENST00000265191 6.7197e-04 6.5137e-01 3.5600e-01 1.2830e+00 +CCDC69 ENST00000355417 4.9125e-12 8.7456e-01 6.0900e-01 1.2830e+00 +TMEM8C ENST00000339996 1.7841e-04 6.8428e-01 3.8800e-01 1.2830e+00 +ADCK1 ENST00000238561 9.4776e-15 9.0530e-01 6.5000e-01 1.2830e+00 +ANGPTL4 ENST00000301455 2.3089e-11 8.6519e-01 5.9700e-01 1.2830e+00 +LITAF ENST00000571688 3.0752e-02 5.0089e-01 2.2700e-01 1.2840e+00 +IL18 ENST00000280357 3.0717e-02 5.0111e-01 2.2700e-01 1.2840e+00 +ZNF132 ENST00000254166 1.0294e-12 8.8352e-01 6.2100e-01 1.2840e+00 +POLE3 ENST00000374171 3.0709e-02 5.0116e-01 2.2700e-01 1.2840e+00 +LDOC1 ENST00000370526 5.2431e-01 0.0000e+00 0.0000e+00 1.2840e+00 +NUPL2 ENST00000258742 9.5131e-09 8.2164e-01 5.4200e-01 1.2840e+00 +RNF125 ENST00000217740 4.6358e-05 7.1250e-01 4.1700e-01 1.2840e+00 +C1orf177 ENST00000371273 2.1352e-13 8.9198e-01 6.3200e-01 1.2840e+00 +COA1 ENST00000395879 8.8335e-03 5.6473e-01 2.7700e-01 1.2850e+00 +KCNJ1 ENST00000392664 4.6255e-05 7.1276e-01 4.1700e-01 1.2850e+00 +TECTB ENST00000369422 4.7666e-10 8.4593e-01 5.7200e-01 1.2850e+00 +MB ENST00000397326 3.0636e-02 5.0161e-01 2.2700e-01 1.2850e+00 +ERMN ENST00000397283 1.1805e-05 7.3694e-01 4.4300e-01 1.2850e+00 +ANKDD1A ENST00000380230 7.7415e-17 9.2623e-01 6.7800e-01 1.2850e+00 +C11orf49 ENST00000378615 2.2431e-11 8.6662e-01 5.9800e-01 1.2850e+00 +MKKS ENST00000347364 2.1265e-09 8.3490e-01 5.5800e-01 1.2850e+00 +GTDC1 ENST00000392869 1.0127e-12 8.8426e-01 6.2100e-01 1.2850e+00 +TTLL9 ENST00000375938 3.1982e-18 9.3721e-01 6.9300e-01 1.2850e+00 +TTC7A ENST00000319190 1.5359e-31 1.0074e+00 7.9600e-01 1.2850e+00 +ASB15 ENST00000451558 1.8400e-15 9.1426e-01 6.6100e-01 1.2860e+00 +BPIFB2 ENST00000170150 4.7491e-12 8.7615e-01 6.1000e-01 1.2860e+00 +EPHA10 ENST00000373048 1.2428e-26 9.8829e-01 7.6700e-01 1.2860e+00 +UGT1A5 ENST00000373414 9.3665e-09 8.2265e-01 5.4200e-01 1.2860e+00 +TMPRSS11A ENST00000334830 1.8331e-15 9.1441e-01 6.6100e-01 1.2860e+00 +SLC41A3 ENST00000315891 2.0709e-13 8.9330e-01 6.3300e-01 1.2860e+00 +ZNF732 ENST00000419098 9.8159e-02 4.1479e-01 1.6800e-01 1.2860e+00 +C17orf98 ENST00000398575 8.8152e-03 5.6508e-01 2.7700e-01 1.2860e+00 +EGFL6 ENST00000380602 9.9818e-13 8.8491e-01 6.2200e-01 1.2860e+00 +SERP1 ENST00000479209 2.6523e-01 2.7914e-01 9.8000e-02 1.2860e+00 +OR5P3 ENST00000328375 9.8170e-02 4.1476e-01 1.6800e-01 1.2860e+00 +TAS1R2 ENST00000375371 7.6139e-17 9.2684e-01 6.7800e-01 1.2860e+00 +NSG1 ENST00000421177 8.8286e-03 5.6482e-01 2.7700e-01 1.2860e+00 +TTC9C ENST00000316461 1.7609e-04 6.8594e-01 3.8900e-01 1.2860e+00 +CASP10 ENST00000286186 4.6392e-12 8.7726e-01 6.1100e-01 1.2870e+00 +ATP13A5 ENST00000342358 2.4077e-49 1.0582e+00 8.7400e-01 1.2870e+00 +PRPSAP1 ENST00000446526 1.7124e-07 7.9466e-01 5.0800e-01 1.2870e+00 +RHOF ENST00000267205 1.7569e-04 6.8623e-01 3.8900e-01 1.2870e+00 +UNC5CL ENST00000244565 2.0365e-13 8.9403e-01 6.3300e-01 1.2870e+00 +PCK1 ENST00000319441 8.7476e-15 9.0852e-01 6.5300e-01 1.2870e+00 +PEBP4 ENST00000256404 4.5750e-05 7.1402e-01 4.1800e-01 1.2870e+00 +CBLN3 ENST00000267406 6.6248e-04 6.5337e-01 3.5700e-01 1.2870e+00 +NARF ENST00000309794 9.7836e-13 8.8582e-01 6.2200e-01 1.2870e+00 +PMEL ENST00000449260 3.0571e-18 9.3877e-01 6.9500e-01 1.2870e+00 +TMEM192 ENST00000306480 2.9274e-06 7.5891e-01 4.6700e-01 1.2870e+00 +SYNDIG1L ENST00000331628 8.7901e-03 5.6557e-01 2.7700e-01 1.2870e+00 +MACC1 ENST00000400331 6.0053e-19 9.4485e-01 7.0300e-01 1.2880e+00 +ZNF442 ENST00000242804 3.0480e-02 5.0258e-01 2.2800e-01 1.2880e+00 +MBLAC2 ENST00000316610 4.5418e-05 7.1486e-01 4.1900e-01 1.2880e+00 +HAPLN2 ENST00000255039 7.1205e-07 7.7820e-01 4.8900e-01 1.2880e+00 +SAMD10 ENST00000369886 6.5861e-04 6.5420e-01 3.5700e-01 1.2880e+00 +FAM19A4 ENST00000295569 6.5997e-04 6.5391e-01 3.5700e-01 1.2880e+00 +CES2 ENST00000317091 3.5781e-16 9.2249e-01 6.7100e-01 1.2880e+00 +FCHSD1 ENST00000435817 1.3536e-31 1.0104e+00 7.9900e-01 1.2880e+00 +ADAMDEC1 ENST00000256412 3.6295e-16 9.2195e-01 6.7100e-01 1.2880e+00 +ASPRV1 ENST00000320256 8.7846e-03 5.6568e-01 2.7700e-01 1.2880e+00 +PECR ENST00000265322 4.0029e-08 8.1005e-01 5.2600e-01 1.2880e+00 +B3GALTL ENST00000343307 7.1449e-17 9.2917e-01 6.8000e-01 1.2890e+00 +TVP23A ENST00000299866 1.6882e-07 7.9575e-01 5.0900e-01 1.2890e+00 +SRD5A1 ENST00000274192 1.1557e-05 7.3914e-01 4.4500e-01 1.2890e+00 +EMC6 ENST00000397133 5.2298e-01 0.0000e+00 0.0000e+00 1.2890e+00 +C9orf171 ENST00000343036 1.6930e-07 7.9554e-01 5.0900e-01 1.2890e+00 +NSUN3 ENST00000314622 9.0405e-09 8.2494e-01 5.4400e-01 1.2890e+00 +TRIML2 ENST00000512729 1.1540e-05 7.3929e-01 4.4500e-01 1.2890e+00 +MYL6 ENST00000550697 6.5343e-04 6.5531e-01 3.5800e-01 1.2900e+00 +TAF1C ENST00000567759 1.4604e-24 9.8039e-01 7.5300e-01 1.2900e+00 +BPIFB4 ENST00000375483 4.6976e-21 9.6009e-01 7.2400e-01 1.2900e+00 +CASP14 ENST00000427043 2.8684e-06 7.6082e-01 4.6800e-01 1.2900e+00 +C15orf65 ENST00000569691 2.6387e-01 2.8039e-01 9.8000e-02 1.2900e+00 +ORM1 ENST00000259396 1.1456e-05 7.4005e-01 4.4500e-01 1.2900e+00 +MMAA ENST00000281317 9.3982e-13 8.8763e-01 6.2400e-01 1.2900e+00 +RMND5B ENST00000515098 1.9471e-13 8.9598e-01 6.3400e-01 1.2900e+00 +OR51F1 ENST00000343430 3.0324e-02 5.0356e-01 2.2800e-01 1.2900e+00 +PON1 ENST00000222381 9.8142e-11 8.5978e-01 5.8700e-01 1.2900e+00 +MICU1 ENST00000361114 1.9344e-13 8.9626e-01 6.3500e-01 1.2910e+00 +DYTN ENST00000452335 5.7188e-19 9.4651e-01 7.0400e-01 1.2910e+00 +HSPA1A ENST00000375651 3.0228e-02 5.0417e-01 2.2800e-01 1.2910e+00 +FAM200B ENST00000422728 2.0087e-09 8.3833e-01 5.6000e-01 1.2910e+00 +CDK11A ENST00000404249 1.3850e-17 9.3647e-01 6.8900e-01 1.2910e+00 +TSPAN11 ENST00000261177 6.9450e-07 7.8031e-01 4.9000e-01 1.2910e+00 +RAB32 ENST00000367495 6.5061e-04 6.5593e-01 3.5800e-01 1.2910e+00 +IQCJ ENST00000451172 6.5220e-04 6.5558e-01 3.5800e-01 1.2910e+00 +FAM32A ENST00000263384 3.0275e-02 5.0387e-01 2.2800e-01 1.2910e+00 +GPR153 ENST00000377893 6.8764e-07 7.8116e-01 4.9100e-01 1.2920e+00 +MISP ENST00000215582 4.3142e-12 8.8070e-01 6.1300e-01 1.2920e+00 +CILP ENST00000261883 5.3654e-26 9.8924e-01 7.6500e-01 1.2920e+00 +C1QTNF9 ENST00000382071 1.1372e-05 7.4082e-01 4.4600e-01 1.2920e+00 +PLA2G2A ENST00000375111 9.7278e-02 4.1673e-01 1.6900e-01 1.2920e+00 +CD207 ENST00000410009 2.8182e-06 7.6247e-01 4.6900e-01 1.2920e+00 +CLEC4E ENST00000299663 1.1378e-05 7.4076e-01 4.4600e-01 1.2920e+00 +DUSP13 ENST00000372700 1.1320e-05 7.4129e-01 4.4600e-01 1.2920e+00 +NRTN ENST00000303212 3.0223e-02 5.0420e-01 2.2800e-01 1.2920e+00 +AVPR1A ENST00000299178 6.8987e-07 7.8088e-01 4.9100e-01 1.2920e+00 +KLK7 ENST00000391807 6.4670e-04 6.5678e-01 3.5900e-01 1.2930e+00 +MRPL35 ENST00000337109 2.3926e-03 6.1740e-01 3.2200e-01 1.2930e+00 +CCZ1B ENST00000316731 8.9699e-13 8.8975e-01 6.2500e-01 1.2930e+00 +MTNR1B ENST00000257068 6.4771e-04 6.5656e-01 3.5800e-01 1.2930e+00 +CALCB ENST00000533448 9.7127e-02 4.1706e-01 1.6900e-01 1.2930e+00 +C20orf27 ENST00000217195 8.6621e-03 5.6811e-01 2.7900e-01 1.2930e+00 +LRRC28 ENST00000301981 2.0078e-11 8.7215e-01 6.0200e-01 1.2930e+00 +OPN4 ENST00000372071 9.0073e-13 8.8956e-01 6.2500e-01 1.2930e+00 +MB21D1 ENST00000370315 8.6912e-09 8.2750e-01 5.4600e-01 1.2930e+00 +ZNF793 ENST00000445217 1.9629e-09 8.3972e-01 5.6100e-01 1.2930e+00 +MEPE ENST00000424957 8.6273e-03 5.6881e-01 2.7900e-01 1.2940e+00 +CCDC63 ENST00000308208 5.2679e-19 9.4931e-01 7.0600e-01 1.2940e+00 +SELENBP1 ENST00000368868 3.2268e-16 9.2641e-01 6.7400e-01 1.2940e+00 +CCDC102B ENST00000360242 3.2182e-16 9.2652e-01 6.7400e-01 1.2940e+00 +APMAP ENST00000217456 9.3261e-11 8.6247e-01 5.8900e-01 1.2940e+00 +FNDC8 ENST00000158009 1.7064e-04 6.8996e-01 3.9100e-01 1.2940e+00 +ZNF573 ENST00000590414 1.9945e-11 8.7248e-01 6.0200e-01 1.2940e+00 +C7orf72 ENST00000297001 3.7700e-08 8.1428e-01 5.2900e-01 1.2940e+00 +SYNE4 ENST00000324444 4.1880e-12 8.8212e-01 6.1400e-01 1.2940e+00 +LMAN2L ENST00000377079 1.9629e-11 8.7328e-01 6.0300e-01 1.2950e+00 +PSRC1 ENST00000369909 8.5560e-09 8.2852e-01 5.4600e-01 1.2950e+00 +C4BPB ENST00000243611 4.3958e-05 7.1862e-01 4.2100e-01 1.2950e+00 +GPR62 ENST00000322241 2.6246e-01 2.8169e-01 9.9000e-02 1.2950e+00 +GPR171 ENST00000309180 1.6964e-04 6.9071e-01 3.9200e-01 1.2950e+00 +S1PR4 ENST00000246115 2.3778e-03 6.1838e-01 3.2200e-01 1.2950e+00 +GPR119 ENST00000276218 8.6183e-03 5.6899e-01 2.7900e-01 1.2950e+00 +ALPP ENST00000392027 1.8144e-13 8.9906e-01 6.3700e-01 1.2950e+00 +RNF187 ENST00000305943 9.6678e-02 4.1806e-01 1.7000e-01 1.2950e+00 +ZNF430 ENST00000261560 8.6151e-03 5.6905e-01 2.7900e-01 1.2950e+00 +LRRC69 ENST00000448384 1.1180e-05 7.4258e-01 4.4700e-01 1.2950e+00 +LRRC72 ENST00000401542 2.7753e-06 7.6391e-01 4.7000e-01 1.2950e+00 +CENPO ENST00000380834 1.8941e-09 8.4187e-01 5.6200e-01 1.2960e+00 +HTR1D ENST00000374619 6.4061e-04 6.5812e-01 3.5900e-01 1.2960e+00 +FRMD1 ENST00000283309 3.6693e-14 9.0749e-01 6.4700e-01 1.2960e+00 +ERCC1 ENST00000013807 1.5933e-07 8.0022e-01 5.1200e-01 1.2960e+00 +ZNF20 ENST00000334213 9.6582e-02 4.1828e-01 1.7000e-01 1.2960e+00 +PCDHB3 ENST00000231130 1.5891e-07 8.0042e-01 5.1200e-01 1.2960e+00 +KRT20 ENST00000167588 9.0776e-11 8.6390e-01 5.9000e-01 1.2960e+00 +MAVS ENST00000428216 6.7045e-07 7.8331e-01 4.9200e-01 1.2960e+00 +CAPS2 ENST00000409445 6.0736e-24 9.8228e-01 7.5200e-01 1.2970e+00 +ARHGDIB ENST00000228945 6.3770e-04 6.5877e-01 3.6000e-01 1.2970e+00 +DNMT3L ENST00000270172 8.4150e-13 8.9266e-01 6.2700e-01 1.2970e+00 +ANGPTL5 ENST00000334289 4.1332e-10 8.5394e-01 5.7700e-01 1.2970e+00 +NDUFS6 ENST00000274137 9.6359e-02 4.1878e-01 1.7000e-01 1.2970e+00 +DZIP1L ENST00000327532 2.3897e-25 9.8937e-01 7.6300e-01 1.2970e+00 +WDR90 ENST00000293879 1.2637e-64 1.0917e+00 9.2200e-01 1.2970e+00 +ZAR1 ENST00000327939 4.3531e-05 7.1975e-01 4.2100e-01 1.2970e+00 +RNF215 ENST00000382363 1.8704e-09 8.4263e-01 5.6300e-01 1.2970e+00 +IL20RB ENST00000329582 3.6539e-08 8.1649e-01 5.3100e-01 1.2980e+00 +ZRSR1 ENST00000391338 1.6735e-04 6.9245e-01 3.9300e-01 1.2980e+00 +KIAA0141 ENST00000432126 1.2229e-17 9.4095e-01 6.9300e-01 1.2980e+00 +IL36A ENST00000259211 2.9783e-02 5.0702e-01 2.3000e-01 1.2980e+00 +OR52E2 ENST00000321522 9.6208e-02 4.1912e-01 1.7000e-01 1.2980e+00 +HIATL2 ENST00000602917 9.6194e-02 4.1915e-01 1.7000e-01 1.2980e+00 +IL19 ENST00000340758 4.3250e-05 7.2050e-01 4.2200e-01 1.2980e+00 +NSUN5 ENST00000310326 8.2394e-13 8.9363e-01 6.2800e-01 1.2980e+00 +CFHR4 ENST00000367416 2.3840e-18 9.4749e-01 7.0100e-01 1.2990e+00 +OGG1 ENST00000302036 3.9314e-12 8.8514e-01 6.1600e-01 1.2990e+00 +SSX4 ENST00000376886 5.2030e-01 0.0000e+00 0.0000e+00 1.2990e+00 +AC068533.7 ENST00000450043 4.0488e-10 8.5510e-01 5.7800e-01 1.2990e+00 +ZNF76 ENST00000373953 4.7640e-19 9.5277e-01 7.0800e-01 1.2990e+00 +OR10AD1 ENST00000310248 8.5157e-03 5.7107e-01 2.8000e-01 1.2990e+00 +ALDH1B1 ENST00000377698 2.6981e-06 7.6656e-01 4.7200e-01 1.2990e+00 +PRNP ENST00000379440 6.3182e-04 6.6009e-01 3.6000e-01 1.2990e+00 +CHD1L ENST00000369258 1.0034e-36 1.0357e+00 8.3100e-01 1.2990e+00 +SLC22A12 ENST00000377574 1.6891e-13 9.0219e-01 6.3900e-01 1.2990e+00 +RIT2 ENST00000326695 6.3244e-04 6.5995e-01 3.6000e-01 1.2990e+00 +ZNF285 ENST00000330997 1.6690e-04 6.9280e-01 3.9300e-01 1.2990e+00 +BTNL2 ENST00000454136 8.5607e-11 8.6702e-01 5.9200e-01 1.3000e+00 +METTL24 ENST00000338882 1.0876e-05 7.4545e-01 4.4800e-01 1.3000e+00 +WASH4P ENST00000326592 2.3404e-03 6.2088e-01 3.2300e-01 1.3000e+00 +TCF15 ENST00000246080 5.1981e-01 0.0000e+00 0.0000e+00 1.3000e+00 +APTX ENST00000379813 3.9924e-10 8.5589e-01 5.7800e-01 1.3000e+00 +PVR ENST00000425690 3.9220e-10 8.5690e-01 5.7900e-01 1.3010e+00 +RBM48 ENST00000265732 1.5329e-07 8.0320e-01 5.1400e-01 1.3010e+00 +ANGPTL3 ENST00000371129 1.6455e-13 9.0334e-01 6.4000e-01 1.3010e+00 +CELA3A ENST00000290122 8.0514e-09 8.3248e-01 5.4900e-01 1.3010e+00 +PTGR1 ENST00000407693 3.5375e-08 8.1878e-01 5.3200e-01 1.3010e+00 +HAUS1 ENST00000282058 3.5522e-08 8.1849e-01 5.3200e-01 1.3010e+00 +MORN3 ENST00000355329 1.5357e-07 8.0307e-01 5.1400e-01 1.3010e+00 +REG3A ENST00000393878 6.2895e-04 6.6074e-01 3.6100e-01 1.3010e+00 +PMP2 ENST00000256103 8.4728e-03 5.7195e-01 2.8100e-01 1.3010e+00 +ZC2HC1C ENST00000524913 1.8005e-09 8.4493e-01 5.6400e-01 1.3010e+00 +FAM124B ENST00000409685 1.0746e-05 7.4671e-01 4.4900e-01 1.3020e+00 +HIST1H3C ENST00000540144 2.6064e-01 2.8340e-01 9.9000e-02 1.3020e+00 +TRIM64B ENST00000329862 1.0703e-05 7.4713e-01 4.4900e-01 1.3020e+00 +C1orf159 ENST00000421241 1.6450e-04 6.9466e-01 3.9400e-01 1.3020e+00 +NOL7 ENST00000451315 3.5312e-08 8.1891e-01 5.3200e-01 1.3020e+00 +GPRC6A ENST00000310357 5.5919e-17 9.3827e-01 6.8700e-01 1.3020e+00 +ENDOU ENST00000422538 3.2354e-14 9.1282e-01 6.5100e-01 1.3030e+00 +NME9 ENST00000383180 7.8887e-09 8.3381e-01 5.5000e-01 1.3030e+00 +PLD4 ENST00000392593 7.7337e-13 8.9653e-01 6.3000e-01 1.3030e+00 +XYLB ENST00000207870 1.3597e-22 9.7839e-01 7.4300e-01 1.3030e+00 +EIF4E1B ENST00000318682 6.3895e-07 7.8740e-01 4.9500e-01 1.3030e+00 +NAGA ENST00000396398 1.7703e-11 8.7848e-01 6.0600e-01 1.3030e+00 +PPIL6 ENST00000440797 1.7495e-09 8.4667e-01 5.6500e-01 1.3030e+00 +FGF21 ENST00000593756 2.9439e-02 5.0927e-01 2.3100e-01 1.3030e+00 +OR8B12 ENST00000306842 2.5999e-01 2.8401e-01 1.0000e-01 1.3040e+00 +AFM ENST00000226355 4.2654e-19 9.5659e-01 7.1100e-01 1.3040e+00 +FAM103A1 ENST00000304191 8.3960e-03 5.7355e-01 2.8100e-01 1.3040e+00 +REM2 ENST00000267396 1.0585e-05 7.4828e-01 4.5000e-01 1.3040e+00 +OR56A4 ENST00000330728 8.4121e-03 5.7321e-01 2.8100e-01 1.3040e+00 +BTD ENST00000303498 1.4972e-07 8.0503e-01 5.1500e-01 1.3040e+00 +OR2D3 ENST00000317834 8.4071e-03 5.7331e-01 2.8100e-01 1.3040e+00 +DNAJB8 ENST00000469083 9.5207e-02 4.2140e-01 1.7100e-01 1.3040e+00 +UBE2T ENST00000367274 1.0599e-05 7.4814e-01 4.5000e-01 1.3040e+00 +CLEC4A ENST00000229332 4.1872e-05 7.2425e-01 4.2400e-01 1.3050e+00 +ZSCAN9 ENST00000425468 1.7236e-11 8.7983e-01 6.0700e-01 1.3050e+00 +TRIM15 ENST00000376694 7.7580e-09 8.3490e-01 5.5000e-01 1.3050e+00 +C7orf49 ENST00000393114 2.5971e-01 2.8428e-01 1.0000e-01 1.3050e+00 +HAL ENST00000261208 2.4971e-23 9.8464e-01 7.5100e-01 1.3050e+00 +TMCO4 ENST00000294543 1.6674e-20 9.6677e-01 7.2600e-01 1.3050e+00 +ACAA2 ENST00000285093 3.7065e-10 8.6011e-01 5.8100e-01 1.3060e+00 +MRPL18 ENST00000367034 1.6217e-04 6.9650e-01 3.9500e-01 1.3060e+00 +IGFLR1 ENST00000592537 2.5896e-06 7.7043e-01 4.7400e-01 1.3060e+00 +IGSF22 ENST00000513874 3.9627e-41 1.0537e+00 8.5500e-01 1.3060e+00 +AS3MT ENST00000369880 7.9768e-11 8.7079e-01 5.9500e-01 1.3060e+00 +NAIP ENST00000517649 1.6166e-04 6.9691e-01 3.9500e-01 1.3060e+00 +CLECL1 ENST00000327839 2.5929e-01 2.8468e-01 1.0000e-01 1.3060e+00 +BEST2 ENST00000549706 1.5229e-13 9.0676e-01 6.4200e-01 1.3060e+00 +PRAMEF11 ENST00000535591 6.1604e-04 6.6371e-01 3.6200e-01 1.3060e+00 +PRB3 ENST00000381842 6.2362e-07 7.8947e-01 4.9600e-01 1.3060e+00 +SLURP1 ENST00000246515 2.5934e-01 2.8463e-01 1.0000e-01 1.3060e+00 +PLAC8L1 ENST00000311450 8.3287e-03 5.7496e-01 2.8200e-01 1.3070e+00 +DIABLO ENST00000443649 2.5722e-06 7.7106e-01 4.7500e-01 1.3070e+00 +KLRC1 ENST00000544822 4.1390e-05 7.2559e-01 4.2500e-01 1.3070e+00 +XAGE3 ENST00000346279 9.4852e-02 4.2222e-01 1.7100e-01 1.3070e+00 +CLEC4F ENST00000272367 3.0707e-14 9.1505e-01 6.5300e-01 1.3070e+00 +MS4A6E ENST00000300182 2.9203e-02 5.1084e-01 2.3100e-01 1.3070e+00 +CFTR ENST00000003084 2.1735e-58 1.0903e+00 9.1300e-01 1.3070e+00 +PPP1R3F ENST00000055335 4.1516e-05 7.2524e-01 4.2500e-01 1.3070e+00 +CCDC77 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1.3110e+00 +KRT37 ENST00000225550 3.5166e-10 8.6310e-01 5.8300e-01 1.3110e+00 +TRIM77 ENST00000398290 1.0217e-05 7.5198e-01 4.5200e-01 1.3110e+00 +GDF3 ENST00000329913 4.0734e-05 7.2745e-01 4.2600e-01 1.3110e+00 +ZNF674 ENST00000523374 6.0351e-07 7.9226e-01 4.9800e-01 1.3110e+00 +CRYGC ENST00000282141 6.0610e-04 6.6604e-01 3.6400e-01 1.3110e+00 +WDR54 ENST00000348227 1.5733e-11 8.8446e-01 6.1000e-01 1.3110e+00 +SLC1A7 ENST00000371494 7.5281e-11 8.7389e-01 5.9700e-01 1.3110e+00 +SULT1B1 ENST00000310613 3.2594e-08 8.2459e-01 5.3600e-01 1.3110e+00 +CSRP3 ENST00000533783 1.5859e-04 6.9939e-01 3.9700e-01 1.3110e+00 +OPRK1 ENST00000265572 4.0625e-05 7.2776e-01 4.2600e-01 1.3110e+00 +PCDHB1 ENST00000306549 7.5280e-11 8.7389e-01 5.9700e-01 1.3110e+00 +RP11-65D24.2 ENST00000375713 2.5787e-01 2.8605e-01 1.0000e-01 1.3120e+00 +PRSS37 ENST00000350549 2.4898e-06 7.7413e-01 4.7700e-01 1.3120e+00 +TTC31 ENST00000233623 2.2945e-16 9.3958e-01 6.8400e-01 1.3120e+00 +C17orf62 ENST00000437807 6.0320e-04 6.6673e-01 3.6400e-01 1.3120e+00 +DPEP1 ENST00000393092 3.4730e-10 8.6381e-01 5.8400e-01 1.3120e+00 +DDX25 ENST00000263576 1.8125e-18 9.5727e-01 7.0800e-01 1.3120e+00 +AGTR2 ENST00000371906 8.2345e-03 5.7697e-01 2.8300e-01 1.3120e+00 +LOH12CR2 ENST00000381800 5.1669e-01 0.0000e+00 0.0000e+00 1.3120e+00 +VPS9D1 ENST00000389386 7.2069e-20 9.6719e-01 7.2300e-01 1.3120e+00 +TAS2R40 ENST00000408947 2.8878e-02 5.1302e-01 2.3200e-01 1.3120e+00 +FXYD3 ENST00000604255 1.0105e-05 7.5313e-01 4.5300e-01 1.3130e+00 +ZWINT ENST00000373944 7.2736e-11 8.7574e-01 5.9800e-01 1.3130e+00 +AP4M1 ENST00000359593 4.4873e-17 9.4658e-01 6.9300e-01 1.3130e+00 +MFSD10 ENST00000329687 7.3331e-11 8.7530e-01 5.9800e-01 1.3130e+00 +TPRKB ENST00000272424 8.2100e-03 5.7749e-01 2.8300e-01 1.3130e+00 +TECRL ENST00000381210 3.1983e-12 8.9510e-01 6.2300e-01 1.3130e+00 +PI16 ENST00000373674 7.1384e-09 8.4036e-01 5.5400e-01 1.3130e+00 +CCDC137 ENST00000329214 5.9139e-07 7.9400e-01 4.9900e-01 1.3130e+00 +KLF8 ENST00000468660 2.2471e-03 6.2735e-01 3.2700e-01 1.3130e+00 +OR6S1 ENST00000320704 2.8811e-02 5.1348e-01 2.3300e-01 1.3130e+00 +RCAN3 ENST00000374395 1.5715e-04 7.0058e-01 3.9700e-01 1.3130e+00 +NKX6-2 ENST00000368592 2.8854e-02 5.1319e-01 2.3200e-01 1.3130e+00 +ZNF511 ENST00000361518 1.5695e-04 7.0074e-01 3.9700e-01 1.3130e+00 +TEX30 ENST00000376032 6.0198e-04 6.6703e-01 3.6400e-01 1.3130e+00 +NFE2L3 ENST00000056233 7.1842e-11 8.7641e-01 5.9900e-01 1.3140e+00 +C6orf58 ENST00000329722 7.0978e-09 8.4074e-01 5.5400e-01 1.3140e+00 +ADRA1D ENST00000379453 4.0117e-05 7.2923e-01 4.2700e-01 1.3140e+00 +RP11-944L7.5 ENST00000419137 9.3652e-02 4.2503e-01 1.7200e-01 1.3140e+00 +ZP4 ENST00000366570 1.7419e-18 9.5871e-01 7.0900e-01 1.3140e+00 +MPDU1 ENST00000250124 1.0051e-05 7.5370e-01 4.5300e-01 1.3140e+00 +CARTPT ENST00000296777 9.3729e-02 4.2485e-01 1.7200e-01 1.3140e+00 +MTERFD3 ENST00000552029 2.4640e-06 7.7512e-01 4.7700e-01 1.3140e+00 +MARCH8 ENST00000395771 5.8689e-07 7.9465e-01 4.9900e-01 1.3140e+00 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1.0100e-01 1.3160e+00 +MINOS1-NBL1 ENST00000602662 2.8653e-02 5.1456e-01 2.3300e-01 1.3160e+00 +MRPL46 ENST00000312475 1.3615e-07 8.1241e-01 5.2000e-01 1.3160e+00 +TMEM18 ENST00000281017 2.2182e-03 6.2942e-01 3.2800e-01 1.3170e+00 +CLEC4C ENST00000542353 5.7708e-07 7.9609e-01 5.0000e-01 1.3170e+00 +ASCC1 ENST00000342444 2.6051e-14 9.2213e-01 6.5800e-01 1.3170e+00 +FEV ENST00000295727 8.1114e-03 5.7964e-01 2.8400e-01 1.3170e+00 +ARL13A ENST00000450049 5.9177e-04 6.6950e-01 3.6500e-01 1.3170e+00 +UBE2U ENST00000371076 1.3492e-07 8.1312e-01 5.2000e-01 1.3170e+00 +SLC2A11 ENST00000398356 6.2349e-13 9.0653e-01 6.3700e-01 1.3170e+00 +CD84 ENST00000311224 6.9102e-09 8.4250e-01 5.5500e-01 1.3170e+00 +EPYC ENST00000261172 5.7495e-07 7.9641e-01 5.0000e-01 1.3170e+00 +CDA ENST00000375071 8.1038e-03 5.7980e-01 2.8400e-01 1.3180e+00 +NAGPA ENST00000312251 3.0095e-12 8.9807e-01 6.2500e-01 1.3180e+00 +FKRP ENST00000318584 9.8362e-06 7.5596e-01 4.5500e-01 1.3180e+00 +ZFP37 ENST00000374227 6.1213e-13 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1.5283e-04 7.0420e-01 3.9900e-01 1.3200e+00 +FOXRED1 ENST00000263578 1.9872e-16 9.4524e-01 6.8800e-01 1.3200e+00 +TRIM42 ENST00000286349 3.0721e-19 9.6813e-01 7.2000e-01 1.3200e+00 +KRTAP10-7 ENST00000380102 9.7068e-06 7.5736e-01 4.5600e-01 1.3200e+00 +BOP1 ENST00000307404 9.2793e-02 4.2708e-01 1.7300e-01 1.3200e+00 +SLC25A2 ENST00000239451 2.2001e-03 6.3074e-01 3.2800e-01 1.3200e+00 +PDXP ENST00000215904 2.5559e-01 2.8827e-01 1.0100e-01 1.3200e+00 +PRDM9 ENST00000296682 4.8301e-27 1.0143e+00 7.8700e-01 1.3200e+00 +BCDIN3D ENST00000333924 3.8663e-05 7.3354e-01 4.2900e-01 1.3210e+00 +LRAT ENST00000336356 2.8354e-02 5.1664e-01 2.3400e-01 1.3210e+00 +TCP10L2 ENST00000366832 2.9683e-08 8.3126e-01 5.4000e-01 1.3210e+00 +TSPYL1 ENST00000368608 5.6210e-07 7.9835e-01 5.0200e-01 1.3210e+00 +C4orf48 ENST00000409248 5.1423e-01 0.0000e+00 0.0000e+00 1.3210e+00 +ADA ENST00000372874 2.8825e-12 9.0018e-01 6.2700e-01 1.3210e+00 +ZNF157 ENST00000377073 9.6717e-06 7.5774e-01 4.5600e-01 1.3210e+00 +RAB41 ENST00000276066 5.8306e-04 6.7164e-01 3.6700e-01 1.3210e+00 +KRT72 ENST00000293745 1.3674e-11 8.9165e-01 6.1500e-01 1.3220e+00 +TNFRSF4 ENST00000379236 1.5133e-04 7.0548e-01 4.0000e-01 1.3220e+00 +PCYOX1L ENST00000274569 6.5627e-11 8.8130e-01 6.0200e-01 1.3220e+00 +PKIG ENST00000372889 5.1408e-01 0.0000e+00 0.0000e+00 1.3220e+00 +SLC29A3 ENST00000373189 1.2925e-07 8.1646e-01 5.2200e-01 1.3220e+00 +C15orf61 ENST00000342683 9.2485e-02 4.2782e-01 1.7400e-01 1.3220e+00 +OTUD6B ENST00000285420 1.2841e-07 8.1697e-01 5.2200e-01 1.3230e+00 +GJB3 ENST00000373366 2.1767e-03 6.3246e-01 3.2900e-01 1.3230e+00 +SNX24 ENST00000261369 9.5459e-06 7.5912e-01 4.5700e-01 1.3230e+00 +CTSG ENST00000216336 9.5595e-06 7.5897e-01 4.5600e-01 1.3230e+00 +PPAPDC3 ENST00000372264 7.9976e-03 5.8216e-01 2.8600e-01 1.3230e+00 +OR6C2 ENST00000322678 9.2283e-02 4.2831e-01 1.7400e-01 1.3230e+00 +MRPL17 ENST00000288937 2.8198e-02 5.1774e-01 2.3500e-01 1.3230e+00 +ZNF160 ENST00000429604 2.8175e-02 5.1790e-01 2.3500e-01 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6.8328e-01 3.7300e-01 1.3430e+00 +RP11-178L8.4 ENST00000568879 3.4739e-05 7.4616e-01 4.3700e-01 1.3430e+00 +UTF1 ENST00000304477 5.0847e-01 0.0000e+00 0.0000e+00 1.3430e+00 +SPATA9 ENST00000274432 3.4805e-05 7.4593e-01 4.3700e-01 1.3430e+00 +CYB561D2 ENST00000418577 1.3776e-04 7.1784e-01 4.0700e-01 1.3440e+00 +ANKRD37 ENST00000335174 5.3673e-04 6.8377e-01 3.7300e-01 1.3440e+00 +CCDC11 ENST00000398545 9.6973e-19 9.8036e-01 7.2500e-01 1.3440e+00 +MPST ENST00000397129 3.4664e-05 7.4641e-01 4.3700e-01 1.3440e+00 +STEAP3 ENST00000393110 5.3195e-09 8.5987e-01 5.6700e-01 1.3440e+00 +MCEE ENST00000244217 2.6913e-02 5.2713e-01 2.3900e-01 1.3440e+00 +ANKRD49 ENST00000544612 5.3732e-04 6.8361e-01 3.7300e-01 1.3440e+00 +COQ3 ENST00000254759 2.4344e-08 8.4553e-01 5.4900e-01 1.3440e+00 +EVI2A ENST00000247270 2.0438e-03 6.4273e-01 3.3500e-01 1.3440e+00 +HES5 ENST00000378453 2.4882e-01 2.9515e-01 1.0300e-01 1.3440e+00 +TMEM139 ENST00000359333 7.5458e-03 5.9268e-01 2.9100e-01 1.3450e+00 +LYVE1 ENST00000256178 4.7185e-07 8.1344e-01 5.1100e-01 1.3450e+00 +CXCL16 ENST00000293778 3.4546e-05 7.4682e-01 4.3700e-01 1.3450e+00 +SLC25A34 ENST00000294454 4.7127e-07 8.1355e-01 5.1100e-01 1.3450e+00 +PPP1R14C ENST00000361131 2.0320e-03 6.4369e-01 3.3500e-01 1.3450e+00 +RDH11 ENST00000381346 1.0807e-07 8.3052e-01 5.3100e-01 1.3450e+00 +IL26 ENST00000229134 5.3514e-04 6.8421e-01 3.7400e-01 1.3450e+00 +RGS5 ENST00000530507 5.3488e-04 6.8428e-01 3.7400e-01 1.3450e+00 +TIGD7 ENST00000396862 2.0699e-12 9.1665e-01 6.3800e-01 1.3450e+00 +C15orf43 ENST00000340827 2.0249e-06 7.9379e-01 4.8900e-01 1.3450e+00 +TAF1D ENST00000448108 8.4009e-06 7.7265e-01 4.6500e-01 1.3460e+00 +SLFN12 ENST00000394562 4.6915e-07 8.1394e-01 5.1100e-01 1.3460e+00 +AGER ENST00000375076 6.3528e-16 9.5736e-01 6.9200e-01 1.3460e+00 +GPR182 ENST00000300098 1.3704e-04 7.1853e-01 4.0800e-01 1.3460e+00 +SLC35G6 ENST00000412468 5.3288e-04 6.8483e-01 3.7400e-01 1.3460e+00 +FCGR2A ENST00000271450 2.0054e-06 7.9472e-01 4.8900e-01 1.3460e+00 +FHAD1 ENST00000375995 1.3667e-04 7.1888e-01 4.0800e-01 1.3460e+00 +SPATA31E1 ENST00000325643 2.6776e-02 5.2817e-01 2.3900e-01 1.3470e+00 +AGTR1 ENST00000542281 5.3161e-04 6.8519e-01 3.7400e-01 1.3470e+00 +HSPB11 ENST00000194214 2.0199e-03 6.4467e-01 3.3600e-01 1.3470e+00 +HSPB6 ENST00000592984 8.8703e-02 4.3732e-01 1.7700e-01 1.3470e+00 +AQP11 ENST00000313578 5.3022e-04 6.8557e-01 3.7400e-01 1.3470e+00 +FAM98C ENST00000252530 1.0622e-07 8.3188e-01 5.3200e-01 1.3470e+00 +ORM2 ENST00000431067 2.0003e-06 7.9496e-01 4.8900e-01 1.3470e+00 +UQCRH ENST00000311672 2.0194e-03 6.4471e-01 3.3600e-01 1.3470e+00 +GALR1 ENST00000299727 5.3174e-04 6.8515e-01 3.7400e-01 1.3470e+00 +GOSR2 ENST00000225567 4.6633e-07 8.1446e-01 5.1200e-01 1.3470e+00 +AAR2 ENST00000373932 8.3057e-06 7.7387e-01 4.6500e-01 1.3480e+00 +PCDHB15 ENST00000231173 9.7376e-12 9.0939e-01 6.2800e-01 1.3480e+00 +ZNF215 ENST00000278319 6.1857e-16 9.5848e-01 6.9300e-01 1.3480e+00 +BMP8A ENST00000331593 1.9786e-06 7.9601e-01 4.9000e-01 1.3480e+00 +C9orf131 ENST00000312292 4.6321e-18 9.7742e-01 7.1900e-01 1.3480e+00 +POMZP3 ENST00000310842 5.2926e-04 6.8584e-01 3.7400e-01 1.3480e+00 +GJC3 ENST00000312891 5.2869e-04 6.8600e-01 3.7400e-01 1.3480e+00 +ENOSF1 ENST00000340116 9.0272e-19 9.8307e-01 7.2700e-01 1.3480e+00 +DHCR7 ENST00000355527 3.9490e-13 9.2831e-01 6.5200e-01 1.3490e+00 +ZNF169 ENST00000395395 9.5983e-12 9.1015e-01 6.2800e-01 1.3490e+00 +CENPQ ENST00000335783 1.0450e-07 8.3317e-01 5.3300e-01 1.3490e+00 +BTNL9 ENST00000327705 7.8754e-14 9.3681e-01 6.6300e-01 1.3490e+00 +WDYHV1 ENST00000287387 8.2435e-06 7.7467e-01 4.6600e-01 1.3490e+00 +LONP2 ENST00000285737 4.2411e-28 1.0400e+00 8.0900e-01 1.3490e+00 +BPHL ENST00000380379 4.5804e-07 8.1602e-01 5.1300e-01 1.3490e+00 +IVD ENST00000487418 1.5329e-14 9.4562e-01 6.7500e-01 1.3500e+00 +CCDC170 ENST00000239374 8.6099e-24 1.0181e+00 7.7700e-01 1.3500e+00 +THEG ENST00000342640 5.0204e-09 8.6376e-01 5.6900e-01 1.3500e+00 +GINM1 ENST00000367419 5.0270e-09 8.6367e-01 5.6900e-01 1.3500e+00 +JAGN1 ENST00000307768 7.4462e-03 5.9512e-01 2.9200e-01 1.3500e+00 +PDCL3 ENST00000264254 8.2348e-06 7.7478e-01 4.6600e-01 1.3500e+00 +URGCP-MRPS24 ENST00000603700 5.2507e-04 6.8702e-01 3.7500e-01 1.3500e+00 +FLYWCH1 ENST00000416288 8.6719e-19 9.8460e-01 7.2900e-01 1.3500e+00 +HSD17B1 ENST00000585807 1.3421e-04 7.2130e-01 4.0900e-01 1.3510e+00 +RGL3 ENST00000393423 9.9866e-32 1.0568e+00 8.3300e-01 1.3510e+00 +NUDT22 ENST00000279206 4.5224e-07 8.1713e-01 5.1300e-01 1.3510e+00 +YIPF7 ENST00000332990 8.1847e-06 7.7543e-01 4.6600e-01 1.3510e+00 +ARL2BP ENST00000219204 3.3482e-05 7.5054e-01 4.3900e-01 1.3510e+00 +CCDC109B ENST00000394650 2.2776e-08 8.5037e-01 5.5300e-01 1.3510e+00 +CDK15 ENST00000450471 2.2449e-17 9.7369e-01 7.1300e-01 1.3510e+00 +TUBB1 ENST00000217133 1.0217e-07 8.3496e-01 5.3400e-01 1.3520e+00 +GSTK1 ENST00000479303 1.9374e-06 7.9803e-01 4.9100e-01 1.3520e+00 +LRRC40 ENST00000370952 6.0015e-21 1.0019e+00 7.5200e-01 1.3520e+00 +B3GAT2 ENST00000230053 3.3253e-05 7.5136e-01 4.4000e-01 1.3520e+00 +PPIF ENST00000225174 1.9919e-03 6.4698e-01 3.3700e-01 1.3520e+00 +METTL2A ENST00000311506 3.7556e-13 9.3076e-01 6.5400e-01 1.3520e+00 +PCDHGA8 ENST00000398604 4.2794e-18 9.8052e-01 7.2200e-01 1.3520e+00 +MS4A4A ENST00000337908 8.0964e-06 7.7659e-01 4.6700e-01 1.3530e+00 +H1FX ENST00000333762 8.7710e-02 4.3993e-01 1.7800e-01 1.3530e+00 +PAOX ENST00000278060 4.8573e-09 8.6598e-01 5.7100e-01 1.3530e+00 +RFPL3S ENST00000400234 8.7770e-02 4.3977e-01 1.7800e-01 1.3530e+00 +ITPA ENST00000380113 1.0144e-07 8.3553e-01 5.3400e-01 1.3530e+00 +NDUFS5 ENST00000372969 2.6413e-02 5.3097e-01 2.4100e-01 1.3530e+00 +CEP72 ENST00000264935 1.5766e-19 9.9244e-01 7.3800e-01 1.3530e+00 +KYNU ENST00000264170 4.1806e-18 9.8144e-01 7.2200e-01 1.3530e+00 +FNDC9 ENST00000312349 7.3799e-03 5.9677e-01 2.9300e-01 1.3530e+00 +HLA-DOB ENST00000438763 1.9197e-06 7.9892e-01 4.9200e-01 1.3530e+00 +COMTD1 ENST00000372538 3.3099e-05 7.5191e-01 4.4000e-01 1.3530e+00 +METTL12 ENST00000532971 1.9838e-03 6.4765e-01 3.3700e-01 1.3530e+00 +SLC11A1 ENST00000233202 1.5485e-19 9.9312e-01 7.3800e-01 1.3540e+00 +H2AFJ ENST00000544848 2.4627e-01 2.9785e-01 1.0400e-01 1.3540e+00 +IMPG1 ENST00000369950 1.3662e-29 1.0498e+00 8.2100e-01 1.3540e+00 +SLCO1B1 ENST00000256958 1.1086e-21 1.0081e+00 7.6000e-01 1.3540e+00 +MROH6 ENST00000398882 4.1528e-18 9.8170e-01 7.2300e-01 1.3540e+00 +MRPL24 ENST00000361531 1.9123e-06 7.9929e-01 4.9200e-01 1.3540e+00 +ZNF251 ENST00000292562 1.8294e-12 9.2292e-01 6.4300e-01 1.3540e+00 +GNG2 ENST00000335281 5.0556e-01 0.0000e+00 0.0000e+00 1.3540e+00 +TP53TG5 ENST00000372726 4.4430e-07 8.1867e-01 5.1400e-01 1.3540e+00 +METTL22 ENST00000381920 7.2912e-14 9.4043e-01 6.6600e-01 1.3540e+00 +SDCCAG3 ENST00000357365 3.6526e-13 9.3212e-01 6.5500e-01 1.3540e+00 +DPPA2 ENST00000478945 4.7882e-09 8.6695e-01 5.7200e-01 1.3550e+00 +GPR37L1 ENST00000367282 1.0195e-09 8.8004e-01 5.8800e-01 1.3550e+00 +ENDOV ENST00000518137 1.0129e-09 8.8045e-01 5.8800e-01 1.3550e+00 +LSM5 ENST00000450169 2.6283e-02 5.3199e-01 2.4100e-01 1.3550e+00 +NLRP12 ENST00000324134 3.6493e-28 1.0444e+00 8.1300e-01 1.3550e+00 +LYNX1 ENST00000335822 2.6317e-02 5.3173e-01 2.4100e-01 1.3550e+00 +ERCC8 ENST00000265038 2.7974e-15 9.5655e-01 6.8700e-01 1.3550e+00 +TMEM144 ENST00000296529 4.3842e-11 9.0356e-01 6.1700e-01 1.3550e+00 +C5AR2 ENST00000595464 2.4585e-01 2.9830e-01 1.0400e-01 1.3550e+00 +CXorf36 ENST00000398000 3.2801e-05 7.5299e-01 4.4100e-01 1.3550e+00 +UPK1B ENST00000264234 2.1842e-08 8.5342e-01 5.5500e-01 1.3560e+00 +TMEM91 ENST00000392002 2.6278e-02 5.3203e-01 2.4100e-01 1.3560e+00 +CDK5RAP1 ENST00000346416 7.7821e-19 9.8874e-01 7.3200e-01 1.3560e+00 +NABP1 ENST00000425611 3.2763e-05 7.5313e-01 4.4100e-01 1.3560e+00 +TRMT44 ENST00000389737 2.0315e-22 1.0143e+00 7.6800e-01 1.3560e+00 +R3HDML ENST00000217043 1.8840e-06 8.0072e-01 4.9300e-01 1.3560e+00 +ATG10 ENST00000282185 2.1789e-08 8.5360e-01 5.5500e-01 1.3560e+00 +CLHC1 ENST00000401408 5.5753e-21 1.0045e+00 7.5400e-01 1.3560e+00 +RAB38 ENST00000243662 1.9671e-03 6.4906e-01 3.3800e-01 1.3560e+00 +BBS10 ENST00000393262 1.7467e-12 9.2528e-01 6.4400e-01 1.3570e+00 +KLF17 ENST00000372299 4.6604e-09 8.6878e-01 5.7300e-01 1.3570e+00 +GRAMD2 ENST00000309731 3.4911e-13 9.3434e-01 6.5600e-01 1.3570e+00 +C1orf173 ENST00000326665 1.0824e-42 1.0962e+00 8.9100e-01 1.3570e+00 +CHODL ENST00000299295 2.1485e-08 8.5462e-01 5.5500e-01 1.3580e+00 +FAM210B ENST00000371384 8.7064e-02 4.4165e-01 1.7900e-01 1.3580e+00 +KLC3 ENST00000391946 3.8573e-18 9.8461e-01 7.2500e-01 1.3580e+00 +APOBEC3B ENST00000333467 5.2144e-16 9.6578e-01 6.9800e-01 1.3580e+00 +GGT2 ENST00000401924 1.2986e-04 7.2569e-01 4.1200e-01 1.3580e+00 +MYL1 ENST00000352451 1.3017e-04 7.2538e-01 4.1100e-01 1.3580e+00 +BST1 ENST00000265016 4.2099e-11 9.0584e-01 6.1900e-01 1.3580e+00 +CKMT1B ENST00000300283 3.2331e-05 7.5471e-01 4.4200e-01 1.3580e+00 +COMMD7 ENST00000278980 9.7494e-08 8.3868e-01 5.3600e-01 1.3580e+00 +BARD1 ENST00000260947 1.3777e-24 1.0280e+00 7.8700e-01 1.3580e+00 +THAP3 ENST00000054650 7.2819e-03 5.9925e-01 2.9400e-01 1.3580e+00 +SLC22A5 ENST00000245407 5.2651e-16 9.6536e-01 6.9800e-01 1.3580e+00 +CCDC103 ENST00000417826 5.0909e-04 6.9163e-01 3.7800e-01 1.3590e+00 +NME6 ENST00000421967 4.2713e-07 8.2211e-01 5.1600e-01 1.3590e+00 +SLC51B ENST00000334287 2.4475e-01 2.9948e-01 1.0500e-01 1.3590e+00 +SLC5A9 ENST00000236495 9.2114e-27 1.0403e+00 8.0400e-01 1.3590e+00 +WDSUB1 ENST00000409990 6.7458e-14 9.4411e-01 6.6900e-01 1.3590e+00 +FBLL1 ENST00000338333 8.6897e-02 4.4211e-01 1.7900e-01 1.3590e+00 +TRIM4 ENST00000355947 8.5020e-12 9.1663e-01 6.3300e-01 1.3590e+00 +SLFN5 ENST00000299977 1.7046e-12 9.2653e-01 6.4500e-01 1.3590e+00 +GTF2A2 ENST00000396060 2.6061e-02 5.3375e-01 2.4200e-01 1.3590e+00 +IFI35 ENST00000438323 4.2821e-07 8.2189e-01 5.1600e-01 1.3590e+00 +C12orf29 ENST00000356891 2.1077e-08 8.5603e-01 5.5600e-01 1.3600e+00 +OPN1MW2 ENST00000369929 2.4464e-01 2.9961e-01 1.0500e-01 1.3600e+00 +FAHD2B ENST00000414820 9.5913e-08 8.3998e-01 5.3700e-01 1.3600e+00 +PCBD2 ENST00000512783 2.6044e-02 5.3389e-01 2.4200e-01 1.3600e+00 +OR1L8 ENST00000304865 8.6690e-02 4.4267e-01 1.8000e-01 1.3600e+00 +TMEM213 ENST00000442682 8.6669e-02 4.4272e-01 1.8000e-01 1.3600e+00 +CNFN ENST00000222032 2.6008e-02 5.3418e-01 2.4200e-01 1.3600e+00 +MOCS3 ENST00000244051 1.8387e-06 8.0307e-01 4.9400e-01 1.3600e+00 +FDX1 ENST00000260270 8.6575e-02 4.4298e-01 1.8000e-01 1.3610e+00 +RP11-701P16.2 ENST00000508020 2.4418e-01 3.0011e-01 1.0500e-01 1.3610e+00 +SLC25A45 ENST00000398802 4.2329e-07 8.2289e-01 5.1700e-01 1.3610e+00 +CRISP1 ENST00000335847 1.8344e-06 8.0330e-01 4.9400e-01 1.3610e+00 +PRH1 ENST00000428168 7.2243e-03 6.0073e-01 2.9500e-01 1.3610e+00 +CAPNS2 ENST00000457326 1.9337e-03 6.5192e-01 3.4000e-01 1.3610e+00 +CCR10 ENST00000332438 5.0508e-04 6.9281e-01 3.7800e-01 1.3610e+00 +TBXA2R ENST00000411851 1.2823e-04 7.2738e-01 4.1300e-01 1.3610e+00 +PVALB ENST00000216200 8.6602e-02 4.4290e-01 1.8000e-01 1.3610e+00 +LXN ENST00000264265 1.8254e-06 8.0377e-01 4.9500e-01 1.3610e+00 +TMCO1 ENST00000367881 9.4100e-10 8.8511e-01 5.9100e-01 1.3620e+00 +TBX10 ENST00000335385 2.0686e-08 8.5740e-01 5.5700e-01 1.3620e+00 +TMEM26 ENST00000399298 2.0721e-08 8.5728e-01 5.5700e-01 1.3620e+00 +KCNE4 ENST00000604125 2.4409e-01 3.0020e-01 1.0500e-01 1.3620e+00 +TEX35 ENST00000319416 9.4330e-08 8.4131e-01 5.3800e-01 1.3620e+00 +KLK2 ENST00000325321 1.2775e-04 7.2789e-01 4.1300e-01 1.3620e+00 +SHMT1 ENST00000316694 1.2750e-14 9.5404e-01 6.8100e-01 1.3620e+00 +PRSS53 ENST00000280606 9.3515e-17 9.7598e-01 7.1000e-01 1.3630e+00 +FN3K ENST00000300784 2.0577e-08 8.5779e-01 5.5700e-01 1.3630e+00 +C11orf53 ENST00000280325 1.9229e-03 6.5286e-01 3.4000e-01 1.3630e+00 +METTL21A ENST00000411432 5.0104e-04 6.9402e-01 3.7900e-01 1.3630e+00 +RPP14 ENST00000445193 1.9269e-03 6.5251e-01 3.4000e-01 1.3630e+00 +NDUFA4L2 ENST00000393825 8.6367e-02 4.4354e-01 1.8000e-01 1.3630e+00 +POTEJ ENST00000409602 2.0619e-08 8.5764e-01 5.5700e-01 1.3630e+00 +KHDC1L ENST00000370388 8.6279e-02 4.4378e-01 1.8000e-01 1.3630e+00 +KLK12 ENST00000250351 3.1679e-05 7.5715e-01 4.4300e-01 1.3630e+00 +NOD2 ENST00000300589 1.9834e-30 1.0603e+00 8.3200e-01 1.3630e+00 +SUSD5 ENST00000309558 4.0003e-11 9.0873e-01 6.2100e-01 1.3630e+00 +NKIRAS1 ENST00000443659 5.0065e-04 6.9413e-01 3.7900e-01 1.3630e+00 +ERVFRD-1 ENST00000472091 2.5857e-02 5.3539e-01 2.4200e-01 1.3630e+00 +ACSM2A ENST00000573854 3.2754e-23 1.0245e+00 7.7800e-01 1.3640e+00 +FATE1 ENST00000370350 7.1681e-03 6.0219e-01 2.9500e-01 1.3640e+00 +GPR68 ENST00000531499 4.9976e-04 6.9440e-01 3.7900e-01 1.3640e+00 +CYB5R1 ENST00000367249 4.3643e-09 8.7324e-01 5.7600e-01 1.3640e+00 +PPP1R35 ENST00000292330 7.1662e-03 6.0224e-01 2.9500e-01 1.3640e+00 +TUBA3E ENST00000312988 2.0308e-08 8.5875e-01 5.5800e-01 1.3640e+00 +ADTRP ENST00000229583 4.0967e-07 8.2576e-01 5.1900e-01 1.3650e+00 +C3orf62 ENST00000343010 1.2633e-04 7.2939e-01 4.1400e-01 1.3650e+00 +ALG10B ENST00000308742 2.0263e-08 8.5892e-01 5.5800e-01 1.3650e+00 +AC117834.1 ENST00000391681 5.0258e-01 0.0000e+00 0.0000e+00 1.3650e+00 +POLR2J ENST00000292614 7.1512e-03 6.0263e-01 2.9600e-01 1.3650e+00 +ABCG8 ENST00000272286 2.3838e-20 1.0067e+00 7.5200e-01 1.3650e+00 +CCR3 ENST00000545097 1.2636e-04 7.2935e-01 4.1400e-01 1.3650e+00 +LYG1 ENST00000409448 3.1330e-05 7.5848e-01 4.4400e-01 1.3650e+00 +ANKRD53 ENST00000360589 4.0883e-07 8.2594e-01 5.1900e-01 1.3650e+00 +SLC15A3 ENST00000227880 7.7754e-12 9.2144e-01 6.3600e-01 1.3660e+00 +MAP1LC3B ENST00000268607 1.9065e-03 6.5429e-01 3.4100e-01 1.3660e+00 +CD200R1 ENST00000308611 4.3137e-09 8.7403e-01 5.7600e-01 1.3660e+00 +FANCA ENST00000389301 1.5943e-68 1.1525e+00 9.7600e-01 1.3660e+00 +CYP20A1 ENST00000356079 8.8921e-17 9.7811e-01 7.1200e-01 1.3660e+00 +C17orf74 ENST00000333870 7.7303e-12 9.2175e-01 6.3600e-01 1.3660e+00 +PSMB10 ENST00000358514 1.7692e-06 8.0680e-01 4.9700e-01 1.3660e+00 +EFCAB13 ENST00000331493 6.4531e-32 1.0685e+00 8.4300e-01 1.3660e+00 +CRNN ENST00000271835 1.2577e-04 7.2998e-01 4.1400e-01 1.3660e+00 +ITPRIPL1 ENST00000361124 1.8771e-10 8.9977e-01 6.0800e-01 1.3660e+00 +C20orf96 ENST00000360321 1.1780e-14 9.5770e-01 6.8300e-01 1.3670e+00 +TGM6 ENST00000202625 1.1154e-24 1.0348e+00 7.9200e-01 1.3670e+00 +RIPK3 ENST00000216274 1.1874e-14 9.5733e-01 6.8300e-01 1.3670e+00 +ASIC5 ENST00000537611 6.0266e-14 9.4949e-01 6.7200e-01 1.3670e+00 +ATP5I ENST00000304312 8.5765e-02 4.4520e-01 1.8100e-01 1.3670e+00 +MYLK4 ENST00000274643 3.0554e-13 9.4094e-01 6.6100e-01 1.3670e+00 +ATP5SL ENST00000417807 1.9807e-08 8.6059e-01 5.5900e-01 1.3670e+00 +MMP20 ENST00000260228 6.0776e-14 9.4909e-01 6.7200e-01 1.3670e+00 +FCER1A ENST00000368115 3.0826e-05 7.6043e-01 4.4500e-01 1.3680e+00 +FCER2 ENST00000346664 7.6122e-12 9.2259e-01 6.3700e-01 1.3680e+00 +RAD9B ENST00000392672 3.0239e-13 9.4145e-01 6.6100e-01 1.3680e+00 +RP11-105C20.2 ENST00000564533 5.0170e-01 0.0000e+00 0.0000e+00 1.3680e+00 +PILRB ENST00000610247 1.2455e-04 7.3130e-01 4.1500e-01 1.3680e+00 +PIGP ENST00000464265 1.8935e-03 6.5545e-01 3.4100e-01 1.3680e+00 +LCN10 ENST00000497771 3.0786e-05 7.6059e-01 4.4500e-01 1.3680e+00 +RHBDL2 ENST00000289248 8.9365e-08 8.4563e-01 5.4100e-01 1.3690e+00 +WNT10A ENST00000258411 4.1667e-09 8.7640e-01 5.7800e-01 1.3690e+00 +TRIML1 ENST00000332517 3.7040e-11 9.1310e-01 6.2400e-01 1.3690e+00 +UBE2V1 ENST00000340309 1.2406e-04 7.3183e-01 4.1500e-01 1.3690e+00 +ODF3L2 ENST00000315489 2.5553e-02 5.3786e-01 2.4400e-01 1.3690e+00 +SLC34A3 ENST00000538474 5.8863e-14 9.5062e-01 6.7300e-01 1.3690e+00 +BAK1 ENST00000374467 7.4028e-06 7.8621e-01 4.7300e-01 1.3690e+00 +DAD1 ENST00000250498 8.5505e-02 4.4592e-01 1.8100e-01 1.3690e+00 +TMEM184A ENST00000297477 3.6600e-11 9.1378e-01 6.2400e-01 1.3700e+00 +TDRD12 ENST00000421545 2.9169e-13 9.4325e-01 6.6300e-01 1.3700e+00 +XRCC2 ENST00000359321 3.9550e-07 8.2885e-01 5.2100e-01 1.3700e+00 +TSPAN1 ENST00000372003 7.3518e-06 7.8695e-01 4.7300e-01 1.3700e+00 +FETUB ENST00000265029 8.8804e-08 8.4613e-01 5.4100e-01 1.3700e+00 +NTSR1 ENST00000370501 1.9280e-08 8.6258e-01 5.6100e-01 1.3700e+00 +TMEM216 ENST00000515837 1.8855e-03 6.5616e-01 3.4200e-01 1.3700e+00 +FASTKD1 ENST00000453153 4.5631e-29 1.0598e+00 8.2700e-01 1.3710e+00 +PCDHB6 ENST00000231136 1.7745e-10 9.0315e-01 6.1000e-01 1.3710e+00 +ANO7 ENST00000274979 3.4578e-42 1.1057e+00 8.9700e-01 1.3710e+00 +OR4F15 ENST00000332238 8.5180e-02 4.4682e-01 1.8100e-01 1.3710e+00 +ABRACL ENST00000367660 2.4171e-01 3.0283e-01 1.0600e-01 1.3710e+00 +OR5M8 ENST00000327216 2.5433e-02 5.3885e-01 2.4400e-01 1.3710e+00 +CNTD2 ENST00000430325 4.8667e-04 6.9840e-01 3.8100e-01 1.3710e+00 +PFN3 ENST00000358571 5.0096e-01 0.0000e+00 0.0000e+00 1.3710e+00 +SAP25 ENST00000538735 8.5030e-02 4.4724e-01 1.8100e-01 1.3720e+00 +NDUFA5 ENST00000355749 1.8728e-03 6.5730e-01 3.4200e-01 1.3720e+00 +HDHD3 ENST00000238379 1.8719e-03 6.5738e-01 3.4200e-01 1.3720e+00 +CCL4 ENST00000250151 2.4134e-01 3.0324e-01 1.0600e-01 1.3720e+00 +PDCD2 ENST00000541970 3.8955e-07 8.3018e-01 5.2200e-01 1.3720e+00 +DPH1 ENST00000263083 8.0168e-17 9.8250e-01 7.1500e-01 1.3720e+00 +CA2 ENST00000285379 1.6946e-06 8.1098e-01 4.9900e-01 1.3730e+00 +C16orf59 ENST00000361837 7.1044e-12 9.2634e-01 6.3900e-01 1.3730e+00 +MICALL2 ENST00000297508 3.4420e-26 1.0474e+00 8.0700e-01 1.3730e+00 +SLC17A1 ENST00000244527 4.1179e-16 9.7603e-01 7.0600e-01 1.3730e+00 +CCS ENST00000533244 8.6291e-08 8.4844e-01 5.4300e-01 1.3730e+00 +RGPD1 ENST00000559485 7.0125e-03 6.0631e-01 2.9700e-01 1.3730e+00 +SLC26A10 ENST00000320442 2.0972e-15 9.6943e-01 6.9700e-01 1.3730e+00 +SPDYE1 ENST00000258704 3.5518e-11 9.1549e-01 6.2600e-01 1.3730e+00 +IKBKG ENST00000369609 8.4853e-02 4.4774e-01 1.8200e-01 1.3730e+00 +SHCBP1L ENST00000367547 1.5171e-17 9.8969e-01 7.2400e-01 1.3730e+00 +ACTR3C ENST00000539352 7.2147e-06 7.8898e-01 4.7500e-01 1.3740e+00 +FEM1A ENST00000269856 8.3375e-10 8.9283e-01 5.9600e-01 1.3740e+00 +CSN2 ENST00000353151 7.1828e-06 7.8946e-01 4.7500e-01 1.3740e+00 +KLHL34 ENST00000379499 3.0037e-05 7.6355e-01 4.4700e-01 1.3740e+00 +SPRY4 ENST00000344120 4.8210e-04 6.9982e-01 3.8200e-01 1.3740e+00 +PCDHB4 ENST00000194152 7.0275e-12 9.2694e-01 6.4000e-01 1.3740e+00 +ADPRHL1 ENST00000375418 3.4910e-11 9.1648e-01 6.2600e-01 1.3740e+00 +AMBP ENST00000265132 2.7886e-13 9.4550e-01 6.6400e-01 1.3740e+00 +ELOVL2 ENST00000354666 8.3719e-10 8.9257e-01 5.9600e-01 1.3740e+00 +C9orf50 ENST00000372478 1.8577e-08 8.6532e-01 5.6200e-01 1.3750e+00 +CASQ2 ENST00000261448 1.3885e-12 9.3716e-01 6.5300e-01 1.3750e+00 +BDH2 ENST00000296424 8.5318e-08 8.4935e-01 5.4300e-01 1.3750e+00 +CYP4F12 ENST00000550308 1.4740e-17 9.9089e-01 7.2500e-01 1.3750e+00 +CYP4F2 ENST00000221700 7.5803e-17 9.8489e-01 7.1700e-01 1.3750e+00 +TOMM5 ENST00000544379 4.9975e-01 0.0000e+00 0.0000e+00 1.3750e+00 +CDKN1A ENST00000405375 1.8575e-03 6.5869e-01 3.4300e-01 1.3750e+00 +CCDC157 ENST00000405659 7.1565e-22 1.0236e+00 7.7200e-01 1.3750e+00 +ZNF136 ENST00000343979 4.7939e-04 7.0068e-01 3.8200e-01 1.3750e+00 +CD209 ENST00000315599 2.7418e-13 9.4636e-01 6.6500e-01 1.3750e+00 +HAX1 ENST00000328703 8.4813e-08 8.4983e-01 5.4400e-01 1.3750e+00 +SLC25A35 ENST00000380067 1.8465e-08 8.6576e-01 5.6300e-01 1.3750e+00 +KIAA0020 ENST00000397885 3.2052e-26 1.0496e+00 8.0900e-01 1.3760e+00 +CTSW ENST00000307886 6.8595e-12 9.2826e-01 6.4100e-01 1.3760e+00 +PPCDC ENST00000342932 4.7853e-04 7.0095e-01 3.8300e-01 1.3760e+00 +SLC22A13 ENST00000311856 5.3133e-14 9.5557e-01 6.7700e-01 1.3760e+00 +SPINT4 ENST00000279058 8.4396e-02 4.4904e-01 1.8200e-01 1.3760e+00 +TGFBR3L ENST00000565886 8.4471e-02 4.4882e-01 1.8200e-01 1.3760e+00 +MRPS25 ENST00000253686 4.7858e-04 7.0093e-01 3.8300e-01 1.3760e+00 +C21orf33 ENST00000291577 2.9727e-05 7.6481e-01 4.4800e-01 1.3760e+00 +KRTAP5-5 ENST00000399676 8.4477e-02 4.4881e-01 1.8200e-01 1.3760e+00 +CYP27A1 ENST00000258415 5.2916e-19 1.0038e+00 7.4300e-01 1.3760e+00 +CYP39A1 ENST00000275016 3.8748e-16 9.7870e-01 7.0800e-01 1.3760e+00 +ACTRT2 ENST00000378404 4.7660e-04 7.0156e-01 3.8300e-01 1.3770e+00 +EPN3 ENST00000268933 7.4151e-17 9.8584e-01 7.1700e-01 1.3770e+00 +MYL4 ENST00000354968 1.2029e-04 7.3599e-01 4.1700e-01 1.3770e+00 +TMEM251 ENST00000415050 6.9412e-03 6.0825e-01 2.9800e-01 1.3770e+00 +METTL7A ENST00000548553 4.7530e-04 7.0198e-01 3.8300e-01 1.3780e+00 +GABRA6 ENST00000274545 1.3360e-12 9.3918e-01 6.5400e-01 1.3780e+00 +BCL2L12 ENST00000246785 3.8273e-09 8.8222e-01 5.8200e-01 1.3780e+00 +MSLNL ENST00000293892 3.0489e-26 1.0512e+00 8.1000e-01 1.3780e+00 +LURAP1L ENST00000319264 2.5029e-02 5.4224e-01 2.4600e-01 1.3780e+00 +GNB3 ENST00000229264 3.3303e-11 9.1919e-01 6.2800e-01 1.3780e+00 +STX11 ENST00000367568 4.7412e-04 7.0235e-01 3.8300e-01 1.3790e+00 +NUDT13 ENST00000357321 6.6163e-12 9.3024e-01 6.4200e-01 1.3790e+00 +HAS1 ENST00000222115 1.3084e-12 9.4028e-01 6.5500e-01 1.3790e+00 +SLC25A15 ENST00000338625 3.7038e-07 8.3463e-01 5.2400e-01 1.3790e+00 +TMEM200B ENST00000420504 1.8333e-03 6.6092e-01 3.4400e-01 1.3790e+00 +ZNF99 ENST00000596209 2.4950e-02 5.4291e-01 2.4600e-01 1.3800e+00 +LYPD5 ENST00000377950 4.7161e-04 7.0316e-01 3.8400e-01 1.3800e+00 +MRPL3 ENST00000264995 1.3045e-12 9.4044e-01 6.5500e-01 1.3800e+00 +MSS51 ENST00000299432 3.2758e-11 9.2014e-01 6.2900e-01 1.3800e+00 +HES6 ENST00000272937 8.3905e-02 4.5044e-01 1.8300e-01 1.3800e+00 +KIF2B ENST00000268919 1.6069e-10 9.0916e-01 6.1400e-01 1.3800e+00 +TET2 ENST00000540549 4.3334e-54 1.1399e+00 9.4600e-01 1.3800e+00 +THNSL1 ENST00000524413 1.3403e-17 9.9486e-01 7.2800e-01 1.3800e+00 +SURF2 ENST00000371964 6.9279e-06 7.9338e-01 4.7700e-01 1.3810e+00 +RAB37 ENST00000392614 8.1116e-08 8.5342e-01 5.4600e-01 1.3810e+00 +OR2B3 ENST00000377173 6.8596e-03 6.1050e-01 2.9900e-01 1.3810e+00 +CPNE7 ENST00000268720 4.2743e-24 1.0414e+00 7.9400e-01 1.3810e+00 +NKX3-1 ENST00000380871 4.7049e-04 7.0352e-01 3.8400e-01 1.3810e+00 +OR6N2 ENST00000339258 1.8194e-03 6.6221e-01 3.4500e-01 1.3810e+00 +TLR5 ENST00000540964 2.4773e-13 9.5148e-01 6.6800e-01 1.3820e+00 +ORAOV1 ENST00000279147 1.8149e-03 6.6263e-01 3.4500e-01 1.3820e+00 +CYP4F3 ENST00000221307 3.5413e-16 9.8269e-01 7.1100e-01 1.3820e+00 +LRRC61 ENST00000359623 1.8145e-03 6.6267e-01 3.4500e-01 1.3820e+00 +FAIM ENST00000338446 1.1755e-04 7.3912e-01 4.1900e-01 1.3820e+00 +MRPL15 ENST00000260102 1.6024e-06 8.1643e-01 5.0300e-01 1.3820e+00 +SDCBP2 ENST00000360779 3.6357e-07 8.3627e-01 5.2500e-01 1.3820e+00 +DEFA4 ENST00000297435 4.9798e-01 0.0000e+00 0.0000e+00 1.3820e+00 +CASP16 ENST00000428155 1.8103e-03 6.6307e-01 3.4500e-01 1.3830e+00 +CTNNBIP1 ENST00000377263 2.4772e-02 5.4444e-01 2.4700e-01 1.3830e+00 +PRPH ENST00000257860 4.7898e-14 9.6063e-01 6.8000e-01 1.3830e+00 +OR1D5 ENST00000575751 2.4783e-02 5.4434e-01 2.4700e-01 1.3830e+00 +SLC27A6 ENST00000262462 2.4339e-18 1.0032e+00 7.3800e-01 1.3830e+00 +AIG1 ENST00000357847 3.6161e-07 8.3674e-01 5.2600e-01 1.3830e+00 +RIPPLY3 ENST00000329553 8.3551e-02 4.5146e-01 1.8300e-01 1.3830e+00 +PHYKPL ENST00000308158 4.7744e-14 9.6078e-01 6.8000e-01 1.3830e+00 +CDCA4 ENST00000336219 8.3527e-02 4.5153e-01 1.8300e-01 1.3830e+00 +POMC ENST00000405623 1.1658e-04 7.4024e-01 4.2000e-01 1.3840e+00 +RAET1G ENST00000367360 6.8212e-06 7.9506e-01 4.7800e-01 1.3840e+00 +TP53INP1 ENST00000342697 4.6552e-04 7.0514e-01 3.8500e-01 1.3840e+00 +UGT2A2 ENST00000457664 4.7525e-14 9.6101e-01 6.8100e-01 1.3840e+00 +HSPA6 ENST00000309758 6.8282e-06 7.9495e-01 4.7800e-01 1.3840e+00 +ABCG5 ENST00000260645 3.0810e-21 1.0262e+00 7.7000e-01 1.3850e+00 +ANKRD16 ENST00000380094 7.4267e-10 9.0029e-01 6.0100e-01 1.3850e+00 +BAAT ENST00000259407 7.8651e-08 8.5591e-01 5.4700e-01 1.3850e+00 +MSC ENST00000325509 2.4651e-02 5.4549e-01 2.4700e-01 1.3850e+00 +PRM2 ENST00000241808 2.4644e-02 5.4555e-01 2.4700e-01 1.3850e+00 +ZNF230 ENST00000429154 8.3152e-02 4.5262e-01 1.8400e-01 1.3850e+00 +VWA2 ENST00000603594 1.2242e-17 9.9867e-01 7.3100e-01 1.3860e+00 +MOCS2 ENST00000396954 4.6138e-04 7.0650e-01 3.8600e-01 1.3860e+00 +OCM2 ENST00000257627 2.4605e-02 5.4589e-01 2.4700e-01 1.3860e+00 +ST6GALNAC4 ENST00000335791 3.5202e-07 8.3913e-01 5.2700e-01 1.3870e+00 +RFESD ENST00000458310 6.7235e-06 7.9663e-01 4.7900e-01 1.3870e+00 +PPP1R3E ENST00000452015 2.3729e-01 3.0787e-01 1.0800e-01 1.3870e+00 +CYP3A5 ENST00000222982 6.2948e-17 9.9291e-01 7.2300e-01 1.3870e+00 +ACP6 ENST00000369238 2.3344e-13 9.5451e-01 6.7100e-01 1.3870e+00 +C16orf74 ENST00000284245 4.9655e-01 0.0000e+00 0.0000e+00 1.3870e+00 +GNG7 ENST00000382159 4.9663e-01 0.0000e+00 0.0000e+00 1.3870e+00 +TBPL2 ENST00000247219 1.4914e-10 9.1371e-01 6.1800e-01 1.3870e+00 +SLC25A31 ENST00000281154 7.3162e-10 9.0126e-01 6.0200e-01 1.3870e+00 +ATP5H ENST00000301587 4.5999e-04 7.0697e-01 3.8600e-01 1.3870e+00 +GH2 ENST00000332800 2.4553e-02 5.4634e-01 2.4700e-01 1.3870e+00 +LRRC53 ENST00000294635 1.4846e-10 9.1399e-01 6.1800e-01 1.3870e+00 +GALNT8 ENST00000252318 8.0674e-20 1.0181e+00 7.5700e-01 1.3880e+00 +MILR1 ENST00000605096 2.4528e-02 5.4656e-01 2.4800e-01 1.3880e+00 +OR2A12 ENST00000408949 2.4530e-02 5.4654e-01 2.4700e-01 1.3880e+00 +CRYBA4 ENST00000354760 3.4999e-09 8.8840e-01 5.8600e-01 1.3880e+00 +MRM1 ENST00000250156 6.6719e-06 7.9747e-01 4.8000e-01 1.3880e+00 +METTL18 ENST00000310392 2.8027e-05 7.7195e-01 4.5200e-01 1.3880e+00 +SNRPA ENST00000243563 2.8099e-05 7.7164e-01 4.5200e-01 1.3880e+00 +SPACA3 ENST00000269053 1.1484e-04 7.4230e-01 4.2100e-01 1.3880e+00 +GALE ENST00000374497 1.4757e-10 9.1436e-01 6.1800e-01 1.3880e+00 +TMEM235 ENST00000551068 4.5831e-04 7.0753e-01 3.8600e-01 1.3880e+00 +DNAJC28 ENST00000314399 1.6455e-08 8.7434e-01 5.6800e-01 1.3890e+00 +NPC2 ENST00000555619 1.7755e-03 6.6639e-01 3.4700e-01 1.3890e+00 +SLC17A9 ENST00000370351 6.0979e-17 9.9429e-01 7.2400e-01 1.3890e+00 +MLIP ENST00000274897 3.1564e-16 9.8783e-01 7.1400e-01 1.3890e+00 +MYOZ3 ENST00000297130 2.7932e-05 7.7236e-01 4.5200e-01 1.3890e+00 +RNF186 ENST00000375121 8.2589e-02 4.5428e-01 1.8400e-01 1.3890e+00 +IKBIP ENST00000299157 7.6128e-08 8.5855e-01 5.4900e-01 1.3890e+00 +CITED1 ENST00000453707 2.4446e-02 5.4728e-01 2.4800e-01 1.3890e+00 +C16orf58 ENST00000327237 1.1367e-17 1.0018e+00 7.3300e-01 1.3900e+00 +CYP2J2 ENST00000371204 1.6181e-15 9.8130e-01 7.0500e-01 1.3900e+00 +BDH1 ENST00000392379 7.5703e-08 8.5901e-01 5.4900e-01 1.3900e+00 +MTAP ENST00000380172 7.5973e-08 8.5872e-01 5.4900e-01 1.3900e+00 +NECAB2 ENST00000305202 2.2364e-13 9.5670e-01 6.7200e-01 1.3900e+00 +ASRGL1 ENST00000415229 2.7632e-05 7.7368e-01 4.5300e-01 1.3910e+00 +AK3 ENST00000381809 1.1350e-04 7.4390e-01 4.2200e-01 1.3910e+00 +SCRN2 ENST00000290216 5.7373e-12 9.3812e-01 6.4700e-01 1.3910e+00 +TMEM30B ENST00000555868 2.7589e-05 7.7387e-01 4.5300e-01 1.3910e+00 +GSTM2 ENST00000241337 3.3913e-07 8.4244e-01 5.2900e-01 1.3920e+00 +TBXAS1 ENST00000416849 1.4088e-20 1.0266e+00 7.6700e-01 1.3920e+00 +FOXD4L3 ENST00000342833 4.9542e-01 0.0000e+00 0.0000e+00 1.3920e+00 +FAM107B ENST00000181796 7.4318e-08 8.6051e-01 5.5000e-01 1.3920e+00 +TUBAL3 ENST00000380419 7.4351e-08 8.6047e-01 5.5000e-01 1.3920e+00 +FAM187A ENST00000331733 6.5367e-06 7.9970e-01 4.8100e-01 1.3920e+00 +RABEPK ENST00000373538 2.8422e-11 9.2838e-01 6.3400e-01 1.3920e+00 +PTH2R ENST00000272847 1.4112e-20 1.0265e+00 7.6700e-01 1.3920e+00 +ADRA1A ENST00000380586 3.3722e-07 8.4295e-01 5.3000e-01 1.3930e+00 +CCDC129 ENST00000451887 6.5498e-36 1.1031e+00 8.8000e-01 1.3930e+00 +ORC6 ENST00000219097 3.3618e-07 8.4322e-01 5.3000e-01 1.3930e+00 +MARCH10 ENST00000311269 3.2957e-24 1.0503e+00 8.0100e-01 1.3930e+00 +PCK2 ENST00000216780 1.7471e-23 1.0462e+00 7.9500e-01 1.3930e+00 +SPINK14 ENST00000356972 2.4203e-02 5.4943e-01 2.4900e-01 1.3940e+00 +TRAM1L1 ENST00000310754 6.6436e-03 6.1663e-01 3.0200e-01 1.3940e+00 +ARSH ENST00000381130 7.3193e-08 8.6175e-01 5.5100e-01 1.3940e+00 +ATP5S ENST00000311459 6.4510e-06 8.0114e-01 4.8200e-01 1.3940e+00 +RGS13 ENST00000391995 4.4790e-04 7.1105e-01 3.8800e-01 1.3940e+00 +CDKN2D ENST00000393599 4.9473e-01 0.0000e+00 0.0000e+00 1.3940e+00 +C1orf220 ENST00000319387 2.3559e-01 3.0986e-01 1.0800e-01 1.3940e+00 +QPCTL ENST00000012049 1.5671e-08 8.7799e-01 5.7100e-01 1.3940e+00 +SLC2A10 ENST00000359271 1.5672e-08 8.7798e-01 5.7100e-01 1.3940e+00 +KRT78 ENST00000304620 1.4942e-15 9.8501e-01 7.0800e-01 1.3950e+00 +ABHD14A ENST00000273596 6.4241e-06 8.0160e-01 4.8200e-01 1.3950e+00 +SPA17 ENST00000532692 6.6161e-03 6.1743e-01 3.0300e-01 1.3950e+00 +DNASE1L2 ENST00000564065 3.3152e-07 8.4446e-01 5.3000e-01 1.3950e+00 +FDCSP ENST00000317987 8.1818e-02 4.5657e-01 1.8500e-01 1.3950e+00 +PMVK ENST00000368467 2.7113e-05 7.7600e-01 4.5400e-01 1.3950e+00 +KRTAP10-5 ENST00000400372 4.4641e-04 7.1156e-01 3.8800e-01 1.3950e+00 +MND1 ENST00000240488 3.2813e-09 8.9289e-01 5.8900e-01 1.3950e+00 +OR2V2 ENST00000328275 8.1893e-02 4.5635e-01 1.8500e-01 1.3950e+00 +SLC35B3 ENST00000379660 1.3646e-10 9.1917e-01 6.2100e-01 1.3950e+00 +C1orf109 ENST00000358011 1.4731e-06 8.2467e-01 5.0800e-01 1.3960e+00 +KRT36 ENST00000328119 2.0568e-13 9.6101e-01 6.7500e-01 1.3960e+00 +CRLF2 ENST00000381567 3.3104e-07 8.4459e-01 5.3100e-01 1.3960e+00 +C21orf2 ENST00000397956 3.2910e-07 8.4512e-01 5.3100e-01 1.3960e+00 +TOR1AIP2 ENST00000367612 3.2484e-09 8.9359e-01 5.8900e-01 1.3960e+00 +LRRC27 ENST00000368614 1.0059e-17 1.0070e+00 7.3700e-01 1.3970e+00 +PM20D1 ENST00000367136 1.8989e-18 1.0134e+00 7.4600e-01 1.3970e+00 +KRTAP3-2 ENST00000391587 4.9412e-01 0.0000e+00 0.0000e+00 1.3970e+00 +KRTAP4-8 ENST00000333822 2.4058e-02 5.5074e-01 2.4900e-01 1.3970e+00 +MED28 ENST00000237380 1.1083e-04 7.4716e-01 4.2400e-01 1.3970e+00 +HEYL ENST00000372852 3.2662e-07 8.4579e-01 5.3100e-01 1.3970e+00 +ZNF878 ENST00000547628 8.1539e-02 4.5741e-01 1.8500e-01 1.3970e+00 +IRAK1BP1 ENST00000369940 1.4490e-06 8.2630e-01 5.0900e-01 1.3980e+00 +ZNF426 ENST00000535489 6.3008e-06 8.0372e-01 4.8300e-01 1.3980e+00 +C12orf39 ENST00000256969 1.1029e-04 7.4783e-01 4.2400e-01 1.3980e+00 +MS4A15 ENST00000405633 4.4265e-04 7.1286e-01 3.8900e-01 1.3980e+00 +ZNF17 ENST00000601808 2.3465e-01 3.1097e-01 1.0900e-01 1.3980e+00 +GPANK1 ENST00000375906 3.2444e-07 8.4639e-01 5.3200e-01 1.3980e+00 +CPA2 ENST00000222481 1.4033e-15 9.8794e-01 7.1000e-01 1.3990e+00 +GLYATL3 ENST00000371197 7.0711e-08 8.6456e-01 5.5300e-01 1.3990e+00 +SNX32 ENST00000308342 1.8347e-18 1.0149e+00 7.4700e-01 1.3990e+00 +CTHRC1 ENST00000330295 2.6661e-05 7.7805e-01 4.5600e-01 1.3990e+00 +RSPO1 ENST00000356545 1.4418e-06 8.2679e-01 5.0900e-01 1.3990e+00 +TMEM106C ENST00000429772 1.5025e-08 8.8115e-01 5.7300e-01 1.3990e+00 +ZNF841 ENST00000389534 2.3931e-02 5.5189e-01 2.5000e-01 1.3990e+00 +C5orf38 ENST00000334000 1.7218e-03 6.7169e-01 3.5000e-01 1.3990e+00 +TEX26 ENST00000380473 3.1421e-09 8.9592e-01 5.9100e-01 1.3990e+00 +LTB4R2 ENST00000543919 4.3854e-04 7.1431e-01 3.9000e-01 1.4000e+00 +TFB1M ENST00000367166 6.3927e-10 9.1008e-01 6.0800e-01 1.4000e+00 +NDUFA4 ENST00000339600 2.3901e-02 5.5216e-01 2.5000e-01 1.4000e+00 +ROMO1 ENST00000374078 2.3400e-01 3.1175e-01 1.0900e-01 1.4000e+00 +AC024592.12 ENST00000586349 2.3907e-02 5.5211e-01 2.5000e-01 1.4000e+00 +LYPLAL1 ENST00000366928 2.6427e-05 7.7913e-01 4.5600e-01 1.4000e+00 +MYRFL ENST00000535034 3.0843e-09 8.9722e-01 5.9200e-01 1.4010e+00 +MS4A3 ENST00000278865 2.6344e-05 7.7952e-01 4.5600e-01 1.4010e+00 +INA ENST00000369849 1.4818e-08 8.8220e-01 5.7300e-01 1.4010e+00 +CPA4 ENST00000222482 9.3852e-18 1.0100e+00 7.3900e-01 1.4010e+00 +KCNH6 ENST00000583023 7.1244e-31 1.0898e+00 8.5500e-01 1.4010e+00 +POLR1C ENST00000372389 6.3221e-10 9.1081e-01 6.0800e-01 1.4010e+00 +BHMT ENST00000274353 3.7390e-14 9.7290e-01 6.8900e-01 1.4010e+00 +SCN2B ENST00000278947 1.7119e-03 6.7269e-01 3.5000e-01 1.4010e+00 +ZNF524 ENST00000591046 8.1085e-02 4.5880e-01 1.8600e-01 1.4010e+00 +TMEM42 ENST00000302392 8.0845e-02 4.5953e-01 1.8600e-01 1.4020e+00 +HSBP1 ENST00000433866 2.3354e-01 3.1230e-01 1.0900e-01 1.4020e+00 +CYP2C9 ENST00000260682 1.2709e-10 9.2358e-01 6.2400e-01 1.4020e+00 +KRT26 ENST00000335552 7.0954e-15 9.8175e-01 7.0000e-01 1.4020e+00 +ARID3C ENST00000378909 3.0544e-09 8.9791e-01 5.9200e-01 1.4020e+00 +ACPP ENST00000351273 2.5463e-16 9.9756e-01 7.2100e-01 1.4030e+00 +DPM3 ENST00000368399 2.3318e-01 3.1275e-01 1.0900e-01 1.4030e+00 +P2RX2 ENST00000343948 9.6508e-13 9.5653e-01 6.6600e-01 1.4030e+00 +PDE11A ENST00000286063 8.6896e-37 1.1142e+00 8.9100e-01 1.4040e+00 +OTOP2 ENST00000331427 3.5925e-14 9.7491e-01 6.9000e-01 1.4040e+00 +CCDC74B ENST00000310463 1.2420e-10 9.2502e-01 6.2500e-01 1.4040e+00 +FAM101A ENST00000324038 2.3296e-01 3.1301e-01 1.0900e-01 1.4040e+00 +KRTAP10-11 ENST00000334670 4.3329e-04 7.1617e-01 3.9100e-01 1.4040e+00 +MAD2L1BP ENST00000451025 1.4439e-08 8.8416e-01 5.7500e-01 1.4040e+00 +ATP6V0D2 ENST00000285393 2.4683e-11 9.3668e-01 6.4000e-01 1.4040e+00 +MYL6B ENST00000553066 6.0924e-06 8.0741e-01 4.8600e-01 1.4050e+00 +UBXN2A ENST00000309033 1.3932e-06 8.3018e-01 5.1100e-01 1.4050e+00 +CCDC17 ENST00000528266 3.9155e-22 1.0457e+00 7.8800e-01 1.4050e+00 +ACTL10 ENST00000330271 8.0520e-02 4.6053e-01 1.8700e-01 1.4050e+00 +M1AP ENST00000290536 3.1588e-19 1.0246e+00 7.5800e-01 1.4050e+00 +ZNF345 ENST00000529555 1.4292e-08 8.8493e-01 5.7500e-01 1.4050e+00 +GYG1 ENST00000345003 4.8291e-12 9.4780e-01 6.5400e-01 1.4050e+00 +C1orf174 ENST00000361605 1.0680e-04 7.5226e-01 4.2700e-01 1.4050e+00 +ATG4C ENST00000317868 4.6740e-17 1.0060e+00 7.3200e-01 1.4050e+00 +GABRP ENST00000518525 1.8174e-13 9.6744e-01 6.8000e-01 1.4050e+00 +CCDC87 ENST00000333861 3.5141e-14 9.7602e-01 6.9100e-01 1.4050e+00 +ZNF181 ENST00000492450 9.4669e-13 9.5757e-01 6.6700e-01 1.4050e+00 +C6orf201 ENST00000380175 6.4377e-03 6.2275e-01 3.0500e-01 1.4060e+00 +SERTM1 ENST00000315190 4.9156e-01 0.0000e+00 0.0000e+00 1.4060e+00 +C4orf51 ENST00000438731 6.0318e-06 8.0852e-01 4.8600e-01 1.4060e+00 +PFN4 ENST00000313213 1.6894e-03 6.7499e-01 3.5100e-01 1.4060e+00 +P2RY12 ENST00000302632 1.6859e-03 6.7536e-01 3.5200e-01 1.4060e+00 +SCGB2A1 ENST00000244930 2.3239e-01 3.1370e-01 1.1000e-01 1.4060e+00 +MALL ENST00000272462 2.3241e-01 3.1367e-01 1.1000e-01 1.4060e+00 +DBX2 ENST00000332700 6.0563e-06 8.0807e-01 4.8600e-01 1.4060e+00 +SLC26A11 ENST00000361193 3.0064e-19 1.0267e+00 7.6000e-01 1.4070e+00 +KRTAP10-3 ENST00000391620 2.3538e-02 5.5552e-01 2.5200e-01 1.4070e+00 +MUC21 ENST00000376296 8.0201e-02 4.6152e-01 1.8700e-01 1.4070e+00 +CXorf58 ENST00000379211 3.0653e-07 8.5148e-01 5.3500e-01 1.4070e+00 +TPPP2 ENST00000321760 2.3554e-02 5.5536e-01 2.5100e-01 1.4070e+00 +SPHK1 ENST00000323374 3.0327e-07 8.5244e-01 5.3600e-01 1.4080e+00 +NUDT15 ENST00000258662 1.6748e-03 6.7651e-01 3.5200e-01 1.4080e+00 +KRT83 ENST00000293670 3.3665e-14 9.7819e-01 6.9300e-01 1.4080e+00 +FAM83A ENST00000518448 3.0324e-07 8.5245e-01 5.3600e-01 1.4080e+00 +WBP1 ENST00000233615 6.5841e-08 8.7041e-01 5.5700e-01 1.4080e+00 +SCIMP ENST00000574081 4.2680e-04 7.1851e-01 3.9200e-01 1.4080e+00 +BST2 ENST00000252593 4.2516e-04 7.1911e-01 3.9300e-01 1.4090e+00 +CETN3 ENST00000283122 1.0528e-04 7.5424e-01 4.2800e-01 1.4090e+00 +ERICH2 ENST00000409885 6.3781e-03 6.2457e-01 3.0600e-01 1.4090e+00 +ASPDH ENST00000389208 1.3545e-06 8.3297e-01 5.1300e-01 1.4090e+00 +SCGN ENST00000377961 2.3395e-11 9.3986e-01 6.4200e-01 1.4090e+00 +TRIM51 ENST00000449290 1.3832e-08 8.8741e-01 5.7700e-01 1.4090e+00 +TMEM82 ENST00000375782 3.0094e-07 8.5313e-01 5.3600e-01 1.4090e+00 +ZNF525 ENST00000474037 2.3167e-01 3.1458e-01 1.1000e-01 1.4090e+00 +C12orf43 ENST00000288757 1.0484e-04 7.5482e-01 4.2800e-01 1.4100e+00 +CHMP4C ENST00000297265 2.9916e-07 8.5366e-01 5.3600e-01 1.4100e+00 +OR1J4 ENST00000340750 7.9793e-02 4.6280e-01 1.8800e-01 1.4100e+00 +C9orf89 ENST00000375464 5.9279e-06 8.1043e-01 4.8700e-01 1.4100e+00 +KISS1 ENST00000367194 4.9039e-01 0.0000e+00 0.0000e+00 1.4100e+00 +TMEM14A ENST00000211314 2.3377e-02 5.5703e-01 2.5200e-01 1.4100e+00 +IER3IP1 ENST00000256433 2.3402e-02 5.5679e-01 2.5200e-01 1.4100e+00 +IFT27 ENST00000433985 5.8825e-06 8.1128e-01 4.8800e-01 1.4110e+00 +PTTG1 ENST00000393964 4.2161e-04 7.2042e-01 3.9300e-01 1.4110e+00 +TSPAN4 ENST00000397404 6.4243e-08 8.7243e-01 5.5800e-01 1.4110e+00 +SLC29A2 ENST00000357440 3.2307e-14 9.8028e-01 6.9400e-01 1.4110e+00 +ZNF391 ENST00000244576 6.4452e-08 8.7216e-01 5.5800e-01 1.4110e+00 +CCDC68 ENST00000591504 8.7053e-13 9.6215e-01 6.7000e-01 1.4110e+00 +KRTAP1-4 ENST00000377747 2.3104e-01 3.1536e-01 1.1000e-01 1.4120e+00 +SPACA7 ENST00000283550 1.3290e-06 8.3486e-01 5.1400e-01 1.4120e+00 +ITGB3BP ENST00000371092 2.9577e-07 8.5469e-01 5.3700e-01 1.4120e+00 +GPX7 ENST00000361314 5.8451e-06 8.1198e-01 4.8800e-01 1.4120e+00 +RPH3AL ENST00000331302 4.4376e-12 9.5260e-01 6.5700e-01 1.4120e+00 +ZDHHC24 ENST00000310442 4.2080e-04 7.2071e-01 3.9300e-01 1.4120e+00 +C3orf33 ENST00000534941 5.8421e-06 8.1204e-01 4.8800e-01 1.4120e+00 +TRAP1 ENST00000246957 1.5965e-29 1.0916e+00 8.5200e-01 1.4120e+00 +VIP ENST00000367244 4.1995e-04 7.2103e-01 3.9400e-01 1.4120e+00 +VSTM1 ENST00000338372 6.3720e-08 8.7310e-01 5.5800e-01 1.4120e+00 +MS4A8 ENST00000300226 2.4834e-05 7.8679e-01 4.6100e-01 1.4130e+00 +FDX1L ENST00000393708 1.6520e-03 6.7891e-01 3.5300e-01 1.4130e+00 +NIPAL2 ENST00000341166 4.3665e-12 9.5353e-01 6.5800e-01 1.4130e+00 +SERPINB8 ENST00000397985 2.7764e-09 9.0464e-01 5.9600e-01 1.4130e+00 +SPSB4 ENST00000310546 4.1849e-04 7.2158e-01 3.9400e-01 1.4130e+00 +TMEM92 ENST00000300433 6.3256e-03 6.2620e-01 3.0700e-01 1.4130e+00 +STYXL1 ENST00000248600 1.3247e-08 8.9070e-01 5.7900e-01 1.4140e+00 +LRRC15 ENST00000439944 2.7349e-09 9.0571e-01 5.9700e-01 1.4140e+00 +MMP10 ENST00000279441 5.9070e-15 9.9073e-01 7.0700e-01 1.4140e+00 +ARSI ENST00000328668 5.9580e-15 9.9031e-01 7.0700e-01 1.4140e+00 +ASB4 ENST00000325885 1.1180e-10 9.3161e-01 6.3000e-01 1.4140e+00 +FAH ENST00000407106 4.0347e-17 1.0126e+00 7.3700e-01 1.4140e+00 +DDX28 ENST00000332395 1.3284e-08 8.9049e-01 5.7900e-01 1.4140e+00 +MRPL16 ENST00000300151 2.4706e-05 7.8742e-01 4.6100e-01 1.4140e+00 +SERF2 ENST00000409960 2.3172e-02 5.5898e-01 2.5300e-01 1.4140e+00 +AVEN ENST00000306730 2.7422e-09 9.0552e-01 5.9700e-01 1.4140e+00 +BTN3A2 ENST00000356386 1.1002e-10 9.3262e-01 6.3000e-01 1.4150e+00 +C14orf119 ENST00000319074 6.2891e-03 6.2734e-01 3.0800e-01 1.4150e+00 +MYADM ENST00000391769 6.2904e-03 6.2730e-01 3.0800e-01 1.4150e+00 +GADD45GIP1 ENST00000316939 1.0261e-04 7.5779e-01 4.3000e-01 1.4150e+00 +RP11-468E2.6 ENST00000558325 1.0270e-04 7.5767e-01 4.3000e-01 1.4150e+00 +PRL ENST00000306482 2.9015e-07 8.5642e-01 5.3800e-01 1.4150e+00 +OR2J1 ENST00000377171 2.3156e-02 5.5913e-01 2.5300e-01 1.4150e+00 +C18orf42 ENST00000434239 4.8916e-01 0.0000e+00 0.0000e+00 1.4150e+00 +IMMP1L ENST00000278200 2.4628e-05 7.8782e-01 4.6100e-01 1.4150e+00 +RNMTL1 ENST00000304478 5.5446e-10 9.1950e-01 6.1400e-01 1.4150e+00 +DNAJC30 ENST00000395176 2.3092e-02 5.5974e-01 2.5300e-01 1.4160e+00 +KCNK16 ENST00000425054 1.0207e-04 7.5853e-01 4.3000e-01 1.4160e+00 +GUCA1A ENST00000394237 4.1429e-04 7.2315e-01 3.9500e-01 1.4160e+00 +C3orf84 ENST00000545770 5.7310e-06 8.1416e-01 4.9000e-01 1.4160e+00 +WFDC8 ENST00000357199 1.3000e-08 8.9214e-01 5.8000e-01 1.4160e+00 +INO80C ENST00000441607 4.1480e-04 7.2296e-01 3.9500e-01 1.4160e+00 +GP2 ENST00000381362 1.6750e-21 1.0494e+00 7.8800e-01 1.4160e+00 +MMP3 ENST00000299855 5.7362e-15 9.9218e-01 7.0800e-01 1.4160e+00 +OR3A1 ENST00000323404 2.3093e-02 5.5974e-01 2.5300e-01 1.4160e+00 +PEX7 ENST00000318471 8.1798e-13 9.6557e-01 6.7300e-01 1.4160e+00 +PRDM7 ENST00000449207 7.3656e-18 1.0206e+00 7.4700e-01 1.4160e+00 +SH2D4A ENST00000265807 3.1396e-22 1.0541e+00 7.9500e-01 1.4160e+00 +ETV3L ENST00000454449 6.1960e-08 8.7542e-01 5.6000e-01 1.4160e+00 +FAM209A ENST00000371328 7.8881e-02 4.6570e-01 1.8900e-01 1.4170e+00 +RP11-96O20.4 ENST00000564080 6.1391e-08 8.7618e-01 5.6000e-01 1.4170e+00 +ZNRF4 ENST00000222033 4.8866e-01 0.0000e+00 0.0000e+00 1.4170e+00 +GLT1D1 ENST00000281703 6.1378e-08 8.7620e-01 5.6000e-01 1.4170e+00 +CEACAM4 ENST00000221954 6.1219e-08 8.7641e-01 5.6100e-01 1.4170e+00 +RGS2 ENST00000235382 5.6973e-06 8.1481e-01 4.9000e-01 1.4170e+00 +MEIOB ENST00000412554 2.9857e-14 9.8431e-01 6.9700e-01 1.4170e+00 +RANGRF ENST00000226105 2.4357e-05 7.8919e-01 4.6200e-01 1.4170e+00 +OR2G2 ENST00000320065 2.2995e-02 5.6068e-01 2.5400e-01 1.4180e+00 +PDC ENST00000391997 1.0134e-04 7.5953e-01 4.3100e-01 1.4180e+00 +ISOC1 ENST00000173527 6.0952e-08 8.7677e-01 5.6100e-01 1.4180e+00 +SAMD13 ENST00000370673 6.2299e-03 6.2921e-01 3.0800e-01 1.4180e+00 +RP11-89K11.1 ENST00000560292 4.8828e-01 0.0000e+00 0.0000e+00 1.4180e+00 +ETV2 ENST00000402764 2.6344e-09 9.0838e-01 5.9900e-01 1.4180e+00 +OR2G3 ENST00000320002 7.8577e-02 4.6668e-01 1.8900e-01 1.4190e+00 +MPHOSPH6 ENST00000258169 4.1070e-04 7.2451e-01 3.9500e-01 1.4190e+00 +TINAG ENST00000259782 3.4300e-25 1.0748e+00 8.2300e-01 1.4190e+00 +GJA10 ENST00000369352 5.3123e-10 9.2237e-01 6.1600e-01 1.4190e+00 +ICT1 ENST00000301585 5.6196e-06 8.1634e-01 4.9100e-01 1.4190e+00 +TMEM225 ENST00000375026 1.6225e-03 6.8207e-01 3.5500e-01 1.4190e+00 +AKR1E2 ENST00000298375 2.0973e-11 9.4641e-01 6.4700e-01 1.4190e+00 +MAGEH1 ENST00000342972 2.2920e-01 3.1766e-01 1.1100e-01 1.4190e+00 +AP002884.3 ENST00000532612 5.5923e-06 8.1688e-01 4.9100e-01 1.4200e+00 +ZNF266 ENST00000592904 2.2887e-02 5.6173e-01 2.5400e-01 1.4200e+00 +ANAPC16 ENST00000299381 2.2882e-02 5.6178e-01 2.5400e-01 1.4200e+00 +TMPRSS12 ENST00000398458 5.6068e-06 8.1659e-01 4.9100e-01 1.4200e+00 +ACSM2B ENST00000329697 6.2689e-26 1.0792e+00 8.2900e-01 1.4200e+00 +ZNF514 ENST00000295208 1.0350e-10 9.3649e-01 6.3300e-01 1.4210e+00 +SPINK7 ENST00000274565 7.8398e-02 4.6725e-01 1.8900e-01 1.4210e+00 +ZNF662 ENST00000328199 7.6715e-13 9.6911e-01 6.7500e-01 1.4210e+00 +MFSD12 ENST00000398558 6.7265e-18 1.0246e+00 7.5000e-01 1.4210e+00 +LRIT3 ENST00000594814 2.0418e-11 9.4803e-01 6.4800e-01 1.4210e+00 +POLR2G ENST00000301788 1.2570e-06 8.4041e-01 5.1700e-01 1.4210e+00 +SLC6A19 ENST00000304460 1.7664e-24 1.0724e+00 8.1800e-01 1.4220e+00 +ROGDI ENST00000322048 2.5516e-09 9.1066e-01 6.0000e-01 1.4220e+00 +ROPN1 ENST00000184183 9.9631e-05 7.6190e-01 4.3200e-01 1.4220e+00 +TRAPPC5 ENST00000317378 2.2841e-01 3.1865e-01 1.1100e-01 1.4220e+00 +C8orf37 ENST00000286688 2.3711e-05 7.9253e-01 4.6400e-01 1.4230e+00 +POLN ENST00000511885 9.4880e-41 1.1415e+00 9.2200e-01 1.4230e+00 +FANCD2OS ENST00000450660 2.2748e-02 5.6309e-01 2.5500e-01 1.4230e+00 +C2orf40 ENST00000238044 4.0522e-04 7.2663e-01 3.9700e-01 1.4230e+00 +KRT76 ENST00000332411 2.7442e-14 9.8865e-01 7.0000e-01 1.4230e+00 +GCSH ENST00000315467 1.6020e-03 6.8432e-01 3.5600e-01 1.4230e+00 +MMD2 ENST00000404774 5.8561e-08 8.8009e-01 5.6300e-01 1.4230e+00 +KCTD18 ENST00000359878 5.8625e-08 8.8000e-01 5.6300e-01 1.4230e+00 +ZDHHC23 ENST00000330212 3.8421e-12 9.6089e-01 6.6300e-01 1.4240e+00 +KTI12 ENST00000371614 4.0289e-04 7.2753e-01 3.9700e-01 1.4240e+00 +FOLR2 ENST00000298223 5.4816e-06 8.1910e-01 4.9300e-01 1.4240e+00 +SSTR3 ENST00000328544 9.9007e-05 7.6278e-01 4.3300e-01 1.4240e+00 +CD8B ENST00000331469 4.0103e-04 7.2826e-01 3.9700e-01 1.4250e+00 +STMND1 ENST00000536551 9.8701e-05 7.6322e-01 4.3300e-01 1.4250e+00 +ATP5J ENST00000457143 6.1310e-03 6.3239e-01 3.1000e-01 1.4250e+00 +ART3 ENST00000355810 5.1018e-15 9.9802e-01 7.1200e-01 1.4250e+00 +TMEM143 ENST00000293261 3.7891e-12 9.6170e-01 6.6400e-01 1.4250e+00 +LDLRAD1 ENST00000371360 1.2294e-06 8.4264e-01 5.1900e-01 1.4250e+00 +LHFPL5 ENST00000360215 4.0199e-04 7.2789e-01 3.9700e-01 1.4250e+00 +GK2 ENST00000358842 5.0156e-10 9.2623e-01 6.1900e-01 1.4250e+00 +MRPS15 ENST00000373116 5.0041e-10 9.2638e-01 6.1900e-01 1.4250e+00 +FPGT-TNNI3K ENST00000557284 3.2476e-48 1.1628e+00 9.5400e-01 1.4250e+00 +B3GALT6 ENST00000379198 2.2667e-02 5.6389e-01 2.5500e-01 1.4250e+00 +C4orf17 ENST00000326581 1.2018e-08 8.9816e-01 5.8400e-01 1.4260e+00 +PYCRL ENST00000220966 2.3380e-05 7.9427e-01 4.6500e-01 1.4260e+00 +ACY3 ENST00000255082 5.4152e-06 8.2046e-01 4.9300e-01 1.4260e+00 +C1orf123 ENST00000294360 1.2226e-06 8.4319e-01 5.1900e-01 1.4260e+00 +LGALS3BP ENST00000262776 2.6790e-07 8.6365e-01 5.4300e-01 1.4260e+00 +TMEM14C ENST00000541412 6.1054e-03 6.3323e-01 3.1000e-01 1.4260e+00 +CYB5A ENST00000340533 1.5821e-03 6.8654e-01 3.5700e-01 1.4270e+00 +FCRLA ENST00000367959 2.4445e-09 9.1373e-01 6.0200e-01 1.4270e+00 +NAPRT1 ENST00000449291 1.1537e-18 1.0347e+00 7.6200e-01 1.4270e+00 +AP3S2 ENST00000336418 2.3273e-05 7.9484e-01 4.6500e-01 1.4270e+00 +GUK1 ENST00000366728 2.3324e-05 7.9457e-01 4.6500e-01 1.4270e+00 +GLTPD1 ENST00000343938 2.2540e-02 5.6516e-01 2.5600e-01 1.4270e+00 +ACRV1 ENST00000533904 1.2111e-06 8.4413e-01 5.2000e-01 1.4270e+00 +DEPTOR ENST00000286234 3.7245e-12 9.6270e-01 6.6400e-01 1.4270e+00 +CCDC113 ENST00000219299 9.3239e-16 1.0075e+00 7.2400e-01 1.4270e+00 +CTB-96E2.2 ENST00000555059 9.7835e-05 7.6445e-01 4.3400e-01 1.4270e+00 +GADL1 ENST00000282538 1.3724e-21 1.0572e+00 7.9400e-01 1.4270e+00 +TNNI3K ENST00000370891 3.0654e-48 1.1641e+00 9.5500e-01 1.4270e+00 +NDUFB4 ENST00000184266 6.0844e-03 6.3391e-01 3.1100e-01 1.4280e+00 +FGF6 ENST00000228837 3.9765e-04 7.2960e-01 3.9800e-01 1.4280e+00 +CTD-2521M24.10 ENST00000594663 6.0820e-03 6.3399e-01 3.1100e-01 1.4280e+00 +DKKL1 ENST00000221498 3.9771e-04 7.2958e-01 3.9800e-01 1.4280e+00 +OR51V1 ENST00000321255 1.5772e-03 6.8710e-01 3.5800e-01 1.4280e+00 +LGALS3 ENST00000254301 2.3207e-05 7.9520e-01 4.6600e-01 1.4280e+00 +LAYN ENST00000375615 1.3423e-13 9.8352e-01 6.9100e-01 1.4280e+00 +TVP23C ENST00000225576 2.3189e-05 7.9530e-01 4.6600e-01 1.4280e+00 +PAMR1 ENST00000278360 6.2624e-32 1.1149e+00 8.7700e-01 1.4290e+00 +AC104794.4 ENST00000425235 2.2483e-02 5.6573e-01 2.5600e-01 1.4290e+00 +CRYAB ENST00000533475 2.2470e-02 5.6586e-01 2.5600e-01 1.4290e+00 +CHRNA10 ENST00000250699 4.7867e-10 9.2938e-01 6.2100e-01 1.4290e+00 +PPM1N ENST00000451287 5.3345e-06 8.2213e-01 4.9400e-01 1.4290e+00 +LILRB5 ENST00000449561 4.4944e-23 1.0687e+00 8.0900e-01 1.4290e+00 +ZSCAN30 ENST00000420878 6.9946e-13 9.7426e-01 6.7900e-01 1.4290e+00 +ADAM21 ENST00000603540 3.5771e-12 9.6505e-01 6.6600e-01 1.4300e+00 +CLEC12A ENST00000355690 2.6022e-07 8.6630e-01 5.4400e-01 1.4300e+00 +ANKRD36 ENST00000420699 8.3217e-86 1.2267e+00 1.0550e+00 1.4300e+00 +FAM92B ENST00000539556 4.7704e-10 9.2961e-01 6.2100e-01 1.4300e+00 +NOX5 ENST00000388866 3.0490e-28 1.0988e+00 8.5200e-01 1.4300e+00 +TBATA ENST00000299290 4.7461e-10 9.2996e-01 6.2100e-01 1.4300e+00 +OR13A1 ENST00000553795 1.5701e-03 6.8790e-01 3.5800e-01 1.4300e+00 +CDKL2 ENST00000429927 3.0975e-17 1.0247e+00 7.4600e-01 1.4310e+00 +RNF175 ENST00000347063 6.8141e-13 9.7572e-01 6.8000e-01 1.4310e+00 +BEST3 ENST00000330891 2.0104e-19 1.0436e+00 7.7200e-01 1.4310e+00 +FAM227B ENST00000299338 4.3472e-23 1.0699e+00 8.1000e-01 1.4310e+00 +RHOT2 ENST00000315082 8.9033e-27 1.0921e+00 8.4200e-01 1.4310e+00 +RBM34 ENST00000408888 4.6408e-15 1.0028e+00 7.1500e-01 1.4310e+00 +OR1E2 ENST00000248384 1.5619e-03 6.8883e-01 3.5900e-01 1.4310e+00 +CDX4 ENST00000373514 6.0181e-03 6.3611e-01 3.1200e-01 1.4320e+00 +STAP2 ENST00000600324 1.6296e-16 1.0184e+00 7.3700e-01 1.4320e+00 +GSDMA ENST00000301659 1.6190e-16 1.0187e+00 7.3700e-01 1.4320e+00 +OAZ3 ENST00000321531 2.2775e-05 7.9755e-01 4.6700e-01 1.4320e+00 +TCEAL7 ENST00000332431 4.8470e-01 0.0000e+00 0.0000e+00 1.4320e+00 +TAAR1 ENST00000275216 3.9183e-04 7.3193e-01 3.9900e-01 1.4320e+00 +RP11-487E13.1 ENST00000512516 2.2554e-01 3.2234e-01 1.1300e-01 1.4330e+00 +HYLS1 ENST00000425380 2.3152e-09 9.1765e-01 6.0500e-01 1.4330e+00 +HPDL ENST00000334815 2.2634e-05 7.9832e-01 4.6700e-01 1.4330e+00 +EXO5 ENST00000372703 2.2661e-05 7.9818e-01 4.6700e-01 1.4330e+00 +ZSCAN21 ENST00000292450 3.4774e-12 9.6671e-01 6.6700e-01 1.4330e+00 +CCDC27 ENST00000294600 2.8657e-28 1.1008e+00 8.5400e-01 1.4330e+00 +ANXA9 ENST00000368947 2.9752e-17 1.0266e+00 7.4700e-01 1.4330e+00 +GCNT3 ENST00000396065 1.1214e-08 9.0351e-01 5.8700e-01 1.4340e+00 +FAM83F ENST00000333407 1.7620e-11 9.5700e-01 6.5400e-01 1.4340e+00 +SERINC4 ENST00000319327 5.5221e-18 1.0335e+00 7.5700e-01 1.4340e+00 +SRA1 ENST00000336283 5.1900e-06 8.2520e-01 4.9600e-01 1.4340e+00 +ZNHIT2 ENST00000310597 2.2483e-05 7.9916e-01 4.6800e-01 1.4340e+00 +FAM124A ENST00000280057 4.5883e-10 9.3226e-01 6.2300e-01 1.4340e+00 +SFRP5 ENST00000266066 5.1843e-06 8.2532e-01 4.9600e-01 1.4340e+00 +INHBE ENST00000266646 1.1184e-08 9.0372e-01 5.8700e-01 1.4340e+00 +OR6C6 ENST00000358433 2.2211e-02 5.6849e-01 2.5700e-01 1.4340e+00 +AC007557.1 ENST00000456163 4.8399e-01 0.0000e+00 0.0000e+00 1.4340e+00 +CCL16 ENST00000293275 2.2498e-01 3.2308e-01 1.1300e-01 1.4350e+00 +RDH12 ENST00000551171 2.2626e-09 9.1931e-01 6.0600e-01 1.4350e+00 +REM1 ENST00000201979 5.3363e-08 8.8786e-01 5.6800e-01 1.4350e+00 +LRR1 ENST00000298288 1.1070e-08 9.0451e-01 5.8800e-01 1.4350e+00 +C10orf128 ENST00000474718 5.9652e-03 6.3789e-01 3.1300e-01 1.4350e+00 +RPA3-AS1 ENST00000406829 2.2503e-01 3.2301e-01 1.1300e-01 1.4350e+00 +DHFRL1 ENST00000394221 2.2496e-01 3.2310e-01 1.1300e-01 1.4350e+00 +AC022431.2 ENST00000438651 2.2173e-02 5.6887e-01 2.5700e-01 1.4350e+00 +OR2C3 ENST00000366487 5.9489e-03 6.3844e-01 3.1300e-01 1.4360e+00 +MRPL54 ENST00000330133 2.2144e-02 5.6917e-01 2.5800e-01 1.4360e+00 +PNPO ENST00000225573 1.1024e-08 9.0484e-01 5.8800e-01 1.4360e+00 +TGM5 ENST00000220420 2.4183e-25 1.0873e+00 8.3200e-01 1.4360e+00 +ANKLE1 ENST00000394458 5.2059e-18 1.0361e+00 7.5800e-01 1.4370e+00 +OR6Q1 ENST00000302622 1.5367e-03 6.9174e-01 3.6000e-01 1.4370e+00 +LYRM7 ENST00000379380 2.2082e-02 5.6981e-01 2.5800e-01 1.4370e+00 +SNAPIN ENST00000368685 1.5332e-03 6.9215e-01 3.6000e-01 1.4370e+00 +AGAP5 ENST00000374094 5.9176e-03 6.3951e-01 3.1300e-01 1.4380e+00 +NCR2 ENST00000373089 2.4749e-07 8.7089e-01 5.4700e-01 1.4380e+00 +CCDC61 ENST00000595358 2.2578e-14 9.9883e-01 7.0700e-01 1.4380e+00 +OR6B2 ENST00000402971 2.2036e-02 5.7028e-01 2.5800e-01 1.4380e+00 +RNF135 ENST00000328381 2.1992e-09 9.2137e-01 6.0700e-01 1.4380e+00 +ATPAF2 ENST00000474627 2.2116e-09 9.2096e-01 6.0700e-01 1.4380e+00 +UGT2B7 ENST00000305231 1.1910e-13 9.9001e-01 6.9600e-01 1.4380e+00 +HRH4 ENST00000256906 5.2213e-08 8.8969e-01 5.6900e-01 1.4380e+00 +SAG ENST00000409110 1.4921e-16 1.0226e+00 7.4000e-01 1.4380e+00 +PRSS33 ENST00000293851 2.4550e-07 8.7163e-01 5.4800e-01 1.4390e+00 +CMPK2 ENST00000256722 1.1285e-06 8.5125e-01 5.2400e-01 1.4390e+00 +PMF1 ENST00000567140 1.0730e-08 9.0694e-01 5.8900e-01 1.4390e+00 +PMF1-BGLAP ENST00000368276 1.0730e-08 9.0694e-01 5.8900e-01 1.4390e+00 +CLEC6A ENST00000382073 1.1269e-06 8.5139e-01 5.2400e-01 1.4390e+00 +RGS4 ENST00000421743 5.1409e-08 8.9100e-01 5.7000e-01 1.4400e+00 +S100A12 ENST00000368737 4.8234e-01 0.0000e+00 0.0000e+00 1.4400e+00 +CYP4F31P ENST00000416266 2.2379e-01 3.2465e-01 1.1300e-01 1.4400e+00 +OR4M1 ENST00000315957 1.5219e-03 6.9348e-01 3.6100e-01 1.4400e+00 +C21orf88 ENST00000380612 2.2348e-01 3.2507e-01 1.1400e-01 1.4410e+00 +GPR152 ENST00000312457 3.7983e-04 7.3688e-01 4.0200e-01 1.4410e+00 +CD300LF ENST00000326165 1.0563e-08 9.0816e-01 5.9000e-01 1.4410e+00 +HKR1 ENST00000324411 1.6877e-19 1.0511e+00 7.7800e-01 1.4410e+00 +SHISA5 ENST00000296444 1.1126e-06 8.5268e-01 5.2500e-01 1.4410e+00 +KLRB1 ENST00000229402 2.4129e-07 8.7322e-01 5.4900e-01 1.4410e+00 +OR13D1 ENST00000318763 5.8770e-03 6.4091e-01 3.1400e-01 1.4410e+00 +PLA2G12A ENST00000243501 3.7886e-04 7.3728e-01 4.0200e-01 1.4410e+00 +MRPL4 ENST00000253099 4.2719e-10 9.3714e-01 6.2600e-01 1.4410e+00 +MS4A5 ENST00000300190 3.7917e-04 7.3716e-01 4.0200e-01 1.4410e+00 +LBX2 ENST00000460508 5.8839e-03 6.4067e-01 3.1400e-01 1.4410e+00 +MCPH1 ENST00000344683 7.7600e-30 1.1145e+00 8.7000e-01 1.4410e+00 +CRABP1 ENST00000299529 5.8779e-03 6.4088e-01 3.1400e-01 1.4410e+00 +RP11-650K20.3 ENST00000551650 4.8213e-01 0.0000e+00 0.0000e+00 1.4410e+00 +HSD3B1 ENST00000369413 2.3984e-07 8.7377e-01 5.4900e-01 1.4420e+00 +RP11-831H9.11 ENST00000528405 2.1838e-02 5.7235e-01 2.5900e-01 1.4420e+00 +C20orf195 ENST00000370098 2.1684e-05 8.0370e-01 4.7000e-01 1.4420e+00 +NRGN ENST00000284292 4.8190e-01 0.0000e+00 0.0000e+00 1.4420e+00 +RP11-201K10.3 ENST00000473363 4.9795e-06 8.2984e-01 4.9900e-01 1.4420e+00 +AL078585.1 ENST00000419182 5.8584e-03 6.4155e-01 3.1400e-01 1.4420e+00 +C19orf60 ENST00000358607 3.7611e-04 7.3845e-01 4.0300e-01 1.4430e+00 +C1orf137 ENST00000369482 2.1781e-02 5.7295e-01 2.5900e-01 1.4430e+00 +KRT7 ENST00000331817 3.0861e-12 9.7374e-01 6.7200e-01 1.4430e+00 +AC018755.1 ENST00000301439 2.1815e-02 5.7260e-01 2.5900e-01 1.4430e+00 +PSMG2 ENST00000317615 2.3824e-07 8.7439e-01 5.4900e-01 1.4430e+00 +CRABP2 ENST00000368222 1.5096e-03 6.9494e-01 3.6200e-01 1.4430e+00 +OR10A5 ENST00000299454 2.1733e-02 5.7346e-01 2.6000e-01 1.4440e+00 +OSGIN1 ENST00000361711 1.5746e-11 9.6394e-01 6.5900e-01 1.4440e+00 +SLC16A11 ENST00000308009 4.9198e-06 8.3120e-01 5.0000e-01 1.4440e+00 +OR6T1 ENST00000321252 1.5036e-03 6.9566e-01 3.6200e-01 1.4440e+00 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5.0600e-01 1.4610e+00 +CCDC24 ENST00000372318 4.3856e-08 9.0450e-01 5.7800e-01 1.4610e+00 +PIK3R6 ENST00000311434 1.5215e-28 1.1223e+00 8.7100e-01 1.4610e+00 +NME1-NME2 ENST00000393198 8.8471e-09 9.2213e-01 5.9900e-01 1.4620e+00 +NME2 ENST00000393193 8.8471e-09 9.2213e-01 5.9900e-01 1.4620e+00 +EP400NL ENST00000443539 4.4654e-06 8.4218e-01 5.0600e-01 1.4620e+00 +ALDH8A1 ENST00000265605 2.4846e-12 9.8675e-01 6.8100e-01 1.4620e+00 +WISP2 ENST00000372868 1.9682e-05 8.1599e-01 4.7800e-01 1.4620e+00 +SRI ENST00000265729 3.4837e-10 9.5128e-01 6.3500e-01 1.4620e+00 +LGALS7B ENST00000314980 2.1829e-01 3.3218e-01 1.1600e-01 1.4620e+00 +BNIP3 ENST00000368636 1.9687e-05 8.1595e-01 4.7800e-01 1.4620e+00 +KRTCAP2 ENST00000295682 3.5184e-04 7.4920e-01 4.0900e-01 1.4620e+00 +ALS2CR12 ENST00000405148 1.3086e-22 1.0885e+00 8.2100e-01 1.4620e+00 +CYB5D2 ENST00000301391 4.4253e-06 8.4321e-01 5.0700e-01 1.4630e+00 +FAM96A ENST00000300030 1.9655e-05 8.1616e-01 4.7800e-01 1.4630e+00 +GPR17 ENST00000544369 8.4259e-05 7.8565e-01 4.4500e-01 1.4630e+00 +HSD17B11 ENST00000358290 2.0771e-07 8.8711e-01 5.5700e-01 1.4630e+00 +KLK3 ENST00000326003 4.4271e-06 8.4317e-01 5.0700e-01 1.4630e+00 +UGT1A7 ENST00000373426 8.6636e-14 1.0077e+00 7.0800e-01 1.4630e+00 +PLEKHB2 ENST00000409158 6.6904e-11 9.6486e-01 6.5200e-01 1.4630e+00 +VWA5A ENST00000456829 2.5953e-29 1.1278e+00 8.7800e-01 1.4630e+00 +TIMM9 ENST00000395159 2.0827e-02 5.8338e-01 2.6400e-01 1.4640e+00 +EFNA4 ENST00000427683 3.5006e-04 7.5002e-01 4.0900e-01 1.4640e+00 +CYP4Z1 ENST00000334194 1.8745e-17 1.0484e+00 7.6300e-01 1.4640e+00 +GLO1 ENST00000373365 9.6718e-07 8.6698e-01 5.3400e-01 1.4640e+00 +KAZALD1 ENST00000370200 9.6662e-07 8.6704e-01 5.3400e-01 1.4640e+00 +GP9 ENST00000307395 4.7575e-01 0.0000e+00 0.0000e+00 1.4640e+00 +GML ENST00000220940 2.1757e-01 3.3320e-01 1.1600e-01 1.4650e+00 +CHP2 ENST00000300113 9.6292e-07 8.6743e-01 5.3400e-01 1.4650e+00 +ST7-OT4 ENST00000397750 2.0808e-02 5.8360e-01 2.6400e-01 1.4650e+00 +TMEM59 ENST00000234831 2.4058e-12 9.8871e-01 6.8200e-01 1.4650e+00 +ZNF763 ENST00000590798 2.0817e-02 5.8349e-01 2.6400e-01 1.4650e+00 +SLC6A18 ENST00000324642 6.7950e-22 1.0858e+00 8.1500e-01 1.4650e+00 +LINC01100 ENST00000473137 7.2755e-02 4.8684e-01 1.9700e-01 1.4660e+00 +KRT79 ENST00000330553 9.8728e-17 1.0428e+00 7.5400e-01 1.4660e+00 +RFPL4AL1 ENST00000341750 2.1729e-01 3.3359e-01 1.1600e-01 1.4660e+00 +SGCB ENST00000381431 9.5805e-07 8.6795e-01 5.3400e-01 1.4660e+00 +NBPF4 ENST00000415641 5.5056e-03 6.5435e-01 3.2100e-01 1.4660e+00 +FAM206A ENST00000322940 4.3558e-06 8.4502e-01 5.0800e-01 1.4660e+00 +LCE3C ENST00000333881 4.7523e-01 0.0000e+00 0.0000e+00 1.4660e+00 +MMP19 ENST00000322569 1.9975e-20 1.0760e+00 8.0000e-01 1.4670e+00 +LCN6 ENST00000341206 1.9255e-05 8.1879e-01 4.7900e-01 1.4670e+00 +C1QBP ENST00000225698 2.0164e-07 8.8989e-01 5.5900e-01 1.4670e+00 +PAGE5 ENST00000289619 2.0689e-02 5.8495e-01 2.6500e-01 1.4670e+00 +MDP1 ENST00000288087 1.9265e-05 8.1872e-01 4.7900e-01 1.4670e+00 +RNASEH2C ENST00000308418 5.4985e-03 6.5462e-01 3.2100e-01 1.4670e+00 +KCTD11 ENST00000333751 5.4961e-03 6.5471e-01 3.2100e-01 1.4670e+00 +CCDC97 ENST00000269967 1.6817e-09 9.4115e-01 6.2000e-01 1.4680e+00 +RP11-181C3.1 ENST00000501499 7.2446e-02 4.8800e-01 1.9800e-01 1.4680e+00 +ZNF747 ENST00000252799 7.2425e-02 4.8808e-01 1.9800e-01 1.4680e+00 +MAS1 ENST00000252660 8.2518e-05 7.8866e-01 4.4700e-01 1.4680e+00 +SERPINB10 ENST00000238508 3.3122e-10 9.5483e-01 6.3800e-01 1.4680e+00 +APOC1 ENST00000588750 2.1685e-01 3.3422e-01 1.1700e-01 1.4680e+00 +MRPL28 ENST00000199706 1.9955e-07 8.9087e-01 5.6000e-01 1.4690e+00 +ZNF415 ENST00000500065 2.1655e-01 3.3465e-01 1.1700e-01 1.4690e+00 +TRIM63 ENST00000374272 4.3041e-13 1.0021e+00 6.9800e-01 1.4690e+00 +DBI ENST00000542275 1.3944e-03 7.0944e-01 3.6900e-01 1.4690e+00 +TMEM74 ENST00000297459 3.4376e-04 7.5299e-01 4.1100e-01 1.4690e+00 +B4GALNT2 ENST00000300404 1.7413e-17 1.0520e+00 7.6600e-01 1.4690e+00 +MANF ENST00000528157 1.3911e-03 7.0987e-01 3.6900e-01 1.4690e+00 +AP5Z1 ENST00000348624 7.2894e-31 1.1392e+00 8.9100e-01 1.4690e+00 +CREB3L3 ENST00000078445 8.0596e-14 1.0117e+00 7.1100e-01 1.4690e+00 +TMEM219 ENST00000566848 8.1671e-05 7.9015e-01 4.4800e-01 1.4700e+00 +KLF11 ENST00000305883 8.3215e-09 9.2702e-01 6.0200e-01 1.4700e+00 +ASNSD1 ENST00000260952 9.2537e-17 1.0461e+00 7.5700e-01 1.4700e+00 +MORN5 ENST00000373764 8.1711e-05 7.9008e-01 4.4800e-01 1.4700e+00 +OR13C9 ENST00000259362 2.0568e-02 5.8634e-01 2.6500e-01 1.4700e+00 +ACKR2 ENST00000422265 1.3880e-03 7.1028e-01 3.7000e-01 1.4700e+00 +CAV3 ENST00000343849 5.4565e-03 6.5622e-01 3.2200e-01 1.4700e+00 +SPATA6 ENST00000371847 3.4185e-21 1.0843e+00 8.1000e-01 1.4700e+00 +APOBEC4 ENST00000308641 8.1741e-05 7.9002e-01 4.4800e-01 1.4700e+00 +STPG2 ENST00000295268 9.3325e-17 1.0456e+00 7.5600e-01 1.4700e+00 +OR5B2 ENST00000302581 7.2121e-02 4.8922e-01 1.9800e-01 1.4710e+00 +XKR8 ENST00000373884 4.0749e-08 9.1082e-01 5.8300e-01 1.4710e+00 +TAL2 ENST00000334077 4.7392e-01 0.0000e+00 0.0000e+00 1.4710e+00 +ENTPD2 ENST00000355097 1.4578e-14 1.0224e+00 7.2400e-01 1.4710e+00 +C3orf49 ENST00000295896 4.0628e-08 9.1108e-01 5.8300e-01 1.4710e+00 +L3HYPDH ENST00000247194 9.2642e-07 8.7142e-01 5.3600e-01 1.4710e+00 +NUTM2B ENST00000429828 2.0467e-02 5.8751e-01 2.6600e-01 1.4720e+00 +OR4N5 ENST00000333629 2.0486e-02 5.8729e-01 2.6600e-01 1.4720e+00 +RGPD2 ENST00000398146 1.3791e-03 7.1148e-01 3.7000e-01 1.4720e+00 +C11orf42 ENST00000316375 4.0440e-08 9.1148e-01 5.8300e-01 1.4720e+00 +C5orf46 ENST00000318315 7.2027e-02 4.8957e-01 1.9800e-01 1.4720e+00 +GFRA4 ENST00000319242 1.3789e-03 7.1151e-01 3.7000e-01 1.4720e+00 +MSGN1 ENST00000281047 7.2006e-02 4.8965e-01 1.9800e-01 1.4720e+00 +ENPP5 ENST00000371383 3.1565e-10 9.5823e-01 6.4000e-01 1.4730e+00 +SLC44A3 ENST00000271227 3.5957e-27 1.1242e+00 8.6700e-01 1.4730e+00 +OR10H5 ENST00000308940 7.1847e-02 4.9026e-01 1.9800e-01 1.4730e+00 +C2orf76 ENST00000409466 5.4177e-03 6.5772e-01 3.2200e-01 1.4730e+00 +LCMT2 ENST00000305641 2.6276e-15 1.0324e+00 7.3700e-01 1.4730e+00 +NDUFA3 ENST00000485876 7.1883e-02 4.9012e-01 1.9800e-01 1.4730e+00 +PHYHD1 ENST00000308941 4.0371e-13 1.0059e+00 7.0100e-01 1.4740e+00 +CKMT2 ENST00000424301 1.6195e-17 1.0556e+00 7.6800e-01 1.4740e+00 +UBE2D4 ENST00000222402 1.8620e-05 8.2309e-01 4.8200e-01 1.4740e+00 +FEZ2 ENST00000379245 1.1496e-11 9.8382e-01 6.7200e-01 1.4740e+00 +GPRIN3 ENST00000609438 4.0589e-13 1.0056e+00 7.0000e-01 1.4740e+00 +RP1-170O19.20 ENST00000470747 5.4042e-03 6.5824e-01 3.2300e-01 1.4740e+00 +KCNK17 ENST00000373231 4.1781e-06 8.4980e-01 5.1100e-01 1.4740e+00 +LST3 ENST00000540229 1.0871e-25 1.1169e+00 8.5500e-01 1.4750e+00 +OR2T5 ENST00000366473 4.7281e-01 0.0000e+00 0.0000e+00 1.4750e+00 +CETN1 ENST00000327228 2.1511e-01 3.3673e-01 1.1700e-01 1.4750e+00 +PRRG2 ENST00000246794 9.0627e-07 8.7369e-01 5.3800e-01 1.4750e+00 +OSCAR ENST00000359649 3.3644e-04 7.5651e-01 4.1300e-01 1.4750e+00 +AZGP1 ENST00000292401 4.1545e-06 8.5045e-01 5.1100e-01 1.4750e+00 +RIBC2 ENST00000538017 2.1427e-12 9.9582e-01 6.8700e-01 1.4750e+00 +OR10D3 ENST00000318666 2.0292e-02 5.8956e-01 2.6700e-01 1.4760e+00 +TRAPPC4 ENST00000533632 4.1207e-06 8.5139e-01 5.1200e-01 1.4760e+00 +OR5B12 ENST00000302572 2.0305e-02 5.8941e-01 2.6700e-01 1.4760e+00 +MSLN ENST00000382862 5.8751e-25 1.1136e+00 8.5000e-01 1.4760e+00 +BBOX1 ENST00000263182 2.0940e-12 9.9724e-01 6.8800e-01 1.4770e+00 +ATAD3B ENST00000308647 1.0032e-22 1.0995e+00 8.2900e-01 1.4770e+00 +PRRC1 ENST00000296666 2.0910e-12 9.9733e-01 6.8800e-01 1.4770e+00 +MRPL43 ENST00000342071 1.8937e-07 8.9580e-01 5.6300e-01 1.4770e+00 +FAM151B ENST00000282226 3.8968e-08 9.1470e-01 5.8500e-01 1.4770e+00 +HOXA7 ENST00000242159 1.3606e-03 7.1399e-01 3.7200e-01 1.4770e+00 +LGALS2 ENST00000215886 2.0219e-02 5.9043e-01 2.6700e-01 1.4780e+00 +TSPAN16 ENST00000316737 4.0908e-06 8.5223e-01 5.1200e-01 1.4780e+00 +HSPA1B ENST00000375650 5.3464e-03 6.6051e-01 3.2400e-01 1.4780e+00 +ZNF343 ENST00000278772 5.3489e-03 6.6041e-01 3.2400e-01 1.4780e+00 +PARP16 ENST00000261888 2.9939e-10 9.6200e-01 6.4300e-01 1.4780e+00 +CPQ ENST00000220763 1.3154e-14 1.0281e+00 7.2800e-01 1.4790e+00 +ZNF419 ENST00000424930 5.3294e-03 6.6119e-01 3.2400e-01 1.4790e+00 +TST ENST00000403892 7.8734e-05 7.9546e-01 4.5100e-01 1.4790e+00 +NSUN6 ENST00000377304 4.9452e-19 1.0730e+00 7.9000e-01 1.4790e+00 +AC074091.13 ENST00000379677 2.1409e-01 3.3822e-01 1.1800e-01 1.4790e+00 +FSCN2 ENST00000334850 3.8311e-13 1.0090e+00 7.0300e-01 1.4790e+00 +MTRF1L ENST00000367233 2.9554e-10 9.6292e-01 6.4300e-01 1.4800e+00 +COX20 ENST00000411948 2.0118e-02 5.9163e-01 2.6800e-01 1.4800e+00 +C16orf90 ENST00000437192 1.3458e-03 7.1603e-01 3.7300e-01 1.4800e+00 +SLC27A3 ENST00000368661 5.2696e-22 1.0965e+00 8.2300e-01 1.4800e+00 +HSPB2 ENST00000304298 3.2989e-04 7.5974e-01 4.1500e-01 1.4800e+00 +NQO2 ENST00000338130 8.7572e-07 8.7726e-01 5.4000e-01 1.4800e+00 +SOAT2 ENST00000301466 5.5830e-28 1.1333e+00 8.7600e-01 1.4800e+00 +NCCRP1 ENST00000339852 7.6409e-09 9.3389e-01 6.0700e-01 1.4800e+00 +UVSSA ENST00000389851 5.4127e-25 1.1168e+00 8.5200e-01 1.4800e+00 +TNNT1 ENST00000588981 7.0202e-14 1.0196e+00 7.1600e-01 1.4800e+00 +SPDYE2 ENST00000507918 4.7151e-01 0.0000e+00 0.0000e+00 1.4800e+00 +EBPL ENST00000242827 7.8199e-05 7.9645e-01 4.5200e-01 1.4810e+00 +DHRS2 ENST00000344777 8.7228e-07 8.7767e-01 5.4000e-01 1.4810e+00 +OR1E1 ENST00000322608 1.3426e-03 7.1648e-01 3.7300e-01 1.4810e+00 +MYEOV2 ENST00000307266 1.3405e-03 7.1677e-01 3.7300e-01 1.4810e+00 +OR4E2 ENST00000408935 5.3058e-03 6.6212e-01 3.2400e-01 1.4810e+00 +LYPD6 ENST00000334166 4.0193e-06 8.5426e-01 5.1400e-01 1.4810e+00 +C1orf216 ENST00000270815 1.3436e-03 7.1633e-01 3.7300e-01 1.4810e+00 +TVP23C-CDRT4 ENST00000522212 8.7378e-07 8.7749e-01 5.4000e-01 1.4810e+00 +GPR1 ENST00000407325 4.0135e-06 8.5443e-01 5.1400e-01 1.4810e+00 +WDR5B ENST00000330689 1.7993e-05 8.2751e-01 4.8400e-01 1.4810e+00 +TMEM106A ENST00000331615 1.8357e-07 8.9874e-01 5.6500e-01 1.4810e+00 +DCAF16 ENST00000382247 3.2917e-04 7.6010e-01 4.1500e-01 1.4810e+00 +EMR3 ENST00000253673 5.3919e-28 1.1346e+00 8.7700e-01 1.4820e+00 +SGK223 ENST00000520004 1.6825e-35 1.1679e+00 9.2800e-01 1.4820e+00 +EVPLL ENST00000399134 6.8978e-14 1.0207e+00 7.1700e-01 1.4820e+00 +ZNF684 ENST00000372699 3.7374e-08 9.1833e-01 5.8700e-01 1.4820e+00 +SLC26A1 ENST00000361661 1.0564e-11 9.8928e-01 6.7600e-01 1.4820e+00 +ZIM3 ENST00000269834 1.7915e-05 8.2807e-01 4.8500e-01 1.4820e+00 +COA4 ENST00000355693 2.1335e-01 3.3933e-01 1.1800e-01 1.4820e+00 +PIH1D2 ENST00000280350 7.5463e-09 9.3490e-01 6.0800e-01 1.4820e+00 +SEC61B ENST00000223641 2.0030e-02 5.9268e-01 2.6800e-01 1.4830e+00 +RASSF3 ENST00000542104 1.7804e-05 8.2888e-01 4.8500e-01 1.4830e+00 +TMEM254 ENST00000372281 1.3335e-03 7.1775e-01 3.7400e-01 1.4830e+00 +ADM2 ENST00000395738 2.0009e-02 5.9293e-01 2.6800e-01 1.4830e+00 +ALLC ENST00000252505 4.2324e-16 1.0475e+00 7.5300e-01 1.4830e+00 +GSTZ1 ENST00000216465 5.5058e-11 9.7798e-01 6.6100e-01 1.4830e+00 +SLC17A3 ENST00000397060 4.9259e-22 1.0994e+00 8.2500e-01 1.4830e+00 +KIAA1024L ENST00000564719 1.3310e-03 7.1811e-01 3.7400e-01 1.4840e+00 +PRLHR ENST00000239032 7.7094e-05 7.9853e-01 4.5300e-01 1.4840e+00 +MYOM2 ENST00000262113 7.0086e-85 1.2702e+00 1.0900e+00 1.4840e+00 +HBE1 ENST00000380237 1.9963e-02 5.9350e-01 2.6800e-01 1.4840e+00 +KLRF1 ENST00000279544 1.8025e-07 9.0048e-01 5.6600e-01 1.4840e+00 +DLEU1 ENST00000378180 4.7033e-01 0.0000e+00 0.0000e+00 1.4840e+00 +ZNF774 ENST00000354377 2.2808e-15 1.0400e+00 7.4200e-01 1.4840e+00 +FAM114A1 ENST00000358869 1.4659e-20 1.0898e+00 8.1000e-01 1.4850e+00 +ADORA2B ENST00000304222 1.7674e-05 8.2983e-01 4.8600e-01 1.4850e+00 +PCYOX1 ENST00000433351 2.2481e-15 1.0408e+00 7.4300e-01 1.4850e+00 +GPR89A ENST00000313835 6.6612e-14 1.0227e+00 7.1900e-01 1.4850e+00 +EXOSC1 ENST00000370902 7.3521e-09 9.3702e-01 6.0900e-01 1.4850e+00 +ZNF664 ENST00000539644 1.3267e-03 7.1871e-01 3.7400e-01 1.4850e+00 +TMEM222 ENST00000374076 3.9417e-06 8.5652e-01 5.1500e-01 1.4850e+00 +MBLAC1 ENST00000398075 2.1273e-01 3.4025e-01 1.1900e-01 1.4850e+00 +TAX1BP3 ENST00000225525 5.2431e-03 6.6465e-01 3.2600e-01 1.4850e+00 +ACYP1 ENST00000238618 7.0318e-02 4.9618e-01 2.0100e-01 1.4860e+00 +CNGA3 ENST00000393504 8.0327e-20 1.0843e+00 8.0200e-01 1.4860e+00 +UGT3A1 ENST00000274278 3.5366e-13 1.0138e+00 7.0600e-01 1.4860e+00 +OR4L1 ENST00000315683 5.2285e-03 6.6524e-01 3.2600e-01 1.4860e+00 +PEX11A ENST00000300056 8.4537e-07 8.8094e-01 5.4200e-01 1.4860e+00 +PRMT3 ENST00000331079 4.9032e-25 1.1207e+00 8.5500e-01 1.4860e+00 +ALPI ENST00000295463 2.4527e-18 1.0715e+00 7.8400e-01 1.4860e+00 +CALHM1 ENST00000329905 1.7556e-05 8.3070e-01 4.8600e-01 1.4860e+00 +EMB ENST00000303221 1.0084e-11 9.9231e-01 6.7800e-01 1.4860e+00 +TPRG1L ENST00000378344 8.4721e-07 8.8071e-01 5.4200e-01 1.4860e+00 +C10orf99 ENST00000372126 2.1211e-01 3.4118e-01 1.1900e-01 1.4870e+00 +NLRP2 ENST00000543010 1.4201e-38 1.1828e+00 9.4800e-01 1.4870e+00 +CISD3 ENST00000439660 1.9823e-02 5.9520e-01 2.6900e-01 1.4870e+00 +LILRA5 ENST00000301219 7.2545e-09 9.3810e-01 6.1000e-01 1.4870e+00 +TMBIM4 ENST00000358230 3.8876e-06 8.5812e-01 5.1600e-01 1.4870e+00 +MUC17 ENST00000306151 7.8985e-63 1.2412e+00 1.0410e+00 1.4870e+00 +POLR2E ENST00000215587 7.2128e-09 9.3857e-01 6.1000e-01 1.4870e+00 +F2RL2 ENST00000296641 1.7486e-05 8.3121e-01 4.8700e-01 1.4870e+00 +SPATA8 ENST00000328504 7.0195e-02 4.9667e-01 2.0100e-01 1.4870e+00 +DCXR ENST00000306869 8.3510e-07 8.8221e-01 5.4300e-01 1.4880e+00 +DHRS7 ENST00000216500 9.8631e-12 9.9376e-01 6.7900e-01 1.4880e+00 +MYL9 ENST00000279022 1.9797e-02 5.9552e-01 2.6900e-01 1.4880e+00 +SERPINA6 ENST00000341584 8.3448e-07 8.8229e-01 5.4300e-01 1.4880e+00 +PPP1R42 ENST00000324682 1.7442e-05 8.3154e-01 4.8700e-01 1.4880e+00 +HDHD2 ENST00000300605 3.8702e-06 8.5864e-01 5.1600e-01 1.4880e+00 +TCTEX1D2 ENST00000325318 3.2126e-04 7.6412e-01 4.1700e-01 1.4880e+00 +GJA3 ENST00000241125 1.3126e-03 7.2071e-01 3.7500e-01 1.4880e+00 +TEX13A ENST00000413579 1.9784e-02 5.9568e-01 2.6900e-01 1.4880e+00 +NMRK1 ENST00000361092 3.5697e-08 9.2236e-01 5.9000e-01 1.4890e+00 +BEST1 ENST00000449131 1.8214e-12 1.0059e+00 6.9400e-01 1.4890e+00 +ABHD15 ENST00000307201 3.5459e-08 9.2294e-01 5.9000e-01 1.4890e+00 +SERPINB1 ENST00000380739 3.5486e-08 9.2288e-01 5.9000e-01 1.4890e+00 +CD48 ENST00000368046 1.7302e-05 8.3259e-01 4.8700e-01 1.4890e+00 +GPRIN2 ENST00000374314 3.8557e-06 8.5908e-01 5.1700e-01 1.4890e+00 +MIA ENST00000263369 1.7345e-05 8.3227e-01 4.8700e-01 1.4890e+00 +SNRNP35 ENST00000412157 7.1094e-09 9.3975e-01 6.1100e-01 1.4890e+00 +FXYD7 ENST00000270310 5.1947e-03 6.6663e-01 3.2700e-01 1.4890e+00 +SPINK2 ENST00000248701 6.9796e-02 4.9826e-01 2.0200e-01 1.4900e+00 +LINC00935 ENST00000548380 5.1864e-03 6.6697e-01 3.2700e-01 1.4900e+00 +NUP62CL ENST00000372466 1.3073e-03 7.2148e-01 3.7500e-01 1.4900e+00 +C9orf40 ENST00000376854 6.9726e-02 4.9854e-01 2.0200e-01 1.4910e+00 +COQ7 ENST00000321998 3.8080e-06 8.6052e-01 5.1700e-01 1.4910e+00 +IL11 ENST00000264563 3.1772e-04 7.6596e-01 4.1800e-01 1.4910e+00 +RAD51C ENST00000337432 6.1906e-14 1.0269e+00 7.2200e-01 1.4910e+00 +SRXN1 ENST00000381962 6.9723e-02 4.9856e-01 2.0200e-01 1.4910e+00 +SLX4IP ENST00000334534 1.7889e-12 1.0071e+00 6.9500e-01 1.4910e+00 +SPATA19 ENST00000299140 3.5133e-08 9.2375e-01 5.9100e-01 1.4910e+00 +SPATA32 ENST00000331780 1.3702e-09 9.5667e-01 6.3100e-01 1.4910e+00 +MREG ENST00000263268 1.7187e-07 9.0501e-01 5.6800e-01 1.4910e+00 +RPL10L ENST00000298283 5.1677e-03 6.6775e-01 3.2700e-01 1.4910e+00 +C22orf31 ENST00000216071 1.7066e-07 9.0569e-01 5.6900e-01 1.4920e+00 +CHRAC1 ENST00000220913 6.9520e-02 4.9937e-01 2.0200e-01 1.4920e+00 +KCNE3 ENST00000310128 4.6820e-01 0.0000e+00 0.0000e+00 1.4920e+00 +TIGD3 ENST00000309880 2.6300e-10 9.7132e-01 6.4900e-01 1.4920e+00 +FXYD4 ENST00000476166 3.1646e-04 7.6663e-01 4.1800e-01 1.4920e+00 +KERA ENST00000266719 1.7098e-07 9.0551e-01 5.6900e-01 1.4920e+00 +EFHD1 ENST00000264059 5.1487e-03 6.6853e-01 3.2800e-01 1.4920e+00 +MZB1 ENST00000302125 3.1626e-04 7.6673e-01 4.1800e-01 1.4920e+00 +POTEM ENST00000551509 3.1637e-04 7.6667e-01 4.1800e-01 1.4920e+00 +NDUFA12 ENST00000327772 7.4270e-05 8.0400e-01 4.5600e-01 1.4930e+00 +ZNF490 ENST00000311437 3.1512e-04 7.6733e-01 4.1900e-01 1.4930e+00 +OR8D2 ENST00000357438 2.1061e-01 3.4346e-01 1.2000e-01 1.4930e+00 +SNUPN ENST00000564644 1.1094e-14 1.0376e+00 7.3500e-01 1.4930e+00 +ENO4 ENST00000409522 8.0499e-07 8.8607e-01 5.4500e-01 1.4940e+00 +NAA38 ENST00000249299 5.1229e-03 6.6962e-01 3.2800e-01 1.4940e+00 +CD302 ENST00000259053 3.7405e-06 8.6261e-01 5.1900e-01 1.4940e+00 +RPL37A ENST00000491306 5.1255e-03 6.6951e-01 3.2800e-01 1.4940e+00 +FAM181B ENST00000329203 6.9368e-02 4.9999e-01 2.0200e-01 1.4940e+00 +NMB ENST00000394588 1.9529e-02 5.9885e-01 2.7100e-01 1.4940e+00 +LY96 ENST00000284818 7.4167e-05 8.0420e-01 4.5600e-01 1.4940e+00 +CD8A ENST00000409511 1.6806e-05 8.3638e-01 4.9000e-01 1.4950e+00 +TMEM97 ENST00000226230 3.1267e-04 7.6863e-01 4.1900e-01 1.4950e+00 +MIF4GD ENST00000577542 6.7828e-09 9.4360e-01 6.1300e-01 1.4950e+00 +OR2J2 ENST00000377167 1.9489e-02 5.9935e-01 2.7100e-01 1.4950e+00 +C17orf107 ENST00000381365 6.9270e-02 5.0039e-01 2.0200e-01 1.4950e+00 +DHRS7B ENST00000395511 6.7664e-09 9.4380e-01 6.1300e-01 1.4950e+00 +FAM151A ENST00000302250 6.5453e-17 1.0637e+00 7.6900e-01 1.4950e+00 +GALM ENST00000272252 4.8791e-11 9.8627e-01 6.6700e-01 1.4950e+00 +BPIFA2 ENST00000253362 8.0124e-07 8.8656e-01 5.4600e-01 1.4950e+00 +HRG ENST00000232003 5.8888e-14 1.0299e+00 7.2400e-01 1.4950e+00 +REEP6 ENST00000233596 1.6861e-05 8.3595e-01 4.8900e-01 1.4950e+00 +ITPRIP ENST00000278071 4.7954e-11 9.8747e-01 6.6700e-01 1.4960e+00 +IFI44 ENST00000370747 1.9433e-15 1.0487e+00 7.4800e-01 1.4960e+00 +NAT16 ENST00000300303 3.6952e-06 8.6403e-01 5.2000e-01 1.4960e+00 +DUSP15 ENST00000339738 3.7139e-06 8.6344e-01 5.1900e-01 1.4960e+00 +FCGR3A ENST00000367969 3.6955e-06 8.6402e-01 5.2000e-01 1.4960e+00 +SLC14A1 ENST00000436407 5.7661e-14 1.0311e+00 7.2400e-01 1.4960e+00 +C8orf87 ENST00000521906 6.9139e-02 5.0092e-01 2.0300e-01 1.4960e+00 +TBCC ENST00000244625 3.7118e-06 8.6350e-01 5.1900e-01 1.4960e+00 +CTU2 ENST00000453996 3.9682e-22 1.1088e+00 8.3200e-01 1.4960e+00 +METTL21B ENST00000300209 3.1059e-04 7.6975e-01 4.2000e-01 1.4970e+00 +CREG2 ENST00000324768 7.2973e-05 8.0659e-01 4.5700e-01 1.4970e+00 +PRELID2 ENST00000334744 6.6487e-09 9.4525e-01 6.1400e-01 1.4970e+00 +STX10 ENST00000587230 1.3079e-09 9.6025e-01 6.3300e-01 1.4970e+00 +FCRLB ENST00000367948 2.5100e-10 9.7471e-01 6.5100e-01 1.4970e+00 +SERPIND1 ENST00000215727 2.5137e-10 9.7461e-01 6.5100e-01 1.4970e+00 +MRPL49 ENST00000279242 3.1078e-04 7.6964e-01 4.2000e-01 1.4970e+00 +OR4D6 ENST00000300127 5.0885e-03 6.7107e-01 3.2900e-01 1.4970e+00 +DYNLT1 ENST00000367089 7.3232e-05 8.0607e-01 4.5700e-01 1.4970e+00 +SUCLG2 ENST00000493112 5.7163e-14 1.0316e+00 7.2500e-01 1.4970e+00 +ASB5 ENST00000296525 3.0711e-13 1.0224e+00 7.1200e-01 1.4980e+00 +SPATA21 ENST00000335496 1.1342e-17 1.0733e+00 7.8100e-01 1.4980e+00 +LHPP ENST00000368842 1.6345e-07 9.0983e-01 5.7100e-01 1.4980e+00 +RPP25 ENST00000322177 2.0939e-01 3.4533e-01 1.2000e-01 1.4980e+00 +HHIPL2 ENST00000343410 6.7268e-23 1.1163e+00 8.4200e-01 1.4990e+00 +NIPAL1 ENST00000295461 2.4544e-10 9.7635e-01 6.5200e-01 1.4990e+00 +ALG1 ENST00000262374 3.6220e-19 1.0878e+00 8.0100e-01 1.4990e+00 +NRSN1 ENST00000378491 3.0819e-04 7.7104e-01 4.2100e-01 1.4990e+00 +CETP ENST00000200676 1.1892e-23 1.1217e+00 8.4900e-01 1.4990e+00 +PSMF1 ENST00000335877 3.3092e-08 9.2904e-01 5.9400e-01 1.4990e+00 +ZNF214 ENST00000278314 1.1138e-17 1.0742e+00 7.8200e-01 1.4990e+00 +DHRS7C ENST00000330255 3.2734e-08 9.3000e-01 5.9500e-01 1.5000e+00 +ECT2L ENST00000423192 7.8004e-48 1.2202e+00 9.9800e-01 1.5000e+00 +LCE3E ENST00000368789 4.6574e-01 0.0000e+00 0.0000e+00 1.5000e+00 +C1QTNF9B ENST00000382137 3.2529e-08 9.3056e-01 5.9500e-01 1.5010e+00 +TMEM190 ENST00000291934 1.2621e-03 7.2816e-01 3.7900e-01 1.5010e+00 +RABL2B ENST00000395593 7.7226e-07 8.9045e-01 5.4800e-01 1.5010e+00 +GNPDA1 ENST00000508177 1.6024e-07 9.1174e-01 5.7300e-01 1.5010e+00 +HDDC3 ENST00000330334 1.9263e-02 6.0221e-01 2.7200e-01 1.5010e+00 +NRARP ENST00000356628 2.0859e-01 3.4659e-01 1.2100e-01 1.5010e+00 +OR8A1 ENST00000284287 5.0280e-03 6.7365e-01 3.3000e-01 1.5010e+00 +CYB561D1 ENST00000369868 7.1834e-05 8.0892e-01 4.5900e-01 1.5010e+00 +SERPINA12 ENST00000341228 7.7169e-07 8.9052e-01 5.4800e-01 1.5010e+00 +GPR151 ENST00000311104 3.2266e-08 9.3128e-01 5.9600e-01 1.5020e+00 +PAH ENST00000553106 6.4046e-23 1.1184e+00 8.4300e-01 1.5020e+00 +GXYLT2 ENST00000389617 5.3671e-14 1.0354e+00 7.2700e-01 1.5020e+00 +PTGDR ENST00000306051 3.5800e-06 8.6774e-01 5.2200e-01 1.5020e+00 +TRIM49B ENST00000332682 6.3896e-09 9.4852e-01 6.1600e-01 1.5020e+00 +B3GNT4 ENST00000324189 7.6758e-07 8.9109e-01 5.4800e-01 1.5020e+00 +PPIC ENST00000306442 3.0514e-04 7.7271e-01 4.2200e-01 1.5020e+00 +C11orf71 ENST00000325636 2.0849e-01 3.4675e-01 1.2100e-01 1.5020e+00 +CBY1 ENST00000396811 1.2587e-03 7.2867e-01 3.7900e-01 1.5020e+00 +TMEM217 ENST00000336655 7.1339e-05 8.0994e-01 4.5900e-01 1.5030e+00 +TMEM74B ENST00000381894 3.0413e-04 7.7327e-01 4.2200e-01 1.5030e+00 +ATP5J2 ENST00000292475 1.9170e-02 6.0341e-01 2.7300e-01 1.5030e+00 +P2RY13 ENST00000325602 3.0364e-04 7.7354e-01 4.2200e-01 1.5030e+00 +LINC00923 ENST00000503874 2.0785e-01 3.4775e-01 1.2100e-01 1.5040e+00 +GOLGA6A ENST00000290438 1.6100e-05 8.4201e-01 4.9300e-01 1.5040e+00 +CRYGD ENST00000264376 3.0317e-04 7.7380e-01 4.2200e-01 1.5040e+00 +EIF4EBP1 ENST00000338825 2.0762e-01 3.4811e-01 1.2100e-01 1.5050e+00 +FABP2 ENST00000274024 4.9806e-03 6.7571e-01 3.3100e-01 1.5050e+00 +PIGL ENST00000225609 6.1780e-09 9.5132e-01 6.1800e-01 1.5060e+00 +BTG2 ENST00000290551 1.9033e-02 6.0519e-01 2.7400e-01 1.5060e+00 +SLC52A1 ENST00000424747 3.5163e-06 8.6985e-01 5.2300e-01 1.5060e+00 +RP11-111M22.2 ENST00000321844 4.9622e-03 6.7652e-01 3.3100e-01 1.5060e+00 +LGALS9C ENST00000328114 6.2016e-09 9.5100e-01 6.1800e-01 1.5060e+00 +NKD2 ENST00000296849 1.5159e-12 1.0176e+00 7.0200e-01 1.5060e+00 +SLC18B1 ENST00000275227 1.0193e-17 1.0788e+00 7.8500e-01 1.5060e+00 +MAPK15 ENST00000338033 1.8682e-21 1.1109e+00 8.3000e-01 1.5060e+00 +KLHDC7B ENST00000395676 1.1920e-09 9.6745e-01 6.3800e-01 1.5070e+00 +PCDHA2 ENST00000526136 1.0354e-23 1.1275e+00 8.5400e-01 1.5070e+00 +RPRML ENST00000322329 4.6377e-01 0.0000e+00 0.0000e+00 1.5070e+00 +C19orf10 ENST00000262947 3.4923e-06 8.7065e-01 5.2400e-01 1.5070e+00 +GDPD3 ENST00000406256 1.6968e-15 1.0563e+00 7.5400e-01 1.5070e+00 +CKLF ENST00000264001 4.9483e-03 6.7713e-01 3.3200e-01 1.5080e+00 +GOLGA8M ENST00000563027 2.7284e-13 1.0297e+00 7.1700e-01 1.5080e+00 +C8orf44 ENST00000519561 2.0702e-01 3.4908e-01 1.2200e-01 1.5080e+00 +NQO1 ENST00000320623 1.1867e-09 9.6780e-01 6.3800e-01 1.5080e+00 +HDAC10 ENST00000216271 2.9729e-31 1.1698e+00 9.1500e-01 1.5080e+00 +OR4K15 ENST00000305051 1.8946e-02 6.0633e-01 2.7400e-01 1.5080e+00 +DYRK4 ENST00000540757 1.7785e-18 1.0873e+00 7.9600e-01 1.5080e+00 +MS4A7 ENST00000300184 3.4763e-06 8.7119e-01 5.2400e-01 1.5080e+00 +SPATA4 ENST00000280191 1.1841e-09 9.6797e-01 6.3800e-01 1.5080e+00 +TIMM23 ENST00000260867 4.9452e-03 6.7727e-01 3.3200e-01 1.5080e+00 +TRAPPC3L ENST00000368602 1.5719e-05 8.4516e-01 4.9500e-01 1.5090e+00 +GPR35 ENST00000438013 4.9273e-03 6.7806e-01 3.3200e-01 1.5090e+00 +NAMPTL ENST00000440465 1.5141e-07 9.1723e-01 5.7600e-01 1.5090e+00 +CTD-2510F5.6 ENST00000577660 1.8931e-02 6.0653e-01 2.7400e-01 1.5090e+00 +WDR86 ENST00000334493 1.1648e-09 9.6926e-01 6.3900e-01 1.5100e+00 +TSNAXIP1 ENST00000388833 5.2807e-29 1.1601e+00 9.0000e-01 1.5100e+00 +ZNF589 ENST00000354698 4.9175e-03 6.7850e-01 3.3200e-01 1.5100e+00 +DUXA ENST00000554048 3.0459e-08 9.3643e-01 5.9900e-01 1.5100e+00 +EAPP ENST00000250454 2.2259e-10 9.8353e-01 6.5700e-01 1.5100e+00 +ZNF257 ENST00000594947 1.8857e-02 6.0751e-01 2.7500e-01 1.5100e+00 +C14orf28 ENST00000325192 2.2179e-10 9.8380e-01 6.5700e-01 1.5100e+00 +ASB17 ENST00000284142 3.4115e-06 8.7342e-01 5.2500e-01 1.5110e+00 +OR6C75 ENST00000343399 1.8817e-02 6.0803e-01 2.7500e-01 1.5110e+00 +CREG1 ENST00000370509 1.2232e-03 7.3414e-01 3.8200e-01 1.5110e+00 +C6orf229 ENST00000565469 6.7336e-02 5.0845e-01 2.0600e-01 1.5110e+00 +MICU2 ENST00000382374 9.7216e-21 1.1086e+00 8.2400e-01 1.5110e+00 +ZNF668 ENST00000417110 2.9449e-04 7.7870e-01 4.2500e-01 1.5120e+00 +CCDC148 ENST00000283233 1.5603e-30 1.1691e+00 9.1200e-01 1.5120e+00 +ZHX1-C8ORF76 ENST00000357082 1.1430e-09 9.7074e-01 6.4000e-01 1.5120e+00 +DNALI1 ENST00000296218 4.1201e-11 9.9808e-01 6.7500e-01 1.5120e+00 +CD160 ENST00000235933 6.8425e-05 8.1615e-01 4.6300e-01 1.5130e+00 +OTOR ENST00000246081 4.8775e-03 6.8029e-01 3.3300e-01 1.5130e+00 +GGT6 ENST00000574154 2.9754e-08 9.3853e-01 6.0000e-01 1.5130e+00 +TRIM64C ENST00000530230 4.0727e-11 9.9889e-01 6.7500e-01 1.5130e+00 +IFI30 ENST00000407280 2.9645e-08 9.3886e-01 6.0000e-01 1.5130e+00 +CTU1 ENST00000421832 6.7155e-02 5.0923e-01 2.0600e-01 1.5130e+00 +GTPBP8 ENST00000383678 1.4820e-07 9.1931e-01 5.7700e-01 1.5130e+00 +ACPT ENST00000270593 8.6210e-15 1.0521e+00 7.4500e-01 1.5130e+00 +HAUS2 ENST00000260372 3.3829e-06 8.7441e-01 5.2600e-01 1.5130e+00 +TMEM202 ENST00000341689 2.9827e-08 9.3831e-01 6.0000e-01 1.5130e+00 +DCUN1D2 ENST00000478244 2.9667e-08 9.3879e-01 6.0000e-01 1.5130e+00 +ZNF611 ENST00000543227 6.7163e-02 5.0920e-01 2.0600e-01 1.5130e+00 +C9 ENST00000263408 1.6323e-24 1.1373e+00 8.6400e-01 1.5140e+00 +C15orf38 ENST00000357484 1.5397e-05 8.4790e-01 4.9600e-01 1.5140e+00 +OR2A2 ENST00000408979 2.0550e-01 3.5153e-01 1.2200e-01 1.5140e+00 +SMIM7 ENST00000487416 4.8480e-03 6.8163e-01 3.3400e-01 1.5150e+00 +NKX2-8 ENST00000258829 4.8550e-03 6.8131e-01 3.3400e-01 1.5150e+00 +ODAM ENST00000396094 1.5176e-15 1.0625e+00 7.5800e-01 1.5150e+00 +SLC30A8 ENST00000456015 7.4306e-12 1.0126e+00 6.9200e-01 1.5150e+00 +FOXB2 ENST00000376708 6.7467e-05 8.1825e-01 4.6400e-01 1.5160e+00 +SMCO2 ENST00000416383 2.9097e-08 9.4054e-01 6.0100e-01 1.5160e+00 +DNAH14 ENST00000400952 2.6938e-16 1.0717e+00 7.7000e-01 1.5170e+00 +C16orf71 ENST00000299320 4.9108e-20 1.1075e+00 8.2000e-01 1.5170e+00 +OR9A2 ENST00000350513 2.8864e-04 7.8211e-01 4.2700e-01 1.5170e+00 +EIF2B2 ENST00000266126 2.0830e-10 9.8846e-01 6.6000e-01 1.5170e+00 +FAM213B ENST00000419916 1.5148e-05 8.5006e-01 4.9700e-01 1.5170e+00 +OR2T2 ENST00000342927 2.0478e-01 3.5270e-01 1.2300e-01 1.5170e+00 +CTRL ENST00000574481 1.0976e-09 9.7392e-01 6.4200e-01 1.5170e+00 +EVX1 ENST00000496902 6.9817e-07 9.0118e-01 5.5500e-01 1.5170e+00 +ZNF66 ENST00000344519 6.6624e-02 5.1154e-01 2.0700e-01 1.5170e+00 +IFI44L ENST00000370751 1.3464e-12 1.0253e+00 7.0800e-01 1.5170e+00 +CXCL17 ENST00000601181 4.8138e-03 6.8319e-01 3.3500e-01 1.5180e+00 +RGCC ENST00000379359 4.8149e-03 6.8314e-01 3.3500e-01 1.5180e+00 +GINS3 ENST00000426538 1.5050e-05 8.5092e-01 4.9800e-01 1.5180e+00 +PRR18 ENST00000322583 4.6086e-01 0.0000e+00 0.0000e+00 1.5180e+00 +C11orf54 ENST00000528288 2.8718e-08 9.4172e-01 6.0200e-01 1.5180e+00 +ITIH6 ENST00000218436 1.5096e-24 1.1406e+00 8.6700e-01 1.5180e+00 +AP001652.1 ENST00000454512 2.0443e-01 3.5327e-01 1.2300e-01 1.5180e+00 +MRPL13 ENST00000306185 1.4307e-07 9.2275e-01 5.8000e-01 1.5180e+00 +PRSS42 ENST00000429665 5.5685e-09 9.6000e-01 6.2400e-01 1.5190e+00 +ZNF682 ENST00000397165 1.8503e-02 6.1226e-01 2.7700e-01 1.5190e+00 +CHCHD6 ENST00000290913 5.5744e-09 9.5991e-01 6.2400e-01 1.5190e+00 +ECHDC1 ENST00000531967 5.5968e-09 9.5958e-01 6.2400e-01 1.5190e+00 +DPH3 ENST00000488423 6.6294e-02 5.1298e-01 2.0700e-01 1.5200e+00 +CEACAM3 ENST00000357396 1.0670e-09 9.7616e-01 6.4400e-01 1.5200e+00 +MNAT1 ENST00000261245 1.3117e-12 1.0270e+00 7.0900e-01 1.5200e+00 +OR51G1 ENST00000321961 1.1920e-03 7.3914e-01 3.8500e-01 1.5200e+00 +AC011897.1 ENST00000581929 4.7933e-03 6.8413e-01 3.3500e-01 1.5200e+00 +CAPN12 ENST00000328867 1.2260e-33 1.1887e+00 9.3800e-01 1.5200e+00 +ULBP1 ENST00000229708 6.8850e-07 9.0268e-01 5.5600e-01 1.5200e+00 +FAM162A ENST00000477892 3.2417e-06 8.7947e-01 5.2900e-01 1.5210e+00 +CYP4F11 ENST00000402119 1.4678e-21 1.1219e+00 8.3800e-01 1.5210e+00 +C11orf16 ENST00000326053 4.3154e-14 1.0485e+00 7.3700e-01 1.5210e+00 +IFNL1 ENST00000333625 2.8469e-04 7.8446e-01 4.2800e-01 1.5210e+00 +IFI27L1 ENST00000555523 6.6209e-02 5.1336e-01 2.0700e-01 1.5210e+00 +SRMS ENST00000217188 1.2721e-12 1.0290e+00 7.1000e-01 1.5220e+00 +TSSK4 ENST00000339917 5.4619e-09 9.6163e-01 6.2500e-01 1.5220e+00 +HOXB7 ENST00000239165 2.8382e-04 7.8497e-01 4.2800e-01 1.5220e+00 +AKR7A2 ENST00000235835 1.9938e-10 9.9174e-01 6.6200e-01 1.5220e+00 +SLC16A5 ENST00000450736 1.9979e-10 9.9158e-01 6.6200e-01 1.5220e+00 +RSC1A1 ENST00000345034 2.3498e-13 1.0390e+00 7.2400e-01 1.5220e+00 +CAMKMT ENST00000378494 1.3806e-15 1.0679e+00 7.6200e-01 1.5230e+00 +SLC25A41 ENST00000321510 6.8621e-12 1.0180e+00 6.9600e-01 1.5230e+00 +KRBOX1 ENST00000446977 1.8360e-02 6.1423e-01 2.7800e-01 1.5230e+00 +MMP7 ENST00000260227 1.0404e-09 9.7816e-01 6.4500e-01 1.5230e+00 +COA5 ENST00000328709 1.8348e-02 6.1440e-01 2.7800e-01 1.5230e+00 +PAQR6 ENST00000335852 6.5548e-05 8.2259e-01 4.6600e-01 1.5230e+00 +IGFL4 ENST00000377697 1.1794e-03 7.4120e-01 3.8600e-01 1.5230e+00 +APLN ENST00000307484 4.5897e-01 0.0000e+00 0.0000e+00 1.5240e+00 +TAAR8 ENST00000275200 2.8158e-04 7.8633e-01 4.2900e-01 1.5240e+00 +LPA ENST00000447678 6.5917e-89 1.3083e+00 1.1260e+00 1.5240e+00 +RP11-1167A19.2 ENST00000529036 4.5895e-01 0.0000e+00 0.0000e+00 1.5240e+00 +IL4 ENST00000231449 4.7372e-03 6.8674e-01 3.3600e-01 1.5240e+00 +OR51S1 ENST00000322101 2.8152e-04 7.8636e-01 4.2900e-01 1.5240e+00 +MMP13 ENST00000260302 7.8767e-18 1.0921e+00 7.9500e-01 1.5240e+00 +FANCF ENST00000327470 4.5886e-01 0.0000e+00 0.0000e+00 1.5250e+00 +MMP1 ENST00000315274 7.7197e-18 1.0932e+00 7.9600e-01 1.5250e+00 +ZNF763 ENST00000343949 1.8273e-02 6.1544e-01 2.7800e-01 1.5250e+00 +NLRP14 ENST00000299481 5.7416e-36 1.2017e+00 9.5500e-01 1.5250e+00 +KRT15 ENST00000254043 2.3926e-16 1.0783e+00 7.7500e-01 1.5260e+00 +ZDHHC4 ENST00000396706 5.2991e-09 9.6419e-01 6.2700e-01 1.5260e+00 +EVA1A ENST00000233712 6.5594e-02 5.1610e-01 2.0900e-01 1.5260e+00 +GPR135 ENST00000395116 6.4853e-05 8.2419e-01 4.6700e-01 1.5260e+00 +KLHDC9 ENST00000368011 1.0170e-09 9.7997e-01 6.4600e-01 1.5260e+00 +KIAA0825 ENST00000329378 5.2834e-09 9.6444e-01 6.2700e-01 1.5260e+00 +CEACAM7 ENST00000006724 1.3466e-07 9.2870e-01 5.8300e-01 1.5270e+00 +DRAXIN ENST00000294485 1.8935e-10 9.9562e-01 6.6500e-01 1.5270e+00 +C15orf32 ENST00000333334 1.1665e-03 7.4335e-01 3.8700e-01 1.5270e+00 +CFL2 ENST00000341223 6.4399e-05 8.2525e-01 4.6800e-01 1.5270e+00 +LDOC1L ENST00000341255 1.8186e-02 6.1665e-01 2.7900e-01 1.5270e+00 +FCN2 ENST00000291744 3.5646e-11 1.0084e+00 6.8200e-01 1.5270e+00 +ZNF418 ENST00000396147 1.0016e-09 9.8118e-01 6.4700e-01 1.5270e+00 +C7orf76 ENST00000356686 1.8168e-02 6.1692e-01 2.7900e-01 1.5270e+00 +PPP1R3D ENST00000370996 4.7028e-03 6.8837e-01 3.3700e-01 1.5270e+00 +SNAPC1 ENST00000216294 2.3628e-16 1.0790e+00 7.7500e-01 1.5270e+00 +IFIT1 ENST00000371804 2.7793e-04 7.8857e-01 4.3000e-01 1.5280e+00 +OR52H1 ENST00000322653 4.6856e-03 6.8919e-01 3.3700e-01 1.5280e+00 +ETV7 ENST00000340181 3.9605e-14 1.0537e+00 7.4000e-01 1.5280e+00 +AC012123.1 ENST00000426194 1.8166e-02 6.1694e-01 2.7900e-01 1.5280e+00 +CBY3 ENST00000376974 2.7768e-04 7.8872e-01 4.3000e-01 1.5280e+00 +ACOT1 ENST00000311148 6.4141e-05 8.2586e-01 4.6800e-01 1.5280e+00 +NANP ENST00000304788 6.4290e-05 8.2551e-01 4.6800e-01 1.5280e+00 +APLF ENST00000303795 1.3266e-18 1.1021e+00 8.0700e-01 1.5280e+00 +SERTAD3 ENST00000322354 1.8142e-02 6.1728e-01 2.7900e-01 1.5280e+00 +RBKS ENST00000302188 5.1575e-09 9.6649e-01 6.2800e-01 1.5290e+00 +HOXD12 ENST00000406506 2.7657e-04 7.8941e-01 4.3100e-01 1.5290e+00 +LINC00955 ENST00000514422 4.5772e-01 0.0000e+00 0.0000e+00 1.5290e+00 +RNF182 ENST00000488300 4.6762e-03 6.8964e-01 3.3800e-01 1.5290e+00 +FBXW5 ENST00000325285 2.2808e-16 1.0810e+00 7.7700e-01 1.5290e+00 +WDR83 ENST00000418543 6.4459e-12 1.0223e+00 6.9900e-01 1.5290e+00 +GPR142 ENST00000335666 1.8753e-10 9.9635e-01 6.6500e-01 1.5290e+00 +CHEK2 ENST00000382580 1.2103e-24 1.1499e+00 8.7400e-01 1.5300e+00 +SERPINB2 ENST00000457692 6.3773e-12 1.0231e+00 6.9900e-01 1.5300e+00 +MICALCL ENST00000256186 3.7540e-26 1.1588e+00 8.8700e-01 1.5300e+00 +ASGR2 ENST00000380952 9.8145e-10 9.8281e-01 6.4800e-01 1.5300e+00 +CFHR1 ENST00000320493 2.6297e-08 9.4972e-01 6.0700e-01 1.5300e+00 +UGT2A3 ENST00000251566 1.2614e-15 1.0731e+00 7.6600e-01 1.5300e+00 +FKBP11 ENST00000550765 6.4642e-07 9.0948e-01 5.6000e-01 1.5300e+00 +DBNDD1 ENST00000304733 6.3500e-05 8.2738e-01 4.6900e-01 1.5310e+00 +HSD17B14 ENST00000263278 3.4303e-11 1.0111e+00 6.8300e-01 1.5310e+00 +LGALS14 ENST00000360675 2.7470e-04 7.9058e-01 4.3100e-01 1.5310e+00 +ASF1B ENST00000263382 6.3325e-05 8.2780e-01 4.6900e-01 1.5310e+00 +KRTAP10-10 ENST00000380095 4.6536e-03 6.9072e-01 3.3800e-01 1.5310e+00 +SLC28A2 ENST00000347644 1.1277e-27 1.1682e+00 9.0100e-01 1.5310e+00 +SERPINI2 ENST00000476257 6.9523e-15 1.0648e+00 7.5400e-01 1.5310e+00 +TACSTD2 ENST00000371225 4.6571e-03 6.9055e-01 3.3800e-01 1.5310e+00 +MPV17L2 ENST00000599612 6.4336e-07 9.0999e-01 5.6000e-01 1.5310e+00 +TAS2R5 ENST00000247883 1.1523e-03 7.4575e-01 3.8800e-01 1.5310e+00 +WWOX ENST00000566780 1.2376e-15 1.0742e+00 7.6600e-01 1.5320e+00 +TSPO ENST00000329563 2.7398e-04 7.9103e-01 4.3100e-01 1.5320e+00 +KIAA0040 ENST00000545251 2.0102e-01 3.5899e-01 1.2500e-01 1.5320e+00 +TMUB2 ENST00000587989 1.4091e-05 8.5972e-01 5.0300e-01 1.5320e+00 +KLK9 ENST00000376832 1.2997e-07 9.3221e-01 5.8500e-01 1.5320e+00 +FAM127A ENST00000257013 4.5663e-01 0.0000e+00 0.0000e+00 1.5320e+00 +TNFRSF12A ENST00000326577 1.7995e-02 6.1937e-01 2.8000e-01 1.5320e+00 +HOXD11 ENST00000249504 1.1418e-03 7.4755e-01 3.8900e-01 1.5330e+00 +UGT2A1 ENST00000503640 3.8806e-17 1.0915e+00 7.8900e-01 1.5330e+00 +TSACC ENST00000368255 1.7937e-02 6.2020e-01 2.8000e-01 1.5330e+00 +RTP3 ENST00000296142 2.0085e-01 3.5930e-01 1.2500e-01 1.5330e+00 +ZNF57 ENST00000306908 4.6320e-03 6.9176e-01 3.3900e-01 1.5330e+00 +PRADC1 ENST00000258083 1.4051e-05 8.6010e-01 5.0300e-01 1.5330e+00 +TUBB8 ENST00000309812 1.7934e-02 6.2024e-01 2.8000e-01 1.5330e+00 +ALDH3A1 ENST00000457500 3.9013e-17 1.0913e+00 7.8900e-01 1.5330e+00 +CBR1 ENST00000290349 6.2783e-05 8.2910e-01 4.7000e-01 1.5330e+00 +BAD ENST00000394532 4.6237e-03 6.9217e-01 3.3900e-01 1.5330e+00 +C2orf54 ENST00000388934 2.5445e-08 9.5273e-01 6.0900e-01 1.5340e+00 +C18orf32 ENST00000318240 2.0064e-01 3.5965e-01 1.2500e-01 1.5340e+00 +AQP12A ENST00000337801 1.7909e-02 6.2060e-01 2.8000e-01 1.5340e+00 +COA3 ENST00000328434 6.4758e-02 5.1990e-01 2.1000e-01 1.5340e+00 +QPCT ENST00000338415 1.1987e-15 1.0760e+00 7.6800e-01 1.5340e+00 +C9orf69 ENST00000418388 2.0070e-01 3.5955e-01 1.2500e-01 1.5340e+00 +GPR150 ENST00000380007 1.3878e-05 8.6177e-01 5.0400e-01 1.5350e+00 +MFSD9 ENST00000258436 9.3451e-10 9.8674e-01 6.5000e-01 1.5350e+00 +PSMG3 ENST00000288607 2.0030e-01 3.6024e-01 1.2500e-01 1.5350e+00 +HOXA6 ENST00000222728 2.9887e-06 8.8920e-01 5.3500e-01 1.5350e+00 +AC092687.4 ENST00000418835 6.4624e-02 5.2052e-01 2.1000e-01 1.5350e+00 +MT3 ENST00000200691 6.4484e-02 5.2117e-01 2.1100e-01 1.5360e+00 +RCCD1 ENST00000394258 3.2679e-11 1.0147e+00 6.8600e-01 1.5360e+00 +LTB4R2 ENST00000528054 1.3821e-05 8.6232e-01 5.0500e-01 1.5360e+00 +NDUFA11 ENST00000418389 1.7814e-02 6.2197e-01 2.8100e-01 1.5360e+00 +RP1-66C13.4 ENST00000582441 1.7837e-02 6.2163e-01 2.8100e-01 1.5360e+00 +OR51D1 ENST00000357605 4.5855e-03 6.9404e-01 3.4000e-01 1.5360e+00 +AC022532.1 ENST00000420338 6.4374e-02 5.2168e-01 2.1100e-01 1.5370e+00 +C1orf100 ENST00000308105 1.2575e-07 9.3549e-01 5.8800e-01 1.5370e+00 +TM4SF19 ENST00000273695 2.9569e-06 8.9049e-01 5.3500e-01 1.5370e+00 +DCTN3 ENST00000259632 1.2577e-07 9.3548e-01 5.8800e-01 1.5370e+00 +C5orf52 ENST00000409999 6.4408e-02 5.2153e-01 2.1100e-01 1.5370e+00 +DTYMK ENST00000305784 6.1537e-05 8.3215e-01 4.7200e-01 1.5380e+00 +LGALS13 ENST00000221797 1.1274e-03 7.5006e-01 3.9000e-01 1.5380e+00 +DHDH ENST00000221403 9.1294e-10 9.8862e-01 6.5200e-01 1.5380e+00 +LYRM4 ENST00000500576 1.9951e-01 3.6161e-01 1.2600e-01 1.5380e+00 +B3GNT8 ENST00000321702 4.8063e-09 9.7252e-01 6.3200e-01 1.5380e+00 +SEPW1 ENST00000601048 2.6801e-04 7.9483e-01 4.3300e-01 1.5380e+00 +IL11RA ENST00000555003 6.2882e-21 1.1292e+00 8.4000e-01 1.5380e+00 +AGMAT ENST00000375826 1.2369e-07 9.3713e-01 5.8900e-01 1.5390e+00 +AGPAT2 ENST00000371696 1.2360e-07 9.3721e-01 5.8900e-01 1.5390e+00 +KRTAP2-2 ENST00000398477 4.5465e-01 0.0000e+00 0.0000e+00 1.5390e+00 +ZNF77 ENST00000314531 4.5580e-03 6.9539e-01 3.4000e-01 1.5390e+00 +SMIM4 ENST00000477703 1.9943e-01 3.6176e-01 1.2600e-01 1.5390e+00 +AP000349.1 ENST00000598975 4.5549e-03 6.9555e-01 3.4100e-01 1.5390e+00 +SLFN13 ENST00000285013 1.9958e-16 1.0885e+00 7.8200e-01 1.5400e+00 +CMC2 ENST00000219400 1.9910e-01 3.6233e-01 1.2600e-01 1.5400e+00 +TREX2 ENST00000330912 4.5433e-01 0.0000e+00 0.0000e+00 1.5400e+00 +CPNE3 ENST00000521271 1.7777e-25 1.1621e+00 8.8700e-01 1.5400e+00 +FAM3B ENST00000357985 2.4285e-08 9.5702e-01 6.1200e-01 1.5400e+00 +NGB ENST00000298352 4.5474e-03 6.9592e-01 3.4100e-01 1.5400e+00 +CABP4 ENST00000325656 1.6786e-10 1.0048e+00 6.7100e-01 1.5410e+00 +OR2K2 ENST00000302681 1.1135e-03 7.5252e-01 3.9100e-01 1.5410e+00 +ZDHHC11 ENST00000283441 1.1047e-15 1.0808e+00 7.7100e-01 1.5410e+00 +HEBP2 ENST00000607197 6.0829e-05 8.3392e-01 4.7300e-01 1.5410e+00 +RNF32 ENST00000405335 1.1058e-15 1.0807e+00 7.7100e-01 1.5410e+00 +DNAJC22 ENST00000549441 2.9031e-06 8.9270e-01 5.3700e-01 1.5410e+00 +TMEM252 ENST00000377311 1.9897e-01 3.6255e-01 1.2600e-01 1.5410e+00 +KRBOX1 ENST00000418176 1.7643e-02 6.2447e-01 2.8200e-01 1.5410e+00 +SMLR1 ENST00000541421 1.9896e-01 3.6258e-01 1.2600e-01 1.5410e+00 +OR51M1 ENST00000328611 4.5344e-03 6.9657e-01 3.4100e-01 1.5410e+00 +LETM2 ENST00000523983 1.1029e-18 1.1117e+00 8.1400e-01 1.5410e+00 +REG1A ENST00000233735 1.3499e-05 8.6551e-01 5.0600e-01 1.5410e+00 +COX17 ENST00000261070 1.9879e-01 3.6288e-01 1.2600e-01 1.5410e+00 +CENPK ENST00000396679 3.0771e-11 1.0190e+00 6.8900e-01 1.5420e+00 +CERKL ENST00000339098 9.8447e-25 1.1588e+00 8.8100e-01 1.5420e+00 +OR4P4 ENST00000314612 1.7593e-02 6.2521e-01 2.8200e-01 1.5420e+00 +C14orf23 ENST00000399387 1.9871e-01 3.6301e-01 1.2600e-01 1.5420e+00 +FAM25A ENST00000343959 1.9871e-01 3.6301e-01 1.2600e-01 1.5420e+00 +CYP24A1 ENST00000216862 3.1964e-23 1.1490e+00 8.6600e-01 1.5420e+00 +COX7A2 ENST00000370081 4.5177e-03 6.9741e-01 3.4100e-01 1.5420e+00 +RPS6KB2 ENST00000312629 5.9588e-21 1.1318e+00 8.4200e-01 1.5420e+00 +TARM1 ENST00000432826 1.2154e-07 9.3889e-01 5.9000e-01 1.5420e+00 +PRAMEF10 ENST00000235347 1.1128e-03 7.5264e-01 3.9100e-01 1.5420e+00 +ADRB1 ENST00000369295 2.8786e-06 8.9373e-01 5.3700e-01 1.5420e+00 +CCDC134 ENST00000255784 6.0044e-07 9.1751e-01 5.6500e-01 1.5420e+00 +GPR3 ENST00000374024 2.6263e-04 7.9835e-01 4.3500e-01 1.5430e+00 +C1orf227 ENST00000332912 1.9829e-01 3.6375e-01 1.2600e-01 1.5430e+00 +SULT1A1 ENST00000395609 3.0390e-11 1.0200e+00 6.8900e-01 1.5430e+00 +SLC22A10 ENST00000332793 1.8871e-19 1.1201e+00 8.2500e-01 1.5430e+00 +PLEKHG7 ENST00000344636 1.8917e-19 1.1200e+00 8.2400e-01 1.5430e+00 +NRIP2 ENST00000337508 1.6264e-10 1.0072e+00 6.7300e-01 1.5440e+00 +FN3KRP ENST00000269373 4.5570e-09 9.7711e-01 6.3500e-01 1.5440e+00 +ZNF596 ENST00000398612 1.8321e-13 1.0549e+00 7.3500e-01 1.5440e+00 +AC016251.1 ENST00000378936 6.3556e-02 5.2554e-01 2.1200e-01 1.5440e+00 +RAB3D ENST00000222120 1.3302e-05 8.6750e-01 5.0800e-01 1.5440e+00 +TEX33 ENST00000405091 1.2009e-07 9.4009e-01 5.9000e-01 1.5440e+00 +GLTPD2 ENST00000331264 5.9973e-05 8.3608e-01 4.7400e-01 1.5440e+00 +OR6X1 ENST00000327930 1.1048e-03 7.5407e-01 3.9200e-01 1.5440e+00 +EFCAB2 ENST00000366523 5.9198e-07 9.1907e-01 5.6600e-01 1.5440e+00 +TPD52L3 ENST00000344545 1.9798e-01 3.6430e-01 1.2600e-01 1.5450e+00 +NKX2-4 ENST00000351817 4.4783e-03 6.9940e-01 3.4200e-01 1.5450e+00 +NLRX1 ENST00000409109 7.7345e-31 1.1947e+00 9.3200e-01 1.5450e+00 +C2CD4A ENST00000355522 1.7468e-02 6.2707e-01 2.8300e-01 1.5450e+00 +SLCO1B3 ENST00000381545 5.3210e-24 1.1564e+00 8.7500e-01 1.5450e+00 +GSTM5 ENST00000256593 1.1942e-07 9.4066e-01 5.9100e-01 1.5450e+00 +SERPINA11 ENST00000334708 8.5963e-10 9.9350e-01 6.5500e-01 1.5450e+00 +IL17D ENST00000304920 1.9796e-01 3.6434e-01 1.2700e-01 1.5450e+00 +LGALS1 ENST00000215909 4.4880e-03 6.9891e-01 3.4200e-01 1.5450e+00 +IL24 ENST00000391929 5.8826e-07 9.1976e-01 5.6600e-01 1.5450e+00 +OBP2B ENST00000372034 1.3223e-05 8.6831e-01 5.0800e-01 1.5450e+00 +SLC10A6 ENST00000273905 4.5131e-09 9.7794e-01 6.3500e-01 1.5460e+00 +GNAT1 ENST00000232461 9.8532e-13 1.0460e+00 7.2200e-01 1.5460e+00 +S100A7 ENST00000368723 4.5274e-01 0.0000e+00 0.0000e+00 1.5460e+00 +PDRG1 ENST00000202017 2.5916e-04 8.0067e-01 4.3700e-01 1.5470e+00 +CALML4 ENST00000467889 5.9205e-05 8.3806e-01 4.7500e-01 1.5470e+00 +TES ENST00000358204 1.0234e-15 1.0853e+00 7.7400e-01 1.5470e+00 +SAT2 ENST00000269298 2.7832e-06 8.9782e-01 5.4000e-01 1.5480e+00 +C14orf159 ENST00000518868 1.6561e-22 1.1481e+00 8.6200e-01 1.5480e+00 +IFIH1 ENST00000263642 6.9819e-44 1.2467e+00 1.0100e+00 1.5480e+00 +MTHFS ENST00000258874 2.5842e-04 8.0117e-01 4.3700e-01 1.5480e+00 +MOGAT1 ENST00000446656 1.5660e-10 1.0101e+00 6.7500e-01 1.5480e+00 +AC005003.1 ENST00000504184 4.5208e-01 0.0000e+00 0.0000e+00 1.5480e+00 +FIS1 ENST00000223136 1.3020e-05 8.7041e-01 5.0900e-01 1.5480e+00 +BAALC ENST00000309982 4.4356e-03 7.0159e-01 3.4300e-01 1.5490e+00 +TPRX2P ENST00000535362 6.3016e-02 5.2813e-01 2.1300e-01 1.5490e+00 +ABCG2 ENST00000237612 2.0957e-32 1.2054e+00 9.4600e-01 1.5490e+00 +OR52E6 ENST00000329322 1.9683e-01 3.6638e-01 1.2700e-01 1.5490e+00 +ARSF ENST00000381127 3.1126e-14 1.0687e+00 7.5100e-01 1.5490e+00 +ISOC2 ENST00000085068 1.2970e-05 8.7094e-01 5.1000e-01 1.5490e+00 +MEF2BNB ENST00000462790 2.5761e-04 8.0172e-01 4.3700e-01 1.5490e+00 +UCP2 ENST00000310473 1.5497e-10 1.0110e+00 6.7500e-01 1.5490e+00 +THTPA ENST00000288014 2.7667e-06 8.9855e-01 5.4000e-01 1.5490e+00 +IRAK3 ENST00000261233 5.3092e-21 1.1374e+00 8.4600e-01 1.5490e+00 +RASSF4 ENST00000340258 1.7281e-13 1.0587e+00 7.3700e-01 1.5490e+00 +GTPBP6 ENST00000326153 1.1591e-07 9.4365e-01 5.9300e-01 1.5490e+00 +CASP5 ENST00000393141 1.7520e-16 1.0959e+00 7.8700e-01 1.5500e+00 +BET1L ENST00000382762 4.4178e-03 7.0251e-01 3.4400e-01 1.5500e+00 +ATP5L ENST00000300688 4.4259e-03 7.0209e-01 3.4400e-01 1.5500e+00 +C20orf62 ENST00000372910 4.5157e-01 0.0000e+00 0.0000e+00 1.5500e+00 +DNAJC5G ENST00000296097 5.8532e-05 8.3982e-01 4.7600e-01 1.5500e+00 +TMEM141 ENST00000290079 1.0816e-03 7.5831e-01 3.9400e-01 1.5510e+00 +C18orf21 ENST00000592875 5.6865e-07 9.2349e-01 5.6800e-01 1.5510e+00 +ZNF470 ENST00000330619 1.6760e-19 1.1262e+00 8.2900e-01 1.5510e+00 +ROPN1L ENST00000503804 2.7455e-06 8.9949e-01 5.4100e-01 1.5510e+00 +TMEM95 ENST00000330767 2.2408e-08 9.6449e-01 6.1700e-01 1.5510e+00 +SNX20 ENST00000330943 1.2791e-05 8.7283e-01 5.1100e-01 1.5520e+00 +C12orf54 ENST00000314014 1.1347e-07 9.4580e-01 5.9400e-01 1.5520e+00 +NRIP3 ENST00000309166 2.2190e-08 9.6540e-01 6.1700e-01 1.5530e+00 +C14orf180 ENST00000557649 4.3821e-03 7.0438e-01 3.4500e-01 1.5530e+00 +BHLHE23 ENST00000370346 1.9596e-01 3.6794e-01 1.2800e-01 1.5530e+00 +C1orf158 ENST00000288048 2.5309e-04 8.0482e-01 4.3900e-01 1.5530e+00 +CAMP ENST00000296435 4.3897e-03 7.0398e-01 3.4500e-01 1.5530e+00 +PLP2 ENST00000376327 4.3931e-03 7.0380e-01 3.4400e-01 1.5530e+00 +OASL ENST00000257570 2.7573e-11 1.0271e+00 6.9400e-01 1.5530e+00 +HOXC5 ENST00000312492 5.7754e-05 8.4188e-01 4.7700e-01 1.5530e+00 +FITM2 ENST00000396825 2.7203e-06 9.0061e-01 5.4100e-01 1.5530e+00 +LRIT2 ENST00000372113 4.2214e-09 9.8376e-01 6.3900e-01 1.5540e+00 +RAB25 ENST00000361084 1.1227e-07 9.4687e-01 5.9500e-01 1.5540e+00 +TIMM13 ENST00000215570 6.2511e-02 5.3060e-01 2.1400e-01 1.5540e+00 +SPATA3 ENST00000452881 1.0708e-03 7.6033e-01 3.9500e-01 1.5540e+00 +OR1K1 ENST00000277309 1.0697e-03 7.6053e-01 3.9500e-01 1.5540e+00 +GOLGA8G ENST00000525590 1.9562e-01 3.6857e-01 1.2800e-01 1.5540e+00 +PPP1R14B ENST00000309318 4.3794e-03 7.0452e-01 3.4500e-01 1.5540e+00 +NINJ2 ENST00000305108 1.0696e-03 7.6054e-01 3.9500e-01 1.5540e+00 +TEKT4 ENST00000295201 5.2301e-15 1.0820e+00 7.6600e-01 1.5550e+00 +APOL4 ENST00000352371 1.0662e-03 7.6118e-01 3.9600e-01 1.5550e+00 +ZNF267 ENST00000300870 1.7108e-02 6.3255e-01 2.8600e-01 1.5550e+00 +C1orf95 ENST00000366788 4.3627e-03 7.0540e-01 3.4500e-01 1.5550e+00 +MIXL1 ENST00000366810 1.7075e-02 6.3307e-01 2.8600e-01 1.5550e+00 +CIB4 ENST00000288861 1.1150e-07 9.4757e-01 5.9500e-01 1.5550e+00 +CXCR6 ENST00000458629 5.7212e-05 8.4334e-01 4.7800e-01 1.5550e+00 +TMEM52B ENST00000298530 1.0679e-03 7.6086e-01 3.9600e-01 1.5550e+00 +AL589765.1 ENST00000442233 6.2308e-02 5.3160e-01 2.1500e-01 1.5550e+00 +WFDC13 ENST00000305479 1.7094e-02 6.3278e-01 2.8600e-01 1.5550e+00 +KLF16 ENST00000250916 1.9517e-01 3.6940e-01 1.2800e-01 1.5560e+00 +UCN ENST00000296099 4.4958e-01 0.0000e+00 0.0000e+00 1.5560e+00 +HRASLS ENST00000264735 2.5029e-04 8.0678e-01 4.4000e-01 1.5560e+00 +TXNL4B ENST00000268483 4.3549e-03 7.0581e-01 3.4500e-01 1.5560e+00 +RMDN2 ENST00000234195 4.4061e-24 1.1648e+00 8.8200e-01 1.5560e+00 +PLN ENST00000357525 4.4947e-01 0.0000e+00 0.0000e+00 1.5570e+00 +LGSN ENST00000370657 1.5940e-13 1.0640e+00 7.4100e-01 1.5570e+00 +ZNF277 ENST00000361822 8.3182e-22 1.1487e+00 8.5800e-01 1.5570e+00 +BCAS4 ENST00000358791 5.6789e-05 8.4449e-01 4.7900e-01 1.5570e+00 +TNFRSF10A ENST00000221132 5.0697e-15 1.0839e+00 7.6800e-01 1.5570e+00 +GPR132 ENST00000329797 1.6959e-02 6.3488e-01 2.8700e-01 1.5580e+00 +CCDC160 ENST00000517294 1.6983e-02 6.3449e-01 2.8600e-01 1.5580e+00 +OR8G5 ENST00000524943 1.6988e-02 6.3443e-01 2.8600e-01 1.5580e+00 +TMEM25 ENST00000313236 2.6304e-11 1.0306e+00 6.9700e-01 1.5580e+00 +MFNG ENST00000356998 7.6611e-10 1.0030e+00 6.6100e-01 1.5590e+00 +XKR9 ENST00000408926 4.0628e-09 9.8711e-01 6.4100e-01 1.5590e+00 +RP11-934B9.3 ENST00000555591 2.4785e-04 8.0850e-01 4.4100e-01 1.5590e+00 +ARHGAP11B ENST00000428041 2.6229e-06 9.0508e-01 5.4400e-01 1.5590e+00 +C14orf183 ENST00000305273 5.4107e-07 9.2900e-01 5.7200e-01 1.5590e+00 +EMP3 ENST00000270221 2.6151e-06 9.0545e-01 5.4400e-01 1.5600e+00 +C19orf81 ENST00000425202 1.2330e-05 8.7786e-01 5.1400e-01 1.5600e+00 +PPP1R17 ENST00000342032 1.0488e-03 7.6450e-01 3.9700e-01 1.5600e+00 +OR10G8 ENST00000431524 1.6898e-02 6.3585e-01 2.8700e-01 1.5600e+00 +UBB ENST00000302182 1.6904e-02 6.3574e-01 2.8700e-01 1.5600e+00 +TOMM6 ENST00000398884 1.9403e-01 3.7151e-01 1.2900e-01 1.5610e+00 +RPL22L1 ENST00000295830 1.0477e-03 7.6472e-01 3.9800e-01 1.5610e+00 +TRMU ENST00000290846 1.5307e-16 1.1037e+00 7.9300e-01 1.5610e+00 +GNGT2 ENST00000511277 1.9392e-01 3.7173e-01 1.2900e-01 1.5610e+00 +RNF148 ENST00000434824 2.5966e-06 9.0632e-01 5.4500e-01 1.5610e+00 +GJA9 ENST00000357771 4.6528e-12 1.0452e+00 7.1400e-01 1.5610e+00 +SIGLEC11 ENST00000447370 7.8092e-22 1.1518e+00 8.6100e-01 1.5610e+00 +KRT82 ENST00000257974 4.6454e-18 1.1205e+00 8.1500e-01 1.5620e+00 +GPX6 ENST00000361902 2.5820e-06 9.0701e-01 5.4500e-01 1.5620e+00 +ADH5 ENST00000296412 2.5356e-11 1.0334e+00 6.9800e-01 1.5620e+00 +FAM194A ENST00000295910 1.8230e-29 1.2008e+00 9.3200e-01 1.5620e+00 +SLFN11 ENST00000394566 8.2249e-19 1.1272e+00 8.2500e-01 1.5620e+00 +OR11H6 ENST00000315519 1.0427e-03 7.6568e-01 3.9800e-01 1.5620e+00 +AGAP6 ENST00000412531 2.5867e-06 9.0679e-01 5.4500e-01 1.5620e+00 +TPGS1 ENST00000359315 6.1557e-02 5.3536e-01 2.1600e-01 1.5620e+00 +MSRB2 ENST00000376510 5.5352e-05 8.4846e-01 4.8100e-01 1.5630e+00 +TSGA13 ENST00000456951 7.3935e-10 1.0059e+00 6.6300e-01 1.5630e+00 +TAS1R3 ENST00000339381 6.7868e-25 1.1752e+00 8.9300e-01 1.5630e+00 +MRPS21 ENST00000369084 6.1313e-02 5.3660e-01 2.1600e-01 1.5640e+00 +NME4 ENST00000219479 1.0351e-03 7.6718e-01 3.9900e-01 1.5650e+00 +MZT2B ENST00000281871 6.1273e-02 5.3680e-01 2.1700e-01 1.5650e+00 +TUBA3D ENST00000321253 7.2364e-10 1.0077e+00 6.6400e-01 1.5650e+00 +TRIM58 ENST00000366481 1.3450e-10 1.0220e+00 6.8300e-01 1.5650e+00 +LRIT1 ENST00000372105 4.5907e-15 1.0901e+00 7.7200e-01 1.5660e+00 +TCTEX1D1 ENST00000282670 5.4692e-05 8.5033e-01 4.8200e-01 1.5660e+00 +AC073343.1 ENST00000544825 3.8385e-09 9.9212e-01 6.4500e-01 1.5660e+00 +TMCO2 ENST00000372766 5.4723e-05 8.5024e-01 4.8200e-01 1.5660e+00 +NRSN2 ENST00000382291 4.2391e-03 7.1207e-01 3.4800e-01 1.5660e+00 +KLK14 ENST00000391802 1.9965e-08 9.7535e-01 6.2400e-01 1.5670e+00 +SWSAP1 ENST00000312423 4.2206e-03 7.1309e-01 3.4900e-01 1.5670e+00 +ZSCAN32 ENST00000304926 2.4299e-11 1.0366e+00 7.0100e-01 1.5670e+00 +ST8SIA6 ENST00000377602 7.1568e-10 1.0086e+00 6.6500e-01 1.5670e+00 +ZNF799 ENST00000430385 1.6646e-02 6.3986e-01 2.8900e-01 1.5670e+00 +FAM127B ENST00000370775 4.4642e-01 0.0000e+00 0.0000e+00 1.5670e+00 +STOML1 ENST00000316900 2.4189e-11 1.0369e+00 7.0100e-01 1.5670e+00 +TMEM239 ENST00000380585 1.0286e-03 7.6846e-01 3.9900e-01 1.5670e+00 +VNN2 ENST00000326499 4.4480e-15 1.0921e+00 7.7300e-01 1.5680e+00 +IRF7 ENST00000397566 4.4508e-15 1.0920e+00 7.7300e-01 1.5680e+00 +CD300LD ENST00000375352 1.1813e-05 8.8376e-01 5.1700e-01 1.5680e+00 +GYG2 ENST00000381163 7.0587e-10 1.0098e+00 6.6600e-01 1.5680e+00 +KCNJ14 ENST00000391884 2.4991e-06 9.1104e-01 5.4800e-01 1.5680e+00 +HLA-DPA1 ENST00000419277 2.5000e-06 9.1100e-01 5.4800e-01 1.5680e+00 +ADAM18 ENST00000265707 6.8847e-35 1.2306e+00 9.7300e-01 1.5690e+00 +EPGN ENST00000413830 2.3928e-04 8.1474e-01 4.4400e-01 1.5690e+00 +AQP2 ENST00000199280 2.4855e-06 9.1172e-01 5.4800e-01 1.5690e+00 +GRXCR2 ENST00000377976 1.0145e-07 9.5721e-01 6.0100e-01 1.5690e+00 +PBLD ENST00000358769 2.3448e-11 1.0393e+00 7.0200e-01 1.5700e+00 +NPPC ENST00000409852 6.0647e-02 5.4003e-01 2.1800e-01 1.5700e+00 +SMIM13 ENST00000416247 1.9183e-01 3.7568e-01 1.3000e-01 1.5700e+00 +PLA2G5 ENST00000375108 5.3834e-05 8.5281e-01 4.8300e-01 1.5700e+00 +POMK ENST00000331373 1.9487e-08 9.7765e-01 6.2500e-01 1.5700e+00 +ADAT2 ENST00000237283 1.0070e-07 9.5797e-01 6.0200e-01 1.5700e+00 +ACTL7B ENST00000374667 2.4547e-06 9.1327e-01 5.4900e-01 1.5710e+00 +NKX6-3 ENST00000524115 1.6469e-02 6.4275e-01 2.9000e-01 1.5710e+00 +CLEC4D ENST00000299665 2.4548e-06 9.1326e-01 5.4900e-01 1.5710e+00 +GOLGA8Q ENST00000562783 1.0139e-03 7.7139e-01 4.0100e-01 1.5710e+00 +BBIP1 ENST00000454061 4.1740e-03 7.1570e-01 3.5000e-01 1.5710e+00 +CD300C ENST00000330793 1.1640e-05 8.8582e-01 5.1800e-01 1.5710e+00 +EREG ENST00000244869 1.1659e-05 8.8559e-01 5.1800e-01 1.5710e+00 +CYB5R2 ENST00000533558 6.8195e-10 1.0127e+00 6.6700e-01 1.5720e+00 +C17orf58 ENST00000449250 1.9122e-01 3.7687e-01 1.3100e-01 1.5720e+00 +PROKR2 ENST00000546004 2.4388e-06 9.1407e-01 5.4900e-01 1.5720e+00 +FTSJ2 ENST00000242257 2.3612e-04 8.1711e-01 4.4500e-01 1.5720e+00 +CYP11B2 ENST00000323110 7.1321e-19 1.1349e+00 8.3100e-01 1.5720e+00 +HENMT1 ENST00000370032 6.8224e-10 1.0126e+00 6.6700e-01 1.5720e+00 +PCDHA4 ENST00000530339 1.9754e-23 1.1712e+00 8.8300e-01 1.5720e+00 +N6AMT2 ENST00000382758 2.4358e-06 9.1423e-01 5.4900e-01 1.5730e+00 +OR5AP2 ENST00000302981 4.1572e-03 7.1664e-01 3.5100e-01 1.5730e+00 +TEX9 ENST00000352903 6.4247e-22 1.1613e+00 8.6800e-01 1.5730e+00 +RAMP3 ENST00000242249 1.6373e-02 6.4434e-01 2.9100e-01 1.5740e+00 +C10orf35 ENST00000373279 1.6385e-02 6.4415e-01 2.9100e-01 1.5740e+00 +HIGD2A ENST00000274787 1.9087e-01 3.7755e-01 1.3100e-01 1.5740e+00 +OR2A25 ENST00000408898 1.0007e-03 7.7407e-01 4.0200e-01 1.5750e+00 +OR52A1 ENST00000380367 4.1328e-03 7.1803e-01 3.5100e-01 1.5750e+00 +FDFT1 ENST00000220584 4.0998e-15 1.0972e+00 7.7700e-01 1.5750e+00 +C5orf60 ENST00000448248 4.8900e-07 9.4033e-01 5.7900e-01 1.5750e+00 +FAM180A ENST00000338588 1.0025e-03 7.7370e-01 4.0200e-01 1.5750e+00 +UBL5 ENST00000358666 1.6321e-02 6.4522e-01 2.9100e-01 1.5750e+00 +CD164L2 ENST00000374027 1.1451e-05 8.8809e-01 5.1900e-01 1.5750e+00 +TAF8 ENST00000372977 7.3155e-13 1.0665e+00 7.3600e-01 1.5750e+00 +B9D2 ENST00000243578 5.2557e-05 8.5657e-01 4.8500e-01 1.5750e+00 +RASSF7 ENST00000397583 2.2520e-11 1.0424e+00 7.0400e-01 1.5750e+00 +HSPB7 ENST00000311890 1.6292e-02 6.4569e-01 2.9100e-01 1.5760e+00 +RP1-139D8.6 ENST00000372963 6.0033e-02 5.4326e-01 2.1900e-01 1.5760e+00 +TMEM215 ENST00000342743 4.1235e-03 7.1856e-01 3.5100e-01 1.5760e+00 +CASQ1 ENST00000368078 3.8570e-18 1.1309e+00 8.2300e-01 1.5760e+00 +ASIP ENST00000568305 1.6298e-02 6.4560e-01 2.9100e-01 1.5760e+00 +CEACAM19 ENST00000403660 6.6095e-10 1.0153e+00 6.6900e-01 1.5760e+00 +AKIP1 ENST00000309377 1.1363e-05 8.8916e-01 5.2000e-01 1.5760e+00 +C7orf57 ENST00000348904 4.0355e-12 1.0555e+00 7.2100e-01 1.5760e+00 +OR2AG2 ENST00000338569 1.6296e-02 6.4563e-01 2.9100e-01 1.5760e+00 +PPP1R14D ENST00000427255 2.3903e-06 9.1658e-01 5.5100e-01 1.5760e+00 +ZNF544 ENST00000269829 9.9546e-04 7.7515e-01 4.0300e-01 1.5770e+00 +IQCE ENST00000402050 1.3752e-39 1.2545e+00 1.0050e+00 1.5770e+00 +C1orf110 ENST00000367910 4.1139e-03 7.1911e-01 3.5200e-01 1.5770e+00 +MLN ENST00000430124 4.1058e-03 7.1958e-01 3.5200e-01 1.5770e+00 +THUMPD1 ENST00000381337 3.9721e-12 1.0567e+00 7.2200e-01 1.5770e+00 +CTC-260F20.3 ENST00000555938 9.5774e-08 9.6314e-01 6.0500e-01 1.5770e+00 +C1orf54 ENST00000369102 2.3180e-04 8.2043e-01 4.4700e-01 1.5770e+00 +SYNGR2 ENST00000225777 5.1893e-05 8.5858e-01 4.8600e-01 1.5780e+00 +FAM71E1 ENST00000595790 2.3110e-04 8.2097e-01 4.4800e-01 1.5780e+00 +ZNF492 ENST00000456783 1.8998e-01 3.7929e-01 1.3100e-01 1.5780e+00 +TMEM186 ENST00000333050 5.1994e-05 8.5827e-01 4.8600e-01 1.5780e+00 +ZNHIT1 ENST00000305105 2.3592e-06 9.1821e-01 5.5200e-01 1.5780e+00 +CES5A ENST00000521992 7.9418e-29 1.2085e+00 9.3500e-01 1.5780e+00 +C3orf80 ENST00000326474 1.8963e-01 3.7999e-01 1.3200e-01 1.5790e+00 +CLDN8 ENST00000399899 1.6193e-02 6.4737e-01 2.9200e-01 1.5790e+00 +S100A7L2 ENST00000368725 1.8950e-01 3.8023e-01 1.3200e-01 1.5790e+00 +MSMB ENST00000358559 1.6199e-02 6.4727e-01 2.9200e-01 1.5790e+00 +CTD-3214H19.16 ENST00000597959 9.8749e-04 7.7681e-01 4.0400e-01 1.5790e+00 +AUNIP ENST00000374298 3.4534e-09 1.0016e+00 6.5100e-01 1.5790e+00 +CSRP2 ENST00000311083 4.7690e-07 9.4316e-01 5.8000e-01 1.5790e+00 +SLC22A25 ENST00000306494 1.2149e-16 1.1173e+00 8.0300e-01 1.5790e+00 +RPL26L1 ENST00000521476 9.8764e-04 7.7678e-01 4.0400e-01 1.5790e+00 +C12orf56 ENST00000333722 6.8904e-16 1.1091e+00 7.9100e-01 1.5790e+00 +AC002310.13 ENST00000568114 1.8963e-01 3.7997e-01 1.3200e-01 1.5790e+00 +OR3A2 ENST00000408891 2.2954e-04 8.2218e-01 4.4800e-01 1.5800e+00 +LYZL6 ENST00000585556 9.8373e-04 7.7760e-01 4.0400e-01 1.5800e+00 +IL15RA ENST00000379977 2.3320e-06 9.1966e-01 5.5300e-01 1.5800e+00 +AC021218.2 ENST00000377722 5.9572e-02 5.4572e-01 2.2000e-01 1.5800e+00 +AL354898.1 ENST00000277491 2.3398e-06 9.1925e-01 5.5200e-01 1.5800e+00 +NXPE4 ENST00000375478 6.8642e-16 1.1094e+00 7.9200e-01 1.5800e+00 +SRRD ENST00000215917 1.8029e-08 9.8510e-01 6.3000e-01 1.5810e+00 +DNMT3A ENST00000264709 7.3538e-39 1.2550e+00 1.0040e+00 1.5810e+00 +GABARAPL2 ENST00000037243 2.2815e-04 8.2328e-01 4.4900e-01 1.5810e+00 +AL441883.1 ENST00000600057 5.9485e-02 5.4619e-01 2.2000e-01 1.5810e+00 +DPPA5 ENST00000370370 4.0632e-03 7.2205e-01 3.5300e-01 1.5810e+00 +COQ4 ENST00000300452 3.3961e-09 1.0031e+00 6.5200e-01 1.5810e+00 +OR2L13 ENST00000366478 9.8315e-04 7.7772e-01 4.0400e-01 1.5810e+00 +NDUFAF7 ENST00000002125 1.0818e-19 1.1492e+00 8.4600e-01 1.5820e+00 +ABHD12B ENST00000337334 3.7965e-15 1.1021e+00 7.8000e-01 1.5820e+00 +AGR2 ENST00000419304 9.2381e-08 9.6689e-01 6.0700e-01 1.5820e+00 +C2orf70 ENST00000329615 5.0939e-05 8.6151e-01 4.8800e-01 1.5820e+00 +CRIPT ENST00000238892 9.7752e-04 7.7890e-01 4.0500e-01 1.5820e+00 +CHMP4A ENST00000347519 3.3901e-09 1.0032e+00 6.5200e-01 1.5820e+00 +COX6A2 ENST00000287490 1.8881e-01 3.8162e-01 1.3200e-01 1.5820e+00 +CYP2A7 ENST00000301146 3.7792e-15 1.1023e+00 7.8100e-01 1.5820e+00 +DNAJC5B ENST00000276570 2.2936e-06 9.2174e-01 5.5400e-01 1.5830e+00 +SMPD2 ENST00000258052 3.5507e-18 1.1355e+00 8.2600e-01 1.5830e+00 +PRCD ENST00000586148 1.6018e-02 6.5035e-01 2.9300e-01 1.5830e+00 +C1orf105 ENST00000367727 1.1007e-05 8.9362e-01 5.2300e-01 1.5830e+00 +KRT74 ENST00000305620 2.1183e-14 1.0935e+00 7.6800e-01 1.5830e+00 +TSLP ENST00000344895 4.0357e-03 7.2368e-01 3.5400e-01 1.5840e+00 +DHRS4L2 ENST00000335125 4.6376e-07 9.4633e-01 5.8200e-01 1.5840e+00 +TOMM20L ENST00000360945 5.0571e-05 8.6265e-01 4.8900e-01 1.5840e+00 +CLDN6 ENST00000396925 4.0357e-03 7.2368e-01 3.5400e-01 1.5840e+00 +PTGER1 ENST00000292513 9.7345e-04 7.7977e-01 4.0500e-01 1.5840e+00 +TATDN1 ENST00000276692 6.4923e-16 1.1128e+00 7.9400e-01 1.5840e+00 +YIF1A ENST00000376901 6.1818e-10 1.0210e+00 6.7300e-01 1.5840e+00 +FMO3 ENST00000367755 6.5145e-16 1.1126e+00 7.9400e-01 1.5840e+00 +GNG5 ENST00000370641 1.8814e-01 3.8295e-01 1.3200e-01 1.5850e+00 +TMIGD2 ENST00000301272 1.0895e-05 8.9505e-01 5.2400e-01 1.5850e+00 +KLF14 ENST00000310992 1.5980e-02 6.5101e-01 2.9400e-01 1.5850e+00 +PGBD2 ENST00000329291 6.4382e-16 1.1133e+00 7.9400e-01 1.5850e+00 +GPR84 ENST00000551809 3.2998e-09 1.0057e+00 6.5300e-01 1.5850e+00 +SULT1A2 ENST00000395630 3.6786e-12 1.0623e+00 7.2600e-01 1.5850e+00 +C3AR1 ENST00000307637 3.3053e-09 1.0055e+00 6.5300e-01 1.5850e+00 +WFDC3 ENST00000243938 9.0781e-08 9.6871e-01 6.0800e-01 1.5850e+00 +OR2B11 ENST00000318749 2.2477e-04 8.2598e-01 4.5000e-01 1.5850e+00 +SCNN1D ENST00000379116 1.6507e-33 1.2373e+00 9.7300e-01 1.5860e+00 +LGALS12 ENST00000340246 6.5191e-13 1.0746e+00 7.4200e-01 1.5860e+00 +AKR7L ENST00000420396 2.2370e-04 8.2684e-01 4.5100e-01 1.5860e+00 +OR5B17 ENST00000357377 4.4075e-01 0.0000e+00 0.0000e+00 1.5860e+00 +TFF3 ENST00000518498 1.5910e-02 6.5221e-01 2.9400e-01 1.5860e+00 +HMX2 ENST00000339992 4.9891e-05 8.6481e-01 4.9000e-01 1.5870e+00 +ASB16 ENST00000293414 1.0959e-16 1.1235e+00 8.0700e-01 1.5870e+00 +PIFO ENST00000369738 8.9379e-08 9.7034e-01 6.0900e-01 1.5870e+00 +SIAH3 ENST00000400405 9.6340e-04 7.8192e-01 4.0600e-01 1.5870e+00 +C21orf67 ENST00000330551 5.8694e-02 5.5052e-01 2.2200e-01 1.5880e+00 +VIT ENST00000379242 5.4350e-32 1.2323e+00 9.6400e-01 1.5880e+00 +AKR1C1 ENST00000380872 3.5240e-15 1.1068e+00 7.8400e-01 1.5880e+00 +FLYWCH2 ENST00000396958 1.8732e-01 3.8462e-01 1.3300e-01 1.5880e+00 +OXGR1 ENST00000298440 4.9619e-05 8.6567e-01 4.9000e-01 1.5880e+00 +OR4D9 ENST00000329328 9.6084e-04 7.8248e-01 4.0700e-01 1.5880e+00 +TTC36 ENST00000302783 2.2268e-04 8.2767e-01 4.5100e-01 1.5880e+00 +UTS2B ENST00000340524 2.2271e-04 8.2764e-01 4.5100e-01 1.5880e+00 +BBC3 ENST00000449228 3.9762e-03 7.2724e-01 3.5600e-01 1.5890e+00 +RAB26 ENST00000210187 1.6979e-08 9.9091e-01 6.3300e-01 1.5890e+00 +WDR38 ENST00000373574 1.9750e-11 1.0524e+00 7.1100e-01 1.5890e+00 +SSTR5 ENST00000293897 9.5544e-04 7.8365e-01 4.0700e-01 1.5890e+00 +HIST2H2AC ENST00000331380 1.8727e-01 3.8471e-01 1.3300e-01 1.5890e+00 +INSL3 ENST00000379695 1.5764e-02 6.5478e-01 2.9500e-01 1.5900e+00 +APOBEC1 ENST00000229304 1.6791e-08 9.9199e-01 6.3400e-01 1.5900e+00 +OR2T35 ENST00000317450 1.8682e-01 3.8565e-01 1.3300e-01 1.5900e+00 +GBGT1 ENST00000372040 1.0776e-10 1.0398e+00 6.9400e-01 1.5900e+00 +RBP5 ENST00000266560 4.9181e-05 8.6709e-01 4.9100e-01 1.5900e+00 +GIPC2 ENST00000370759 3.1514e-09 1.0098e+00 6.5600e-01 1.5910e+00 +MEA1 ENST00000244711 1.0536e-05 8.9978e-01 5.2600e-01 1.5910e+00 +OR52B6 ENST00000345043 3.9544e-03 7.2856e-01 3.5600e-01 1.5910e+00 +UGT2B11 ENST00000446444 5.9800e-16 1.1179e+00 7.9800e-01 1.5910e+00 +FIBCD1 ENST00000372338 1.9395e-14 1.0994e+00 7.7200e-01 1.5910e+00 +PCDHB11 ENST00000354757 5.8173e-10 1.0262e+00 6.7600e-01 1.5910e+00 +RPP21 ENST00000433076 4.8992e-05 8.6770e-01 4.9100e-01 1.5910e+00 +OR6Y1 ENST00000302617 9.5201e-04 7.8440e-01 4.0800e-01 1.5910e+00 +MRPS16 ENST00000372945 5.8297e-02 5.5273e-01 2.2300e-01 1.5920e+00 +OR10W1 ENST00000395079 1.5720e-02 6.5556e-01 2.9600e-01 1.5920e+00 +MRRF ENST00000344641 4.4057e-07 9.5220e-01 5.8600e-01 1.5920e+00 +SLC18A1 ENST00000440926 2.8012e-21 1.1697e+00 8.7000e-01 1.5920e+00 +CD14 ENST00000302014 4.8813e-05 8.6829e-01 4.9200e-01 1.5920e+00 +SLC36A4 ENST00000326402 1.8141e-17 1.1347e+00 8.2100e-01 1.5920e+00 +TMEM187 ENST00000369982 1.5717e-02 6.5561e-01 2.9600e-01 1.5920e+00 +GLIPR2 ENST00000377960 4.8573e-05 8.6908e-01 4.9200e-01 1.5930e+00 +GLOD4 ENST00000301329 6.0698e-13 1.0797e+00 7.4500e-01 1.5930e+00 +C3orf70 ENST00000335012 4.8695e-05 8.6867e-01 4.9200e-01 1.5930e+00 +C4orf45 ENST00000434826 4.3689e-07 9.5316e-01 5.8600e-01 1.5930e+00 +HIST1H1E ENST00000304218 1.8608e-01 3.8718e-01 1.3400e-01 1.5930e+00 +SEMG2 ENST00000372769 5.8203e-02 5.5326e-01 2.2300e-01 1.5930e+00 +RSPO4 ENST00000217260 8.5962e-08 9.7443e-01 6.1200e-01 1.5930e+00 +RDH16 ENST00000398138 4.3901e-07 9.5261e-01 5.8600e-01 1.5930e+00 +ZSCAN1 ENST00000282326 4.3802e-07 9.5286e-01 5.8600e-01 1.5930e+00 +RHBG ENST00000368249 1.0751e-13 1.0907e+00 7.6000e-01 1.5930e+00 +RP5-850E9.3 ENST00000488788 4.3802e-01 0.0000e+00 0.0000e+00 1.5940e+00 +KLK10 ENST00000309958 4.3662e-07 9.5323e-01 5.8600e-01 1.5940e+00 +FAM198A ENST00000430121 5.7508e-16 1.1204e+00 7.9900e-01 1.5940e+00 +OR4K14 ENST00000305045 9.4256e-04 7.8649e-01 4.0900e-01 1.5940e+00 +SPP1 ENST00000395080 2.1460e-06 9.3015e-01 5.5900e-01 1.5950e+00 +C19orf18 ENST00000314391 4.3311e-07 9.5416e-01 5.8700e-01 1.5950e+00 +NTHL1 ENST00000219066 5.6607e-10 1.0285e+00 6.7800e-01 1.5950e+00 +OR4D10 ENST00000530162 3.9123e-03 7.3114e-01 3.5700e-01 1.5950e+00 +PRDX6 ENST00000340385 4.8237e-05 8.7019e-01 4.9300e-01 1.5950e+00 +CLPSL2 ENST00000403376 1.8580e-01 3.8776e-01 1.3400e-01 1.5950e+00 +TMEM242 ENST00000400788 4.8272e-05 8.7007e-01 4.9300e-01 1.5950e+00 +SPINK9 ENST00000377906 1.5591e-02 6.5787e-01 2.9700e-01 1.5950e+00 +ENTPD3 ENST00000301825 2.6387e-21 1.1728e+00 8.7200e-01 1.5960e+00 +APOA5 ENST00000542499 5.5765e-10 1.0298e+00 6.7900e-01 1.5960e+00 +CST3 ENST00000398411 3.9011e-03 7.3183e-01 3.5800e-01 1.5960e+00 +CALCA ENST00000331587 1.5562e-02 6.5838e-01 2.9700e-01 1.5960e+00 +KRTAP1-5 ENST00000361883 3.9059e-03 7.3153e-01 3.5800e-01 1.5960e+00 +ZNF660 ENST00000322734 4.3113e-07 9.5469e-01 5.8700e-01 1.5960e+00 +RAB20 ENST00000267328 3.8974e-03 7.3206e-01 3.5800e-01 1.5960e+00 +SLC35D2 ENST00000253270 5.8967e-13 1.0818e+00 7.4600e-01 1.5960e+00 +BIN3 ENST00000276416 5.8224e-13 1.0827e+00 7.4700e-01 1.5970e+00 +ZSCAN5C ENST00000534327 2.1218e-06 9.3159e-01 5.6000e-01 1.5970e+00 +PPBP ENST00000296028 5.7739e-02 5.5589e-01 2.2400e-01 1.5970e+00 +PLIN4 ENST00000301286 5.5780e-16 1.1223e+00 8.0100e-01 1.5970e+00 +TEX36 ENST00000368821 2.1489e-04 8.3416e-01 4.5500e-01 1.5970e+00 +MAFF ENST00000338483 1.5514e-02 6.5926e-01 2.9700e-01 1.5970e+00 +ZBP1 ENST00000371173 1.8259e-14 1.1034e+00 7.7500e-01 1.5970e+00 +MAP3K7CL ENST00000399947 8.3352e-08 9.7768e-01 6.1400e-01 1.5970e+00 +GTF2H2 ENST00000330280 1.5519e-02 6.5917e-01 2.9700e-01 1.5970e+00 +MUC12 ENST00000536621 1.2792e-68 1.3409e+00 1.1300e+00 1.5980e+00 +IFT43 ENST00000238628 1.8153e-11 1.0590e+00 7.1600e-01 1.5980e+00 +DARC ENST00000368121 2.1424e-04 8.3471e-01 4.5500e-01 1.5980e+00 +CKMT1A ENST00000413453 4.2467e-07 9.5643e-01 5.8800e-01 1.5980e+00 +SS18L2 ENST00000447630 1.5480e-02 6.5987e-01 2.9800e-01 1.5980e+00 +KLHDC7A ENST00000400664 4.9895e-19 1.1547e+00 8.4500e-01 1.5980e+00 +TM4SF18 ENST00000296059 2.1148e-06 9.3201e-01 5.6000e-01 1.5980e+00 +RDM1 ENST00000293273 1.5827e-08 9.9778e-01 6.3800e-01 1.5980e+00 +AP3S1 ENST00000316788 1.0159e-05 9.0493e-01 5.2900e-01 1.5990e+00 +ANXA8L2 ENST00000374277 9.2573e-04 7.9027e-01 4.1100e-01 1.5990e+00 +HPR ENST00000540303 5.4618e-10 1.0316e+00 6.8000e-01 1.5990e+00 +OR1D2 ENST00000331459 9.2513e-04 7.9041e-01 4.1100e-01 1.5990e+00 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8.3711e-01 4.5600e-01 1.6010e+00 +RGS16 ENST00000367558 1.0062e-05 9.0631e-01 5.3000e-01 1.6010e+00 +OR6K6 ENST00000368144 9.1859e-04 7.9191e-01 4.1100e-01 1.6010e+00 +HLA-DPB1 ENST00000418931 5.3254e-10 1.0338e+00 6.8100e-01 1.6020e+00 +POP5 ENST00000357500 4.1420e-07 9.5931e-01 5.9000e-01 1.6020e+00 +KCNMB1 ENST00000274629 2.0696e-06 9.3476e-01 5.6200e-01 1.6020e+00 +GLYCTK ENST00000436784 9.6521e-11 1.0489e+00 7.0000e-01 1.6020e+00 +BET1 ENST00000222547 3.8328e-03 7.3613e-01 3.6000e-01 1.6020e+00 +PAGE2 ENST00000374968 5.7156e-02 5.5926e-01 2.2500e-01 1.6020e+00 +MC4R ENST00000299766 9.1697e-04 7.9228e-01 4.1200e-01 1.6020e+00 +PDZK1IP1 ENST00000294338 9.1769e-04 7.9211e-01 4.1100e-01 1.6020e+00 +PILRA ENST00000198536 1.7260e-11 1.0630e+00 7.1800e-01 1.6030e+00 +RPL41 ENST00000546591 1.8377e-01 3.9204e-01 1.3500e-01 1.6030e+00 +CFHR3 ENST00000367425 1.7200e-11 1.0633e+00 7.1800e-01 1.6030e+00 +RP11-195F19.5 ENST00000421828 1.5288e-02 6.6340e-01 2.9900e-01 1.6030e+00 +FAM96B ENST00000422424 3.8240e-03 7.3669e-01 3.6000e-01 1.6030e+00 +SPATA31D1 ENST00000344803 3.8158e-03 7.3722e-01 3.6000e-01 1.6040e+00 +GZMA ENST00000274306 2.0457e-06 9.3625e-01 5.6300e-01 1.6040e+00 +ADH1A ENST00000209668 1.7118e-11 1.0636e+00 7.1900e-01 1.6040e+00 +FAM122C ENST00000370784 2.0902e-04 8.3925e-01 4.5700e-01 1.6040e+00 +RP11-770J1.4 ENST00000532619 1.5279e-02 6.6357e-01 2.9900e-01 1.6040e+00 +CLEC19A ENST00000465414 3.7987e-03 7.3832e-01 3.6100e-01 1.6050e+00 +EMC10 ENST00000334976 9.4077e-11 1.0510e+00 7.0200e-01 1.6050e+00 +TMEM88B ENST00000378821 4.3487e-01 0.0000e+00 0.0000e+00 1.6050e+00 +FAM177B ENST00000445590 4.6111e-05 8.7744e-01 4.9700e-01 1.6050e+00 +DTWD2 ENST00000510708 2.8104e-09 1.0204e+00 6.6300e-01 1.6050e+00 +FAM83E ENST00000263266 9.4341e-11 1.0507e+00 7.0200e-01 1.6050e+00 +MS4A13 ENST00000378186 4.6205e-05 8.7711e-01 4.9700e-01 1.6050e+00 +DPP7 ENST00000371579 3.9946e-22 1.1853e+00 8.8600e-01 1.6050e+00 +SPIN2B ENST00000333933 5.6895e-02 5.6078e-01 2.2600e-01 1.6050e+00 +ELMOD3 ENST00000315658 5.0378e-16 1.1287e+00 8.0500e-01 1.6060e+00 +AL627309.1 ENST00000423372 9.0576e-04 7.9488e-01 4.1300e-01 1.6060e+00 +ZNF676 ENST00000397121 1.8308e-01 3.9352e-01 1.3600e-01 1.6060e+00 +CCNI2 ENST00000378731 7.8377e-08 9.8423e-01 6.1800e-01 1.6060e+00 +GAGE2D ENST00000404720 4.3441e-01 0.0000e+00 0.0000e+00 1.6060e+00 +RITA1 ENST00000548278 3.7970e-03 7.3842e-01 3.6100e-01 1.6060e+00 +NEU4 ENST00000325935 4.0412e-07 9.6218e-01 5.9200e-01 1.6060e+00 +OR51L1 ENST00000321543 9.0531e-04 7.9499e-01 4.1300e-01 1.6060e+00 +CLRN2 ENST00000511148 2.0187e-06 9.3795e-01 5.6400e-01 1.6060e+00 +AC079612.1 ENST00000358775 2.0651e-04 8.4147e-01 4.5800e-01 1.6070e+00 +RPL3L ENST00000268661 4.9470e-16 1.1299e+00 8.0600e-01 1.6070e+00 +SMDT1 ENST00000331479 1.8284e-01 3.9406e-01 1.3600e-01 1.6070e+00 +C1orf56 ENST00000368926 9.6918e-06 9.1167e-01 5.3300e-01 1.6080e+00 +PGK2 ENST00000304801 9.6757e-06 9.1190e-01 5.3300e-01 1.6080e+00 +PCDHA9 ENST00000532602 1.8891e-24 1.2044e+00 9.1200e-01 1.6080e+00 +TSPO2 ENST00000373161 8.9910e-04 7.9645e-01 4.1400e-01 1.6080e+00 +CLEC18C ENST00000569347 8.9881e-04 7.9652e-01 4.1400e-01 1.6080e+00 +TBC1D7 ENST00000606214 2.9441e-12 1.0791e+00 7.3700e-01 1.6080e+00 +TRIAP1 ENST00000546954 5.6508e-02 5.6307e-01 2.2700e-01 1.6080e+00 +GP6 ENST00000310373 1.6361e-11 1.0672e+00 7.2100e-01 1.6090e+00 +FRG2B ENST00000425520 1.8217e-01 3.9552e-01 1.3600e-01 1.6090e+00 +TEN1 ENST00000397640 1.5092e-02 6.6709e-01 3.0100e-01 1.6090e+00 +SLPI ENST00000338380 8.9665e-04 7.9703e-01 4.1400e-01 1.6090e+00 +C1orf186 ENST00000331555 4.5250e-05 8.8049e-01 4.9900e-01 1.6090e+00 +LILRA1 ENST00000251372 7.3933e-20 1.1701e+00 8.6100e-01 1.6090e+00 +C3orf79 ENST00000446603 5.6297e-02 5.6434e-01 2.2700e-01 1.6100e+00 +C2orf91 ENST00000378711 8.9143e-04 7.9828e-01 4.1500e-01 1.6100e+00 +SLC22A9 ENST00000279178 4.2676e-19 1.1636e+00 8.5200e-01 1.6100e+00 +ACTRT1 ENST00000371124 3.7403e-03 7.4213e-01 3.6300e-01 1.6110e+00 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7.7000e-01 1.6130e+00 +SAA1 ENST00000405158 1.4930e-02 6.7019e-01 3.0200e-01 1.6130e+00 +LAMP5 ENST00000246070 2.6473e-09 1.0259e+00 6.6600e-01 1.6130e+00 +GSTT2 ENST00000215780 1.4962e-02 6.6958e-01 3.0200e-01 1.6130e+00 +STAR ENST00000276449 8.7679e-11 1.0569e+00 7.0600e-01 1.6130e+00 +TMEM154 ENST00000304385 3.8695e-07 9.6725e-01 5.9500e-01 1.6130e+00 +FOXE3 ENST00000335071 1.8135e-01 3.9733e-01 1.3700e-01 1.6130e+00 +COPZ2 ENST00000006101 7.4565e-08 9.8958e-01 6.2100e-01 1.6140e+00 +TCF23 ENST00000296096 4.4240e-05 8.8417e-01 5.0100e-01 1.6140e+00 +FANCL ENST00000402135 5.9404e-23 1.1981e+00 8.9900e-01 1.6140e+00 +KRT16 ENST00000301653 1.5006e-14 1.1167e+00 7.8400e-01 1.6140e+00 +GSTO2 ENST00000338595 2.6125e-09 1.0272e+00 6.6700e-01 1.6140e+00 +PPP1R3G ENST00000405617 4.4228e-05 8.8421e-01 5.0100e-01 1.6140e+00 +NBPF6 ENST00000444143 1.4909e-02 6.7059e-01 3.0200e-01 1.6140e+00 +MAGEB3 ENST00000361644 4.3183e-01 0.0000e+00 0.0000e+00 1.6140e+00 +PRSS45 ENST00000442359 2.0122e-04 8.4629e-01 4.6100e-01 1.6140e+00 +AP000322.53 ENST00000450895 1.8107e-01 3.9794e-01 1.3700e-01 1.6140e+00 +KDM4D ENST00000335080 4.3196e-01 0.0000e+00 0.0000e+00 1.6140e+00 +TMEM52 ENST00000310991 1.4909e-02 6.7060e-01 3.0200e-01 1.6140e+00 +PHOSPHO2 ENST00000359744 2.0018e-04 8.4726e-01 4.6200e-01 1.6150e+00 +FAM173A ENST00000569529 8.7746e-04 8.0166e-01 4.1600e-01 1.6150e+00 +RPP38 ENST00000378197 2.0088e-04 8.4661e-01 4.6100e-01 1.6150e+00 +C9orf9 ENST00000350499 4.3870e-05 8.8554e-01 5.0100e-01 1.6160e+00 +GYPE ENST00000358615 3.6896e-03 7.4551e-01 3.6400e-01 1.6160e+00 +OR51G2 ENST00000322013 3.6881e-03 7.4561e-01 3.6400e-01 1.6160e+00 +TMEM128 ENST00000254742 1.9994e-04 8.4748e-01 4.6200e-01 1.6160e+00 +MRPS33 ENST00000393008 3.6885e-03 7.4558e-01 3.6400e-01 1.6160e+00 +OR5P2 ENST00000329434 3.6817e-03 7.4604e-01 3.6500e-01 1.6160e+00 +SDR39U1 ENST00000399395 1.5321e-11 1.0725e+00 7.2500e-01 1.6160e+00 +ADH7 ENST00000476959 1.5123e-11 1.0735e+00 7.2500e-01 1.6170e+00 +ZNF337 ENST00000376436 3.6778e-03 7.4631e-01 3.6500e-01 1.6170e+00 +ZNF681 ENST00000402377 3.6792e-03 7.4621e-01 3.6500e-01 1.6170e+00 +GSTM4 ENST00000369836 1.3834e-08 1.0111e+00 6.4600e-01 1.6170e+00 +KIAA0125 ENST00000429431 8.7279e-04 8.0280e-01 4.1700e-01 1.6170e+00 +CTD-2368P22.1 ENST00000550135 1.3762e-08 1.0117e+00 6.4700e-01 1.6170e+00 +NOL3 ENST00000568146 1.9920e-04 8.4818e-01 4.6200e-01 1.6170e+00 +ELSPBP1 ENST00000339841 1.5208e-11 1.0731e+00 7.2500e-01 1.6170e+00 +DUSP28 ENST00000405954 1.7995e-01 4.0045e-01 1.3800e-01 1.6180e+00 +RP11-347C12.3 ENST00000550538 5.5479e-02 5.6931e-01 2.2900e-01 1.6180e+00 +ZC2HC1B ENST00000237275 2.5401e-09 1.0298e+00 6.6900e-01 1.6180e+00 +TM4SF4 ENST00000305354 7.2513e-08 9.9259e-01 6.2300e-01 1.6180e+00 +SDR42E2 ENST00000602312 1.3652e-08 1.0125e+00 6.4700e-01 1.6180e+00 +DHRS9 ENST00000327239 7.2309e-08 9.9289e-01 6.2300e-01 1.6180e+00 +HOXA9 ENST00000343483 4.3591e-05 8.8658e-01 5.0200e-01 1.6180e+00 +RABL2A ENST00000393167 7.2529e-08 9.9257e-01 6.2300e-01 1.6180e+00 +CTSE ENST00000358184 1.4371e-14 1.1197e+00 7.8700e-01 1.6180e+00 +OR2AT4 ENST00000305159 3.6632e-03 7.4730e-01 3.6500e-01 1.6180e+00 +RP11-680G10.1 ENST00000568080 4.3060e-01 0.0000e+00 0.0000e+00 1.6180e+00 +NUDT18 ENST00000309188 1.8736e-06 9.4758e-01 5.6900e-01 1.6190e+00 +ATP6V1F ENST00000492758 1.4736e-02 6.7397e-01 3.0400e-01 1.6190e+00 +ZSCAN4 ENST00000318203 4.3321e-05 8.8760e-01 5.0300e-01 1.6190e+00 +NOXO1 ENST00000397280 8.3428e-11 1.0610e+00 7.0800e-01 1.6190e+00 +RWDD2A ENST00000369724 3.7145e-07 9.7205e-01 5.9800e-01 1.6190e+00 +AIF1 ENST00000376059 1.8793e-06 9.4719e-01 5.6900e-01 1.6190e+00 +HSD3B2 ENST00000543831 7.1760e-08 9.9372e-01 6.2400e-01 1.6190e+00 +ASB10 ENST00000420175 2.6403e-12 1.0874e+00 7.4300e-01 1.6190e+00 +CR1L ENST00000508064 7.6434e-27 1.2279e+00 9.4000e-01 1.6190e+00 +TPBGL ENST00000562197 4.3003e-01 0.0000e+00 0.0000e+00 1.6200e+00 +PRR5-ARHGAP8 ENST00000352766 2.1367e-28 1.2377e+00 9.5400e-01 1.6200e+00 +OLAH ENST00000378217 4.5721e-10 1.0472e+00 6.9000e-01 1.6200e+00 +SMIM17 ENST00000598409 1.4713e-02 6.7441e-01 3.0400e-01 1.6200e+00 +OR5M9 ENST00000279791 3.6459e-03 7.4848e-01 3.6600e-01 1.6200e+00 +GLRX2 ENST00000367440 8.5990e-04 8.0601e-01 4.1900e-01 1.6210e+00 +CTA-299D3.8 ENST00000407505 1.4667e-02 6.7534e-01 3.0400e-01 1.6210e+00 +C2orf73 ENST00000398634 3.6668e-07 9.7358e-01 5.9900e-01 1.6210e+00 +UCMA ENST00000378681 9.0610e-06 9.2139e-01 5.3900e-01 1.6210e+00 +LYRM9 ENST00000379103 1.4671e-02 6.7525e-01 3.0400e-01 1.6210e+00 +CD300LB ENST00000392621 7.0860e-08 9.9509e-01 6.2500e-01 1.6210e+00 +IFNE ENST00000448696 1.4672e-02 6.7525e-01 3.0400e-01 1.6210e+00 +ZNF551 ENST00000282296 5.5038e-02 5.7206e-01 2.3000e-01 1.6220e+00 +OR51I1 ENST00000380211 8.5828e-04 8.0642e-01 4.1900e-01 1.6220e+00 +LYPD4 ENST00000330743 9.0339e-06 9.2182e-01 5.3900e-01 1.6220e+00 +AC019171.1 ENST00000601251 5.5050e-02 5.7198e-01 2.3000e-01 1.6220e+00 +RRP36 ENST00000244496 7.9308e-14 1.1121e+00 7.7400e-01 1.6220e+00 +SLC3A1 ENST00000260649 7.2168e-27 1.2306e+00 9.4200e-01 1.6230e+00 +GPT ENST00000394955 3.5945e-19 1.1735e+00 8.5900e-01 1.6230e+00 +C1QTNF6 ENST00000337843 9.0082e-06 9.2224e-01 5.3900e-01 1.6230e+00 +MYL7 ENST00000223364 1.8314e-06 9.5056e-01 5.7100e-01 1.6230e+00 +AP000769.1 ENST00000309775 5.4792e-02 5.7361e-01 2.3100e-01 1.6240e+00 +FOPNL ENST00000255759 1.8256e-06 9.5097e-01 5.7100e-01 1.6240e+00 +PODNL1 ENST00000339560 4.4042e-13 1.1032e+00 7.6100e-01 1.6240e+00 +FKBPL ENST00000375156 7.9526e-11 1.0651e+00 7.1100e-01 1.6240e+00 +SNX16 ENST00000396330 1.4160e-11 1.0789e+00 7.2900e-01 1.6240e+00 +SNCG ENST00000372017 8.4750e-04 8.0916e-01 4.2000e-01 1.6250e+00 +GATSL2 ENST00000426327 4.2837e-01 0.0000e+00 0.0000e+00 1.6250e+00 +LELP1 ENST00000368747 4.2789e-01 0.0000e+00 0.0000e+00 1.6260e+00 +LTC4S ENST00000292596 8.4628e-04 8.0947e-01 4.2000e-01 1.6260e+00 +FUOM ENST00000368552 1.9189e-04 8.5519e-01 4.6600e-01 1.6260e+00 +HPGDS ENST00000295256 1.8063e-06 9.5236e-01 5.7200e-01 1.6260e+00 +OR10V1 ENST00000307552 8.4587e-04 8.0957e-01 4.2000e-01 1.6260e+00 +CYBA ENST00000261623 8.8678e-06 9.2453e-01 5.4000e-01 1.6260e+00 +RSG1 ENST00000375599 8.8551e-06 9.2474e-01 5.4100e-01 1.6260e+00 +SERPINA1 ENST00000448921 6.8497e-08 9.9878e-01 6.2700e-01 1.6260e+00 +RSPH9 ENST00000372165 2.3881e-09 1.0356e+00 6.7300e-01 1.6260e+00 +AC005481.5 ENST00000409610 4.2807e-01 0.0000e+00 0.0000e+00 1.6260e+00 +HEATR5A ENST00000382464 5.4671e-02 5.7437e-01 2.3100e-01 1.6260e+00 +GPRC5A ENST00000014914 6.7860e-08 9.9980e-01 6.2800e-01 1.6270e+00 +CELA3B ENST00000337107 2.4372e-12 1.0936e+00 7.4700e-01 1.6270e+00 +ZNF440 ENST00000304060 1.4464e-02 6.7941e-01 3.0600e-01 1.6270e+00 +OR5A1 ENST00000302030 8.8011e-06 9.2563e-01 5.4100e-01 1.6270e+00 +PLCXD1 ENST00000381657 4.3087e-10 1.0526e+00 6.9400e-01 1.6270e+00 +TNFSF18 ENST00000404377 1.9152e-04 8.5556e-01 4.6600e-01 1.6270e+00 +C16orf46 ENST00000299578 6.8068e-08 9.9947e-01 6.2700e-01 1.6270e+00 +OR8G1 ENST00000341493 3.5718e-03 7.5363e-01 3.6800e-01 1.6270e+00 +OR9Q1 ENST00000335397 8.3932e-04 8.1127e-01 4.2100e-01 1.6280e+00 +SLFN12L ENST00000260908 7.6581e-11 1.0683e+00 7.1300e-01 1.6280e+00 +LAMTOR4 ENST00000341942 3.5588e-03 7.5455e-01 3.6900e-01 1.6280e+00 +IL13 ENST00000304506 1.4426e-02 6.8019e-01 3.0600e-01 1.6280e+00 +HTR3E ENST00000440596 4.2286e-10 1.0542e+00 6.9500e-01 1.6290e+00 +GOLGA8F ENST00000532622 5.4264e-02 5.7698e-01 2.3200e-01 1.6290e+00 +SMCO3 ENST00000316048 1.4367e-02 6.8139e-01 3.0700e-01 1.6290e+00 +C7orf62 ENST00000297203 4.1459e-05 8.9484e-01 5.0700e-01 1.6290e+00 +RABIF ENST00000367262 1.4371e-02 6.8131e-01 3.0700e-01 1.6290e+00 +KCNRG ENST00000312942 4.1306e-05 8.9545e-01 5.0700e-01 1.6300e+00 +GOLGA6L1 ENST00000316397 2.3586e-12 1.0962e+00 7.4900e-01 1.6300e+00 +CDC42SE1 ENST00000439374 3.5427e-03 7.5570e-01 3.6900e-01 1.6300e+00 +F2RL3 ENST00000248076 4.1298e-05 8.9548e-01 5.0700e-01 1.6300e+00 +LBH ENST00000395323 1.4360e-02 6.8155e-01 3.0700e-01 1.6300e+00 +C19orf70 ENST00000309324 8.3352e-04 8.1278e-01 4.2200e-01 1.6300e+00 +ZNF100 ENST00000358296 1.8933e-04 8.5773e-01 4.6700e-01 1.6300e+00 +HCAR2 ENST00000328880 1.8933e-04 8.5772e-01 4.6700e-01 1.6300e+00 +SLC46A2 ENST00000374228 1.3414e-11 1.0833e+00 7.3200e-01 1.6300e+00 +BANF2 ENST00000545418 1.4314e-02 6.8249e-01 3.0700e-01 1.6310e+00 +OR8B8 ENST00000328064 1.4312e-02 6.8253e-01 3.0700e-01 1.6310e+00 +NAPSA ENST00000253719 7.1709e-14 1.1194e+00 7.8000e-01 1.6310e+00 +ACOT6 ENST00000381139 3.5327e-03 7.5642e-01 3.6900e-01 1.6310e+00 +C2orf80 ENST00000341287 7.5000e-11 1.0701e+00 7.1400e-01 1.6310e+00 +NMS ENST00000376865 1.3331e-11 1.0838e+00 7.3200e-01 1.6310e+00 +EXOG ENST00000287675 1.3331e-11 1.0838e+00 7.3200e-01 1.6310e+00 +IL22 ENST00000538666 1.8843e-04 8.5863e-01 4.6800e-01 1.6310e+00 +C12orf79 ENST00000549802 8.3157e-04 8.1329e-01 4.2200e-01 1.6310e+00 +SELPLG ENST00000228463 1.7680e-01 4.0774e-01 1.4000e-01 1.6310e+00 +FCAR ENST00000355524 6.5959e-08 1.0029e+00 6.2900e-01 1.6320e+00 +OR10G3 ENST00000303532 3.5194e-03 7.5737e-01 3.7000e-01 1.6320e+00 +TMEM140 ENST00000275767 5.3997e-02 5.7870e-01 2.3200e-01 1.6320e+00 +H2AFX ENST00000530167 1.7652e-01 4.0840e-01 1.4000e-01 1.6320e+00 +HOXA4 ENST00000360046 8.5959e-06 9.2909e-01 5.4300e-01 1.6320e+00 +COX6A1P2 ENST00000423336 4.2607e-01 0.0000e+00 0.0000e+00 1.6320e+00 +GP5 ENST00000401815 1.8766e-04 8.5941e-01 4.6800e-01 1.6320e+00 +GRTP1 ENST00000375431 4.0399e-13 1.1097e+00 7.6600e-01 1.6330e+00 +TMEM69 ENST00000372025 1.8670e-04 8.6038e-01 4.6800e-01 1.6330e+00 +SETD6 ENST00000219315 1.8383e-18 1.1741e+00 8.5400e-01 1.6330e+00 +GSTA1 ENST00000334575 1.7305e-06 9.5799e-01 5.7500e-01 1.6330e+00 +CPB1 ENST00000491148 2.6104e-22 1.2075e+00 9.0200e-01 1.6330e+00 +DNASE2B ENST00000370665 3.6644e-16 1.1494e+00 8.2000e-01 1.6330e+00 +SIRPB1 ENST00000381605 2.3107e-12 1.0978e+00 7.5000e-01 1.6330e+00 +TOR3A ENST00000367627 2.3045e-12 1.0980e+00 7.5000e-01 1.6330e+00 +ZNF233 ENST00000391958 1.8665e-04 8.6043e-01 4.6900e-01 1.6330e+00 +PRR22 ENST00000419421 1.4248e-02 6.8385e-01 3.0800e-01 1.6330e+00 +AP4S1 ENST00000216366 1.7275e-06 9.5822e-01 5.7600e-01 1.6330e+00 +MARCKSL1 ENST00000329421 1.4253e-02 6.8376e-01 3.0800e-01 1.6330e+00 +DAP ENST00000230895 3.5018e-03 7.5865e-01 3.7000e-01 1.6340e+00 +TM4SF20 ENST00000304568 1.8620e-04 8.6089e-01 4.6900e-01 1.6340e+00 +RAD51B ENST00000487270 2.0790e-15 1.1418e+00 8.0800e-01 1.6340e+00 +ALKBH7 ENST00000245812 1.7207e-06 9.5874e-01 5.7600e-01 1.6340e+00 +LY6K ENST00000292430 1.4203e-02 6.8480e-01 3.0800e-01 1.6340e+00 +CDRT1 ENST00000312127 3.4983e-03 7.5890e-01 3.7100e-01 1.6340e+00 +MPEG1 ENST00000361050 3.5925e-16 1.1507e+00 8.2100e-01 1.6340e+00 +GALNTL5 ENST00000392800 3.5947e-16 1.1506e+00 8.2100e-01 1.6340e+00 +AC027763.2 ENST00000575889 1.7573e-01 4.1029e-01 1.4100e-01 1.6350e+00 +C4orf40 ENST00000344526 1.8537e-04 8.6174e-01 4.6900e-01 1.6350e+00 +S100A6 ENST00000368720 1.7565e-01 4.1049e-01 1.4100e-01 1.6350e+00 +KLRC3 ENST00000381903 1.7152e-06 9.5916e-01 5.7600e-01 1.6350e+00 +DYDC2 ENST00000372198 3.4876e-03 7.5968e-01 3.7100e-01 1.6350e+00 +TMEM126B ENST00000358867 1.8551e-04 8.6160e-01 4.6900e-01 1.6350e+00 +UPK1A ENST00000222275 7.2141e-11 1.0734e+00 7.1700e-01 1.6350e+00 +IGFBPL1 ENST00000377694 4.0352e-05 8.9933e-01 5.0900e-01 1.6350e+00 +BPIFA1 ENST00000354297 1.1971e-08 1.0258e+00 6.5600e-01 1.6360e+00 +MCTP2 ENST00000357742 6.0300e-52 1.3374e+00 1.0990e+00 1.6360e+00 +AIM2 ENST00000368130 2.1942e-09 1.0437e+00 6.7800e-01 1.6360e+00 +TMEM239 ENST00000380593 8.1616e-04 8.1739e-01 4.2400e-01 1.6360e+00 +HAP1 ENST00000347901 3.3512e-26 1.2374e+00 9.4400e-01 1.6370e+00 +UGT2B10 ENST00000265403 1.0278e-17 1.1692e+00 8.4600e-01 1.6370e+00 +SATL1 ENST00000509231 4.9995e-20 1.1922e+00 8.7800e-01 1.6380e+00 +SBK2 ENST00000413299 3.9689e-05 9.0209e-01 5.1100e-01 1.6380e+00 +CALHM2 ENST00000260743 8.3082e-06 9.3411e-01 5.4600e-01 1.6380e+00 +ENDOG ENST00000372642 1.8287e-04 8.6432e-01 4.7100e-01 1.6380e+00 +GLOD5 ENST00000303227 5.3308e-02 5.8324e-01 2.3400e-01 1.6380e+00 +NR0B2 ENST00000254227 8.3377e-06 9.3359e-01 5.4600e-01 1.6380e+00 +OR13C2 ENST00000542196 1.4056e-02 6.8790e-01 3.1000e-01 1.6380e+00 +WBSCR28 ENST00000320531 1.1786e-08 1.0274e+00 6.5700e-01 1.6380e+00 +GMFG ENST00000597595 1.1758e-08 1.0277e+00 6.5700e-01 1.6380e+00 +TIMM22 ENST00000327158 3.9658e-05 9.0223e-01 5.1100e-01 1.6380e+00 +NUDT14 ENST00000392568 3.9537e-05 9.0274e-01 5.1100e-01 1.6390e+00 +ZNF98 ENST00000357774 3.4454e-03 7.6279e-01 3.7200e-01 1.6390e+00 +FAM216B ENST00000537894 8.1029e-04 8.1898e-01 4.2500e-01 1.6390e+00 +DDI1 ENST00000302259 2.1471e-09 1.0458e+00 6.7900e-01 1.6390e+00 +MRPS17 ENST00000426595 1.1728e-08 1.0279e+00 6.5700e-01 1.6390e+00 +H2BFM ENST00000355016 1.4026e-02 6.8855e-01 3.1000e-01 1.6390e+00 +ERICH1 ENST00000262109 1.1389e-14 1.1360e+00 7.9800e-01 1.6390e+00 +FAM159B ENST00000389074 3.4479e-03 7.6260e-01 3.7200e-01 1.6390e+00 +RP11-211G3.3 ENST00000449623 8.0638e-04 8.2005e-01 4.2600e-01 1.6400e+00 +BHMT2 ENST00000255192 1.9621e-15 1.1457e+00 8.1100e-01 1.6400e+00 +PTX4 ENST00000293922 3.7580e-13 1.1152e+00 7.6900e-01 1.6400e+00 +FAM132A ENST00000330388 6.2063e-08 1.0096e+00 6.3400e-01 1.6400e+00 +TMEM230 ENST00000342308 1.8056e-04 8.6676e-01 4.7200e-01 1.6410e+00 +RPSAP58 ENST00000496398 3.4250e-03 7.6432e-01 3.7300e-01 1.6410e+00 +LY6G5B ENST00000375864 8.1818e-06 9.3638e-01 5.4700e-01 1.6410e+00 +ASB18 ENST00000409749 6.1879e-08 1.0100e+00 6.3400e-01 1.6410e+00 +C4orf22 ENST00000508675 2.0896e-09 1.0485e+00 6.8100e-01 1.6420e+00 +UBQLNL ENST00000380184 2.1123e-12 1.1049e+00 7.5500e-01 1.6420e+00 +ZDHHC11B ENST00000508859 3.6787e-13 1.1169e+00 7.7100e-01 1.6420e+00 +AZU1 ENST00000233997 3.9068e-05 9.0474e-01 5.1200e-01 1.6420e+00 +LDHAL6A ENST00000280706 3.7764e-10 1.0645e+00 7.0100e-01 1.6420e+00 +SRSF10 ENST00000492112 4.2275e-01 0.0000e+00 0.0000e+00 1.6420e+00 +JOSD2 ENST00000598418 1.8012e-04 8.6723e-01 4.7200e-01 1.6420e+00 +AHSA2 ENST00000394457 1.8000e-04 8.6736e-01 4.7200e-01 1.6420e+00 +CYP4A11 ENST00000310638 1.0870e-24 1.2316e+00 9.3200e-01 1.6430e+00 +TMEM159 ENST00000233047 3.4061e-03 7.6574e-01 3.7400e-01 1.6430e+00 +FABP12 ENST00000360464 3.4043e-03 7.6588e-01 3.7400e-01 1.6430e+00 +IGLL1 ENST00000330377 1.3899e-02 6.9128e-01 3.1100e-01 1.6430e+00 +MRPL44 ENST00000258383 2.0628e-09 1.0497e+00 6.8200e-01 1.6440e+00 +P2RY8 ENST00000381297 3.4012e-03 7.6611e-01 3.7400e-01 1.6440e+00 +MXRA7 ENST00000355797 7.9422e-04 8.2341e-01 4.2700e-01 1.6440e+00 +AMY1C ENST00000370079 3.3974e-03 7.6640e-01 3.7400e-01 1.6440e+00 +C20orf197 ENST00000313426 4.2195e-01 0.0000e+00 0.0000e+00 1.6440e+00 +C17orf78 ENST00000300618 2.0653e-09 1.0496e+00 6.8200e-01 1.6440e+00 +PCP4L1 ENST00000504449 5.2717e-02 5.8722e-01 2.3600e-01 1.6440e+00 +PROK2 ENST00000295619 1.3828e-02 6.9283e-01 3.1200e-01 1.6450e+00 +PRR23D1 ENST00000533250 4.2180e-01 0.0000e+00 0.0000e+00 1.6450e+00 +ENDOD1 ENST00000278505 6.5757e-11 1.0815e+00 7.2200e-01 1.6450e+00 +NTS ENST00000256010 3.8527e-05 9.0708e-01 5.1300e-01 1.6450e+00 +SEC14L3 ENST00000215812 3.6612e-23 1.2232e+00 9.1800e-01 1.6460e+00 +C3orf83 ENST00000564146 3.8261e-05 9.0824e-01 5.1400e-01 1.6460e+00 +AC112715.2 ENST00000445534 4.2143e-01 0.0000e+00 0.0000e+00 1.6460e+00 +MAFA ENST00000333480 3.3727e-03 7.6828e-01 3.7500e-01 1.6460e+00 +CST8 ENST00000246012 3.3735e-03 7.6823e-01 3.7500e-01 1.6460e+00 +OR8B3 ENST00000354597 1.3798e-02 6.9348e-01 3.1200e-01 1.6460e+00 +CCT8L2 ENST00000359963 1.5923e-06 9.6906e-01 5.8200e-01 1.6470e+00 +FABP7 ENST00000368444 7.8595e-04 8.2574e-01 4.2800e-01 1.6470e+00 +OR2C1 ENST00000304936 3.8058e-05 9.0914e-01 5.1400e-01 1.6470e+00 +MRPL50 ENST00000374865 3.8088e-05 9.0901e-01 5.1400e-01 1.6470e+00 +TTC34 ENST00000401095 6.4816e-11 1.0828e+00 7.2300e-01 1.6470e+00 +CCDC28A ENST00000332797 3.6463e-10 1.0677e+00 7.0300e-01 1.6470e+00 +PLEKHS1 ENST00000369310 2.1435e-22 1.2181e+00 9.1000e-01 1.6470e+00 +OR6C74 ENST00000343870 3.3696e-03 7.6853e-01 3.7500e-01 1.6470e+00 +OR6J1 ENST00000540461 5.2416e-02 5.8928e-01 2.3600e-01 1.6470e+00 +PRTN3 ENST00000234347 3.8044e-05 9.0920e-01 5.1400e-01 1.6470e+00 +RASL11A ENST00000241463 1.5920e-06 9.6908e-01 5.8200e-01 1.6470e+00 +FAM89B ENST00000530349 5.2310e-02 5.9001e-01 2.3700e-01 1.6480e+00 +CHST4 ENST00000338482 2.0001e-09 1.0527e+00 6.8400e-01 1.6480e+00 +GLYATL2 ENST00000287275 1.5822e-06 9.6991e-01 5.8200e-01 1.6480e+00 +RGS21 ENST00000417209 3.8018e-05 9.0932e-01 5.1500e-01 1.6480e+00 +RNF151 ENST00000569714 1.7597e-04 8.7171e-01 4.7400e-01 1.6480e+00 +IFI6 ENST00000339145 1.3731e-02 6.9497e-01 3.1300e-01 1.6480e+00 +CUTA ENST00000374500 3.0840e-07 9.9436e-01 6.1100e-01 1.6490e+00 +ZSWIM1 ENST00000372523 1.1282e-11 1.0976e+00 7.4100e-01 1.6490e+00 +SH2D6 ENST00000340326 3.7712e-05 9.1069e-01 5.1500e-01 1.6490e+00 +ASCL3 ENST00000325884 1.3684e-02 6.9600e-01 3.1300e-01 1.6490e+00 +CDK20 ENST00000325303 5.9487e-14 1.1332e+00 7.8900e-01 1.6490e+00 +AC091801.1 ENST00000402115 1.7221e-01 4.1896e-01 1.4400e-01 1.6490e+00 +IGFL2 ENST00000434646 7.7735e-04 8.2820e-01 4.3000e-01 1.6500e+00 +OR10G2 ENST00000542433 3.3388e-03 7.7091e-01 3.7600e-01 1.6500e+00 +MPG ENST00000219431 1.9454e-12 1.1115e+00 7.5900e-01 1.6500e+00 +SPG7 ENST00000268704 1.9683e-36 1.2992e+00 1.0300e+00 1.6510e+00 +TP53RK ENST00000372114 7.7469e-04 8.2897e-01 4.3000e-01 1.6510e+00 +FCGR3B ENST00000531221 3.0294e-07 9.9654e-01 6.1300e-01 1.6510e+00 +SAYSD1 ENST00000229903 3.7399e-05 9.1210e-01 5.1600e-01 1.6510e+00 +INMT ENST00000013222 3.3238e-03 7.7209e-01 3.7700e-01 1.6510e+00 +TEX29 ENST00000283547 7.7723e-06 9.4404e-01 5.5200e-01 1.6510e+00 +C8orf48 ENST00000297324 1.7347e-04 8.7449e-01 4.7600e-01 1.6510e+00 +RP11-422N16.3 ENST00000499579 4.1939e-01 0.0000e+00 0.0000e+00 1.6520e+00 +WDR83OS ENST00000596731 3.3142e-03 7.7283e-01 3.7700e-01 1.6520e+00 +FAM167B ENST00000373582 7.7413e-04 8.2913e-01 4.3000e-01 1.6520e+00 +GFER ENST00000248114 1.7308e-04 8.7492e-01 4.7600e-01 1.6520e+00 +AADACL2 ENST00000356517 1.0604e-08 1.0384e+00 6.6300e-01 1.6520e+00 +PRR13 ENST00000429243 1.3585e-02 6.9824e-01 3.1400e-01 1.6520e+00 +FABP6 ENST00000393980 1.5516e-06 9.7253e-01 5.8400e-01 1.6520e+00 +RAB27A ENST00000396307 3.0027e-07 9.9763e-01 6.1300e-01 1.6530e+00 +AL021546.6 ENST00000551806 3.7119e-05 9.1337e-01 5.1700e-01 1.6530e+00 +RP11-286N22.8 ENST00000541135 3.6968e-05 9.1407e-01 5.1700e-01 1.6540e+00 +GOLGA8I ENST00000450802 1.9216e-22 1.2241e+00 9.1500e-01 1.6540e+00 +C1ORF220 ENST00000367636 3.6903e-05 9.1436e-01 5.1700e-01 1.6540e+00 +NANOS2 ENST00000341294 5.1664e-02 5.9453e-01 2.3800e-01 1.6540e+00 +CCL27 ENST00000259631 1.3511e-02 6.9991e-01 3.1500e-01 1.6540e+00 +CCL28 ENST00000361115 5.1599e-02 5.9500e-01 2.3900e-01 1.6540e+00 +LIME1 ENST00000309546 1.7155e-04 8.7665e-01 4.7700e-01 1.6540e+00 +OR4D1 ENST00000268912 1.7181e-04 8.7635e-01 4.7700e-01 1.6540e+00 +A4GALT ENST00000401850 7.6668e-06 9.4609e-01 5.5300e-01 1.6540e+00 +CCDC166 ENST00000542437 3.2900e-03 7.7475e-01 3.7800e-01 1.6550e+00 +ACOT4 ENST00000326303 1.0412e-08 1.0403e+00 6.6500e-01 1.6550e+00 +FLJ00273 ENST00000595331 1.7062e-01 4.2305e-01 1.4500e-01 1.6550e+00 +SNX10 ENST00000338523 3.3891e-10 1.0745e+00 7.0800e-01 1.6550e+00 +C11orf74 ENST00000532470 7.6050e-06 9.4731e-01 5.5300e-01 1.6550e+00 +FAM19A3 ENST00000369630 3.6668e-05 9.1545e-01 5.1800e-01 1.6550e+00 +FKBP14 ENST00000222803 1.5229e-06 9.7505e-01 5.8500e-01 1.6550e+00 +ZNF221 ENST00000251269 7.6431e-04 8.3200e-01 4.3200e-01 1.6550e+00 +EPHX3 ENST00000221730 1.6489e-15 1.1578e+00 8.2000e-01 1.6550e+00 +SLC35E2 ENST00000246421 7.6215e-04 8.3263e-01 4.3200e-01 1.6560e+00 +MOGAT3 ENST00000223114 1.8376e-12 1.1161e+00 7.6200e-01 1.6560e+00 +ALDH3B2 ENST00000349015 3.1881e-13 1.1279e+00 7.7800e-01 1.6560e+00 +TIRAP ENST00000392678 7.6118e-04 8.3292e-01 4.3200e-01 1.6560e+00 +PRSS46 ENST00000463091 3.6604e-05 9.1575e-01 5.1800e-01 1.6560e+00 +TP53I3 ENST00000238721 5.9516e-11 1.0903e+00 7.2800e-01 1.6560e+00 +PDYN ENST00000217305 1.7033e-04 8.7804e-01 4.7800e-01 1.6560e+00 +OBP2A ENST00000539850 1.5163e-06 9.7564e-01 5.8600e-01 1.6560e+00 +PLIN5 ENST00000381848 1.0481e-11 1.1038e+00 7.4600e-01 1.6560e+00 +FAM166A ENST00000344774 1.8249e-12 1.1167e+00 7.6300e-01 1.6570e+00 +GOLGA6L6 ENST00000427390 2.2875e-19 1.2004e+00 8.7900e-01 1.6570e+00 +TMEM156 ENST00000381938 3.3366e-10 1.0760e+00 7.0900e-01 1.6570e+00 +SHISA3 ENST00000319234 3.6402e-05 9.1669e-01 5.1900e-01 1.6570e+00 +AC110619.2 ENST00000404327 1.3399e-02 7.0247e-01 3.1600e-01 1.6570e+00 +AC011366.3 ENST00000523446 4.1766e-01 0.0000e+00 0.0000e+00 1.6570e+00 +HCAR1 ENST00000432564 7.5927e-04 8.3348e-01 4.3200e-01 1.6570e+00 +DTD2 ENST00000310850 7.5939e-04 8.3345e-01 4.3200e-01 1.6570e+00 +SCIN ENST00000297029 1.7180e-36 1.3044e+00 1.0340e+00 1.6570e+00 +APOBEC3D ENST00000216099 1.3595e-18 1.1927e+00 8.6800e-01 1.6570e+00 +PDE6G ENST00000331056 1.3418e-02 7.0203e-01 3.1600e-01 1.6570e+00 +RP11-322L20.1 ENST00000557527 5.1167e-02 5.9809e-01 2.4000e-01 1.6580e+00 +FFAR1 ENST00000246553 7.5686e-04 8.3420e-01 4.3300e-01 1.6580e+00 +TAC4 ENST00000334568 3.6126e-05 9.1799e-01 5.1900e-01 1.6580e+00 +ZNF780B ENST00000434248 3.2592e-03 7.7723e-01 3.7900e-01 1.6580e+00 +RLN3 ENST00000431365 1.3378e-02 7.0295e-01 3.1600e-01 1.6580e+00 +TMEM247 ENST00000434431 3.6077e-05 9.1822e-01 5.1900e-01 1.6590e+00 +PRSS35 ENST00000536636 3.2800e-10 1.0776e+00 7.1000e-01 1.6590e+00 +ZNF788 ENST00000596883 1.3342e-02 7.0378e-01 3.1600e-01 1.6590e+00 +MGP ENST00000228938 3.6072e-05 9.1824e-01 5.1900e-01 1.6590e+00 +PI3 ENST00000243924 1.6965e-01 4.2559e-01 1.4600e-01 1.6590e+00 +LCE1E ENST00000368770 1.6972e-01 4.2540e-01 1.4600e-01 1.6590e+00 +PCDH11Y ENST00000362095 1.6811e-04 8.8059e-01 4.7900e-01 1.6590e+00 +C6orf52 ENST00000259983 3.6111e-05 9.1806e-01 5.1900e-01 1.6590e+00 +ATP5G2 ENST00000394349 7.4577e-06 9.5026e-01 5.5500e-01 1.6590e+00 +PTRH1 ENST00000419060 1.6798e-04 8.8075e-01 4.7900e-01 1.6590e+00 +PTPN20B ENST00000374233 5.1059e-02 5.9887e-01 2.4000e-01 1.6590e+00 +GP1BA ENST00000329125 3.2325e-03 7.7939e-01 3.8000e-01 1.6600e+00 +PEX11G ENST00000221480 5.4033e-08 1.0252e+00 6.4300e-01 1.6600e+00 +APOH ENST00000205948 1.5614e-15 1.1617e+00 8.2200e-01 1.6600e+00 +KRTAP10-1 ENST00000400375 1.6762e-04 8.8116e-01 4.7900e-01 1.6600e+00 +OR5AC2 ENST00000358642 1.3314e-02 7.0444e-01 3.1700e-01 1.6600e+00 +ATOH7 ENST00000373673 5.0896e-02 6.0006e-01 2.4000e-01 1.6610e+00 +CAPSL ENST00000397367 2.8442e-07 1.0043e+00 6.1700e-01 1.6610e+00 +GPR42 ENST00000454971 5.0905e-02 5.9999e-01 2.4000e-01 1.6610e+00 +FAM173B ENST00000511437 1.7847e-09 1.0640e+00 6.9100e-01 1.6620e+00 +AHSG ENST00000411641 3.2090e-10 1.0796e+00 7.1100e-01 1.6620e+00 +ISX ENST00000308700 3.5552e-05 9.2073e-01 5.2100e-01 1.6620e+00 +AC096582.1 ENST00000596600 4.1594e-01 0.0000e+00 0.0000e+00 1.6620e+00 +SMIM18 ENST00000517349 1.6897e-01 4.2739e-01 1.4600e-01 1.6620e+00 +LRRC52 ENST00000294818 7.3202e-06 9.5308e-01 5.5700e-01 1.6620e+00 +KRT33B ENST00000251646 4.4301e-17 1.1810e+00 8.4800e-01 1.6620e+00 +PSCA ENST00000301258 1.6856e-01 4.2851e-01 1.4700e-01 1.6630e+00 +OR4C5 ENST00000319813 3.2052e-03 7.8163e-01 3.8100e-01 1.6630e+00 +ZNF253 ENST00000589717 3.2064e-03 7.8154e-01 3.8100e-01 1.6630e+00 +S100Z ENST00000317593 1.3210e-02 7.0689e-01 3.1800e-01 1.6630e+00 +MRPS14 ENST00000476371 1.6481e-04 8.8448e-01 4.8100e-01 1.6640e+00 +XG ENST00000419513 9.6910e-09 1.0479e+00 6.6900e-01 1.6640e+00 +SERPINA4 ENST00000557004 9.7276e-09 1.0475e+00 6.6900e-01 1.6640e+00 +OR5V1 ENST00000377154 1.3153e-02 7.0822e-01 3.1800e-01 1.6640e+00 +FAM221A ENST00000344962 1.7027e-12 1.1224e+00 7.6600e-01 1.6640e+00 +S100A10 ENST00000368811 1.6843e-01 4.2884e-01 1.4700e-01 1.6640e+00 +WDR55 ENST00000358337 5.0372e-14 1.1457e+00 7.9800e-01 1.6650e+00 +DGAT2L6 ENST00000333026 5.5267e-11 1.0969e+00 7.3200e-01 1.6650e+00 +MPLKIP ENST00000306984 1.6384e-04 8.8565e-01 4.8200e-01 1.6650e+00 +CDKL4 ENST00000378803 5.0101e-14 1.1461e+00 7.9800e-01 1.6650e+00 +CD5L ENST00000368174 4.2297e-17 1.1840e+00 8.5100e-01 1.6660e+00 +DEXI ENST00000331808 4.1450e-01 0.0000e+00 0.0000e+00 1.6660e+00 +RP11-62N21.1 ENST00000504357 5.0351e-02 6.0407e-01 2.4200e-01 1.6660e+00 +TCEANC2 ENST00000234827 2.7615e-07 1.0080e+00 6.2000e-01 1.6660e+00 +KCNK7 ENST00000340313 3.4780e-05 9.2450e-01 5.2300e-01 1.6660e+00 +CNTNAP3B ENST00000377564 9.5945e-29 1.2742e+00 9.8200e-01 1.6660e+00 +C9orf62 ENST00000320778 3.1634e-03 7.8513e-01 3.8300e-01 1.6670e+00 +NDUFB7 ENST00000215565 3.1709e-03 7.8449e-01 3.8200e-01 1.6670e+00 +BTN3A3 ENST00000244519 1.1892e-18 1.2011e+00 8.7400e-01 1.6670e+00 +PLSCR5 ENST00000443512 3.0759e-10 1.0836e+00 7.1400e-01 1.6670e+00 +PABPC3 ENST00000281589 8.4423e-15 1.1577e+00 8.1300e-01 1.6670e+00 +LCA10 ENST00000452593 1.6221e-04 8.8762e-01 4.8300e-01 1.6670e+00 +APOBEC3G ENST00000407997 5.6720e-21 1.2220e+00 9.0400e-01 1.6670e+00 +ZNF778 ENST00000433976 7.1255e-06 9.5719e-01 5.5900e-01 1.6670e+00 +C1orf195 ENST00000376005 1.6768e-01 4.3087e-01 1.4700e-01 1.6670e+00 +MMP26 ENST00000380390 5.3574e-11 1.0997e+00 7.3400e-01 1.6680e+00 +NDUFB6 ENST00000379847 1.6201e-04 8.8786e-01 4.8300e-01 1.6680e+00 +CTC-429P9.4 ENST00000593459 1.3008e-02 7.1170e-01 3.2000e-01 1.6680e+00 +LL22NC03-63E9.3 ENST00000407120 1.6727e-01 4.3200e-01 1.4800e-01 1.6680e+00 +OR2M4 ENST00000306687 3.1458e-03 7.8662e-01 3.8300e-01 1.6690e+00 +SLC2A7 ENST00000400906 5.5393e-21 1.2234e+00 9.0500e-01 1.6690e+00 +SLC25A47 ENST00000361529 8.2217e-15 1.1596e+00 8.1400e-01 1.6690e+00 +RTBDN ENST00000322912 3.0152e-10 1.0855e+00 7.1500e-01 1.6690e+00 +THAP8 ENST00000292894 1.4014e-06 9.8638e-01 5.9200e-01 1.6690e+00 +C6orf118 ENST00000230301 3.2403e-20 1.2179e+00 8.9600e-01 1.6700e+00 +CAMK2N1 ENST00000375078 1.6681e-01 4.3326e-01 1.4800e-01 1.6700e+00 +ZNF688 ENST00000223459 7.0023e-06 9.5986e-01 5.6100e-01 1.6700e+00 +TMEM253 ENST00000418511 1.3919e-06 9.8731e-01 5.9300e-01 1.6700e+00 +RIMBP3B ENST00000434111 4.1247e-01 0.0000e+00 0.0000e+00 1.6710e+00 +SOD3 ENST00000382120 7.2272e-04 8.4471e-01 4.3800e-01 1.6710e+00 +CSDC2 ENST00000306149 3.1220e-03 7.8865e-01 3.8400e-01 1.6710e+00 +ZNF506 ENST00000443905 1.6558e-09 1.0715e+00 6.9600e-01 1.6710e+00 +RP11-484M3.5 ENST00000490594 1.6658e-01 4.3390e-01 1.4800e-01 1.6710e+00 +RP11-597K23.2 ENST00000559788 4.9813e-02 6.0813e-01 2.4300e-01 1.6710e+00 +ZNF224 ENST00000336976 3.1252e-03 7.8838e-01 3.8400e-01 1.6710e+00 +OR10A2 ENST00000307322 3.1211e-03 7.8873e-01 3.8400e-01 1.6720e+00 +MOK ENST00000361847 8.8397e-22 1.2326e+00 9.1700e-01 1.6720e+00 +MED18 ENST00000373842 1.5906e-04 8.9150e-01 4.8500e-01 1.6720e+00 +S100A13 ENST00000368699 4.9652e-02 6.0936e-01 2.4400e-01 1.6720e+00 +MRPS26 ENST00000380325 1.3667e-06 9.8983e-01 5.9400e-01 1.6730e+00 +ZNF587 ENST00000339656 4.9557e-02 6.1009e-01 2.4400e-01 1.6730e+00 +HMSD ENST00000408945 1.2863e-02 7.1524e-01 3.2100e-01 1.6730e+00 +C4orf26 ENST00000435974 4.9615e-02 6.0964e-01 2.4400e-01 1.6730e+00 +POTEH ENST00000343518 5.1283e-11 1.1037e+00 7.3700e-01 1.6730e+00 +OR52A5 ENST00000307388 6.9060e-06 9.6198e-01 5.6200e-01 1.6730e+00 +TMSB4X ENST00000380636 4.1205e-01 0.0000e+00 0.0000e+00 1.6730e+00 +SLC22A1 ENST00000366963 1.4614e-22 1.2393e+00 9.2600e-01 1.6730e+00 +PCDHB14 ENST00000239449 4.5527e-14 1.1534e+00 8.0300e-01 1.6740e+00 +PLET1 ENST00000338832 6.8789e-06 9.6259e-01 5.6200e-01 1.6740e+00 +KCNJ16 ENST00000392670 8.8743e-12 1.1181e+00 7.5500e-01 1.6740e+00 +TEKT5 ENST00000283025 3.0810e-20 1.2209e+00 8.9900e-01 1.6740e+00 +DCD ENST00000293371 1.5781e-04 8.9307e-01 4.8600e-01 1.6740e+00 +TMEM81 ENST00000367167 3.0983e-03 7.9070e-01 3.8500e-01 1.6740e+00 +ZNF528 ENST00000360465 7.1373e-04 8.4759e-01 4.3900e-01 1.6740e+00 +FAM26D ENST00000405399 7.1349e-04 8.4767e-01 4.3900e-01 1.6740e+00 +PCTP ENST00000268896 8.7596e-12 1.1192e+00 7.5600e-01 1.6750e+00 +CTXN1 ENST00000318978 4.1125e-01 0.0000e+00 0.0000e+00 1.6750e+00 +GGTLC1 ENST00000335694 3.3367e-05 9.3169e-01 5.2700e-01 1.6750e+00 +FAM219B ENST00000357635 1.5708e-04 8.9399e-01 4.8600e-01 1.6750e+00 +RP11-352D3.2 ENST00000379526 1.2801e-02 7.1679e-01 3.2200e-01 1.6750e+00 +N6AMT1 ENST00000303775 6.8181e-06 9.6395e-01 5.6300e-01 1.6750e+00 +TNFSF4 ENST00000281834 4.9378e-02 6.1147e-01 2.4500e-01 1.6750e+00 +PGAM1 ENST00000334828 2.5841e-07 1.0163e+00 6.2500e-01 1.6760e+00 +ZNF425 ENST00000378061 3.3190e-05 9.3262e-01 5.2700e-01 1.6760e+00 +DECR1 ENST00000220764 4.4689e-14 1.1549e+00 8.0400e-01 1.6760e+00 +IL20 ENST00000367098 1.3447e-06 9.9207e-01 5.9500e-01 1.6760e+00 +CTD-2117L12.1 ENST00000504333 4.9232e-02 6.1260e-01 2.4500e-01 1.6760e+00 +ZNF211 ENST00000299871 4.9782e-11 1.1064e+00 7.3800e-01 1.6760e+00 +OR6C3 ENST00000379667 3.0733e-03 7.9289e-01 3.8600e-01 1.6760e+00 +DTWD1 ENST00000251250 2.8135e-10 1.0921e+00 7.1900e-01 1.6770e+00 +OR51B2 ENST00000328813 1.2734e-02 7.1846e-01 3.2200e-01 1.6770e+00 +BEAN1 ENST00000536005 6.7615e-06 9.6524e-01 5.6400e-01 1.6770e+00 +GSTA2 ENST00000493422 2.5611e-07 1.0174e+00 6.2500e-01 1.6770e+00 +STX19 ENST00000315099 2.5612e-07 1.0174e+00 6.2500e-01 1.6770e+00 +AMY2A ENST00000414303 8.5411e-12 1.1214e+00 7.5700e-01 1.6780e+00 +RTP2 ENST00000358241 6.7109e-06 9.6640e-01 5.6400e-01 1.6780e+00 +LRRC26 ENST00000371542 1.2698e-02 7.1936e-01 3.2300e-01 1.6780e+00 +U2AF1L4 ENST00000292879 6.7118e-06 9.6638e-01 5.6400e-01 1.6780e+00 +SMCO1 ENST00000397537 1.5503e-04 8.9662e-01 4.8800e-01 1.6780e+00 +CFD ENST00000327726 6.7045e-06 9.6655e-01 5.6400e-01 1.6780e+00 +KRTAP10-8 ENST00000334662 3.2911e-05 9.3409e-01 5.2800e-01 1.6780e+00 +IGSF5 ENST00000380588 3.6345e-17 1.1943e+00 8.5800e-01 1.6780e+00 +ST6GALNAC2 ENST00000225276 7.4720e-15 1.1668e+00 8.1900e-01 1.6780e+00 +MAP1LC3B2 ENST00000306985 1.2693e-02 7.1950e-01 3.2300e-01 1.6780e+00 +KCTD21 ENST00000340067 3.0552e-03 7.9449e-01 3.8700e-01 1.6780e+00 +GPNMB ENST00000381990 2.8803e-27 1.2745e+00 9.7600e-01 1.6780e+00 +ZNF837 ENST00000427624 1.3275e-06 9.9385e-01 5.9600e-01 1.6780e+00 +C1orf87 ENST00000371201 6.1824e-25 1.2608e+00 9.5400e-01 1.6790e+00 +POTEG ENST00000409832 4.8749e-11 1.1083e+00 7.4000e-01 1.6790e+00 +C19orf52 ENST00000270502 1.5460e-04 8.9718e-01 4.8800e-01 1.6790e+00 +CERS4 ENST00000251363 1.3519e-22 1.2437e+00 9.2900e-01 1.6790e+00 +DEFB123 ENST00000376309 4.0956e-01 0.0000e+00 0.0000e+00 1.6790e+00 +AADACL4 ENST00000376221 1.5430e-04 8.9757e-01 4.8800e-01 1.6790e+00 +HPCAL4 ENST00000372844 3.2705e-05 9.3519e-01 5.2900e-01 1.6790e+00 +KRTAP5-3 ENST00000399685 1.6438e-01 4.4008e-01 1.5000e-01 1.6790e+00 +COX6C ENST00000520468 4.8848e-02 6.1562e-01 2.4600e-01 1.6800e+00 +AGRP ENST00000290953 6.9912e-04 8.5238e-01 4.4200e-01 1.6800e+00 +MRPS11 ENST00000325844 4.6918e-08 1.0415e+00 6.5300e-01 1.6800e+00 +ASB12 ENST00000362002 6.9764e-04 8.5287e-01 4.4200e-01 1.6800e+00 +POLE4 ENST00000483063 6.9897e-04 8.5243e-01 4.4200e-01 1.6800e+00 +OR51E1 ENST00000396952 3.0352e-03 7.9628e-01 3.8800e-01 1.6800e+00 +TOP1MT ENST00000329245 2.4353e-34 1.3131e+00 1.0330e+00 1.6800e+00 +ZNF749 ENST00000334181 4.8846e-02 6.1563e-01 2.4600e-01 1.6800e+00 +C21orf49 ENST00000382375 1.6434e-01 4.4019e-01 1.5000e-01 1.6800e+00 +C7orf55 ENST00000297534 1.2631e-02 7.2107e-01 3.2400e-01 1.6800e+00 +OR51B4 ENST00000380224 6.9519e-04 8.5369e-01 4.4200e-01 1.6810e+00 +OR51E2 ENST00000396950 1.5308e-04 8.9916e-01 4.8900e-01 1.6810e+00 +GNG8 ENST00000300873 1.6400e-01 4.4119e-01 1.5000e-01 1.6810e+00 +ZNF543 ENST00000321545 3.5236e-17 1.1964e+00 8.5900e-01 1.6810e+00 +RP11-1C1.5 ENST00000506021 1.2566e-02 7.2272e-01 3.2400e-01 1.6810e+00 +TMEM220 ENST00000341871 1.3033e-06 9.9641e-01 5.9800e-01 1.6810e+00 +CRISP2 ENST00000339139 1.4437e-12 1.1361e+00 7.7600e-01 1.6810e+00 +C9orf85 ENST00000334731 3.2225e-05 9.3778e-01 5.3000e-01 1.6820e+00 +CA1 ENST00000523953 4.7481e-11 1.1107e+00 7.4100e-01 1.6820e+00 +PRND ENST00000305817 1.2539e-02 7.2340e-01 3.2500e-01 1.6820e+00 +C3orf35 ENST00000328376 4.8577e-02 6.1777e-01 2.4700e-01 1.6830e+00 +DEFB126 ENST00000382398 4.0842e-01 0.0000e+00 0.0000e+00 1.6830e+00 +MAGEF1 ENST00000317897 3.0065e-03 7.9887e-01 3.8900e-01 1.6830e+00 +CNR2 ENST00000536471 6.5369e-06 9.7047e-01 5.6700e-01 1.6830e+00 +CTD-2207O23.12 ENST00000599312 4.0842e-01 0.0000e+00 0.0000e+00 1.6830e+00 +SLC25A48 ENST00000412661 1.5155e-04 9.0117e-01 4.9000e-01 1.6830e+00 +ADRB3 ENST00000345060 2.4637e-07 1.0223e+00 6.2800e-01 1.6830e+00 +DECR2 ENST00000219481 2.6455e-10 1.0981e+00 7.2300e-01 1.6840e+00 +PRH2 ENST00000396400 1.2493e-02 7.2461e-01 3.2500e-01 1.6840e+00 +VSIG4 ENST00000374737 1.4953e-09 1.0818e+00 7.0200e-01 1.6840e+00 +RPL36AL ENST00000298289 4.8413e-02 6.1909e-01 2.4700e-01 1.6840e+00 +PTS ENST00000280362 6.4613e-06 9.7229e-01 5.6800e-01 1.6850e+00 +ZFAND2A ENST00000316495 2.9921e-03 8.0018e-01 3.9000e-01 1.6850e+00 +C12orf60 ENST00000330828 4.8314e-02 6.1988e-01 2.4800e-01 1.6850e+00 +PRTFDC1 ENST00000320152 2.3671e-13 1.1517e+00 7.9400e-01 1.6850e+00 +EXOSC8 ENST00000389704 6.9378e-15 1.1723e+00 8.2300e-01 1.6850e+00 +FAM203A ENST00000347708 1.2417e-02 7.2657e-01 3.2600e-01 1.6860e+00 +UQCRQ ENST00000378670 4.8250e-02 6.2041e-01 2.4800e-01 1.6860e+00 +C1orf170 ENST00000433179 1.1667e-15 1.1826e+00 8.3700e-01 1.6860e+00 +CMTM3 ENST00000424011 1.4974e-04 9.0360e-01 4.9100e-01 1.6860e+00 +UNC93A ENST00000230256 1.1634e-15 1.1828e+00 8.3700e-01 1.6860e+00 +ENO3 ENST00000323997 1.5718e-19 1.2236e+00 8.9500e-01 1.6860e+00 +GPX2 ENST00000389614 1.4995e-04 9.0332e-01 4.9100e-01 1.6860e+00 +GCHFR ENST00000260447 4.8251e-02 6.2040e-01 2.4800e-01 1.6860e+00 +RFPL1 ENST00000354373 1.2421e-02 7.2646e-01 3.2600e-01 1.6860e+00 +PIP ENST00000291009 6.8286e-04 8.5787e-01 4.4400e-01 1.6860e+00 +AC093157.1 ENST00000593496 4.0694e-01 0.0000e+00 0.0000e+00 1.6870e+00 +TRIM54 ENST00000296098 5.5065e-18 1.2096e+00 8.7500e-01 1.6870e+00 +GALR2 ENST00000329003 6.3829e-06 9.7419e-01 5.6900e-01 1.6870e+00 +RP11-520P18.5 ENST00000562505 4.8050e-02 6.2203e-01 2.4800e-01 1.6870e+00 +ADI1 ENST00000327435 3.1509e-05 9.4174e-01 5.3200e-01 1.6870e+00 +TBC1D29 ENST00000580161 6.7880e-04 8.5927e-01 4.4500e-01 1.6870e+00 +SBK3 ENST00000420723 6.7934e-04 8.5908e-01 4.4500e-01 1.6870e+00 +FRAT2 ENST00000371019 4.7967e-02 6.2271e-01 2.4900e-01 1.6880e+00 +BLOC1S6 ENST00000220531 8.0385e-09 1.0681e+00 6.8200e-01 1.6880e+00 +USMG5 ENST00000369825 4.8038e-02 6.2213e-01 2.4900e-01 1.6880e+00 +SAA4 ENST00000278222 1.2346e-02 7.2845e-01 3.2700e-01 1.6880e+00 +KRTAP4-5 ENST00000343246 1.6174e-01 4.4784e-01 1.5200e-01 1.6890e+00 +AP000350.10 ENST00000433835 4.3956e-08 1.0491e+00 6.5800e-01 1.6890e+00 +DEFB1 ENST00000297439 4.0590e-01 0.0000e+00 0.0000e+00 1.6890e+00 +VIMP ENST00000398226 1.4301e-09 1.0864e+00 7.0500e-01 1.6890e+00 +TMEM255B ENST00000375353 7.7218e-12 1.1303e+00 7.6300e-01 1.6890e+00 +KRT33A ENST00000007735 3.1937e-17 1.2032e+00 8.6400e-01 1.6890e+00 +C11orf52 ENST00000278601 3.0999e-05 9.4462e-01 5.3400e-01 1.6900e+00 +MIF ENST00000215754 1.2262e-02 7.3067e-01 3.2800e-01 1.6900e+00 +IL1R2 ENST00000332549 6.5372e-15 1.1769e+00 8.2600e-01 1.6900e+00 +C1orf131 ENST00000366649 4.4098e-11 1.1175e+00 7.4600e-01 1.6900e+00 +HSBP1L1 ENST00000451882 4.7800e-02 6.2409e-01 2.4900e-01 1.6900e+00 +PYURF ENST00000273968 1.6154e-01 4.4843e-01 1.5300e-01 1.6900e+00 +HBM ENST00000356815 1.2271e-02 7.3043e-01 3.2800e-01 1.6900e+00 +CACNG6 ENST00000252729 3.0970e-05 9.4479e-01 5.3400e-01 1.6900e+00 +TM2D3 ENST00000333202 7.9392e-09 1.0694e+00 6.8300e-01 1.6900e+00 +UGT2B28 ENST00000335568 5.2426e-18 1.2129e+00 8.7700e-01 1.6910e+00 +AL450307.1 ENST00000341866 2.9332e-03 8.0565e-01 3.9200e-01 1.6910e+00 +GIMAP2 ENST00000223293 4.0527e-01 0.0000e+00 0.0000e+00 1.6910e+00 +ASB14 ENST00000487349 1.1236e-22 1.2543e+00 9.3700e-01 1.6910e+00 +CXCL9 ENST00000264888 2.9304e-03 8.0592e-01 3.9200e-01 1.6910e+00 +ZNF433 ENST00000344980 1.2227e-02 7.3161e-01 3.2800e-01 1.6910e+00 +RILP ENST00000301336 4.3414e-11 1.1190e+00 7.4700e-01 1.6910e+00 +ISG15 ENST00000379389 4.0527e-01 0.0000e+00 0.0000e+00 1.6910e+00 +ONECUT3 ENST00000382349 2.9219e-03 8.0673e-01 3.9300e-01 1.6920e+00 +AGXT2 ENST00000231420 3.7108e-28 1.2913e+00 9.9200e-01 1.6920e+00 +AP000350.4 ENST00000406213 4.0483e-01 0.0000e+00 0.0000e+00 1.6920e+00 +ZNF138 ENST00000440155 4.7594e-02 6.2579e-01 2.5000e-01 1.6920e+00 +THRSP ENST00000281030 2.9238e-03 8.0654e-01 3.9300e-01 1.6920e+00 +RAET1E ENST00000357183 2.3144e-07 1.0303e+00 6.3300e-01 1.6920e+00 +CTRC ENST00000375949 1.2851e-12 1.1459e+00 7.8200e-01 1.6920e+00 +PLAC9 ENST00000372263 2.9210e-03 8.0681e-01 3.9300e-01 1.6920e+00 +DEFB127 ENST00000382388 4.0494e-01 0.0000e+00 0.0000e+00 1.6920e+00 +C2orf72 ENST00000373640 1.6112e-01 4.4971e-01 1.5300e-01 1.6920e+00 +DUSP23 ENST00000368107 6.6600e-04 8.6375e-01 4.4700e-01 1.6920e+00 +HYAL4 ENST00000223026 3.0998e-17 1.2052e+00 8.6600e-01 1.6920e+00 +OR4B1 ENST00000309562 2.9268e-03 8.0626e-01 3.9300e-01 1.6920e+00 +FAM9B ENST00000327220 3.0570e-05 9.4710e-01 5.3500e-01 1.6930e+00 +ZNF880 ENST00000422689 2.9110e-03 8.0776e-01 3.9300e-01 1.6930e+00 +OR52W1 ENST00000311352 6.6442e-04 8.6431e-01 4.4800e-01 1.6930e+00 +ZNF439 ENST00000304030 1.2179e-02 7.3290e-01 3.2900e-01 1.6930e+00 +C1orf192 ENST00000367974 6.1884e-06 9.7905e-01 5.7200e-01 1.6930e+00 +RERGL ENST00000229002 2.4541e-10 1.1054e+00 7.2800e-01 1.6930e+00 +SELO ENST00000380903 5.1473e-18 1.2141e+00 8.7800e-01 1.6930e+00 +ICAM4 ENST00000340992 1.2077e-06 1.0071e+00 6.0400e-01 1.6930e+00 +NKG7 ENST00000221978 1.4538e-04 9.0960e-01 4.9400e-01 1.6930e+00 +NXF5 ENST00000537026 3.7443e-14 1.1687e+00 8.1400e-01 1.6930e+00 +ZNF593 ENST00000374266 6.6476e-04 8.6419e-01 4.4800e-01 1.6930e+00 +C3orf18 ENST00000357203 6.6265e-04 8.6495e-01 4.4800e-01 1.6940e+00 +RGR ENST00000359452 2.4228e-10 1.1067e+00 7.2900e-01 1.6940e+00 +MRPS6 ENST00000399312 6.6140e-04 8.6539e-01 4.4800e-01 1.6940e+00 +MRPS17 ENST00000285298 1.2147e-02 7.3378e-01 3.2900e-01 1.6940e+00 +PACRGL ENST00000503585 1.2636e-12 1.1474e+00 7.8300e-01 1.6940e+00 +ZNF90 ENST00000418063 2.9038e-03 8.0845e-01 3.9400e-01 1.6940e+00 +ISG20 ENST00000306072 2.8990e-03 8.0890e-01 3.9400e-01 1.6940e+00 +PTH ENST00000282091 1.2093e-02 7.3523e-01 3.3000e-01 1.6950e+00 +SAMD5 ENST00000367474 1.2095e-02 7.3520e-01 3.2900e-01 1.6950e+00 +AL645608.1 ENST00000598827 1.2096e-02 7.3515e-01 3.2900e-01 1.6950e+00 +L34079.2 ENST00000594374 2.8967e-03 8.0913e-01 3.9400e-01 1.6950e+00 +GOLGA6B ENST00000421285 1.2579e-12 1.1478e+00 7.8400e-01 1.6950e+00 +RP11-664I21.6 ENST00000524433 4.0392e-01 0.0000e+00 0.0000e+00 1.6950e+00 +C21orf58 ENST00000291691 1.2579e-12 1.1478e+00 7.8400e-01 1.6950e+00 +PATE3 ENST00000445202 4.7274e-02 6.2848e-01 2.5100e-01 1.6950e+00 +GATC ENST00000551765 6.5888e-04 8.6630e-01 4.4900e-01 1.6950e+00 +ABHD14B ENST00000483233 1.4378e-04 9.1187e-01 4.9600e-01 1.6950e+00 +SERPINA10 ENST00000393096 4.1522e-11 1.1231e+00 7.4900e-01 1.6960e+00 +TLCD2 ENST00000330676 6.0895e-06 9.8159e-01 5.7300e-01 1.6960e+00 +GIMAP1 ENST00000307194 4.0351e-01 0.0000e+00 0.0000e+00 1.6960e+00 +MMP27 ENST00000260229 6.3444e-22 1.2520e+00 9.3100e-01 1.6960e+00 +FKBP7 ENST00000424785 4.1828e-08 1.0550e+00 6.6200e-01 1.6960e+00 +PCP2 ENST00000311069 3.0021e-05 9.5033e-01 5.3700e-01 1.6960e+00 +MUC3A ENST00000379458 4.0349e-01 0.0000e+00 0.0000e+00 1.6960e+00 +EIF3CL ENST00000398943 1.2059e-02 7.3618e-01 3.3000e-01 1.6960e+00 +CBR4 ENST00000306193 6.0745e-06 9.8198e-01 5.7300e-01 1.6960e+00 +CEACAM21 ENST00000401445 1.2439e-12 1.1487e+00 7.8400e-01 1.6960e+00 +ZNF561 ENST00000302851 3.0091e-05 9.4991e-01 5.3700e-01 1.6960e+00 +PAQR4 ENST00000318782 1.1796e-06 1.0104e+00 6.0600e-01 1.6970e+00 +COX18 ENST00000295890 6.0435e-15 1.1829e+00 8.3100e-01 1.6970e+00 +C19orf25 ENST00000436106 4.0313e-01 0.0000e+00 0.0000e+00 1.6970e+00 +CYSLTR1 ENST00000373304 1.2030e-02 7.3696e-01 3.3000e-01 1.6970e+00 +ASAH2B ENST00000374006 1.5960e-01 4.5435e-01 1.5400e-01 1.6970e+00 +DAO ENST00000228476 6.2271e-22 1.2531e+00 9.3200e-01 1.6970e+00 +NTF4 ENST00000301411 1.2031e-02 7.3694e-01 3.3000e-01 1.6970e+00 +AC040977.1 ENST00000593646 4.7001e-02 6.3080e-01 2.5200e-01 1.6970e+00 +SLC38A11 ENST00000409149 6.0327e-15 1.1830e+00 8.3100e-01 1.6970e+00 +OOEP ENST00000370359 1.4291e-04 9.1310e-01 4.9600e-01 1.6970e+00 +ANKRD60 ENST00000457363 2.9807e-05 9.5161e-01 5.3800e-01 1.6980e+00 +MT1F ENST00000334350 4.6878e-02 6.3186e-01 2.5200e-01 1.6980e+00 +RXFP4 ENST00000368318 6.0080e-06 9.8372e-01 5.7400e-01 1.6980e+00 +CTB-167G5.5 ENST00000600193 2.8638e-03 8.1231e-01 3.9500e-01 1.6980e+00 +CD52 ENST00000374213 4.0282e-01 0.0000e+00 0.0000e+00 1.6980e+00 +C5AR1 ENST00000355085 4.0249e-01 0.0000e+00 0.0000e+00 1.6980e+00 +ELP5 ENST00000396628 2.0780e-13 1.1624e+00 8.0200e-01 1.6980e+00 +AP000889.3 ENST00000600612 6.5002e-04 8.6952e-01 4.5000e-01 1.6990e+00 +TRIM49C ENST00000448984 1.4152e-04 9.1511e-01 4.9700e-01 1.6990e+00 +ZNF140 ENST00000355557 1.1679e-06 1.0119e+00 6.0700e-01 1.6990e+00 +C1orf168 ENST00000343433 1.3041e-41 1.3571e+00 1.0900e+00 1.6990e+00 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4.5100e-01 1.7010e+00 +MSR1 ENST00000262101 2.1571e-20 1.2429e+00 9.1500e-01 1.7010e+00 +C16orf89 ENST00000315997 1.6287e-16 1.2055e+00 8.6000e-01 1.7020e+00 +C5orf48 ENST00000357147 6.4286e-04 8.7217e-01 4.5100e-01 1.7020e+00 +DNAL4 ENST00000216068 2.8273e-03 8.1592e-01 3.9700e-01 1.7020e+00 +MVD ENST00000301012 2.7438e-17 1.2138e+00 8.7200e-01 1.7020e+00 +COX6B2 ENST00000593184 6.4242e-04 8.7233e-01 4.5200e-01 1.7020e+00 +PSKH2 ENST00000276616 7.2081e-09 1.0802e+00 6.9000e-01 1.7020e+00 +XAF1 ENST00000361842 6.8151e-12 1.1415e+00 7.7100e-01 1.7020e+00 +PTPLA ENST00000361271 1.2914e-09 1.0971e+00 7.1200e-01 1.7020e+00 +AP000758.1 ENST00000595283 4.0102e-01 0.0000e+00 0.0000e+00 1.7020e+00 +GRXCR1 ENST00000399770 3.9439e-11 1.1280e+00 7.5300e-01 1.7020e+00 +SDPR ENST00000304141 7.2412e-09 1.0797e+00 6.8900e-01 1.7020e+00 +MRPL52 ENST00000355151 2.1598e-07 1.0392e+00 6.3800e-01 1.7020e+00 +PTRH2 ENST00000470557 6.3822e-04 8.7390e-01 4.5200e-01 1.7030e+00 +MOB3A ENST00000357066 2.9101e-05 9.5591e-01 5.4000e-01 1.7030e+00 +C5orf58 ENST00000521850 4.6419e-02 6.3583e-01 2.5300e-01 1.7030e+00 +COMT ENST00000361682 1.1377e-06 1.0156e+00 6.0900e-01 1.7030e+00 +CMC4 ENST00000369484 1.5810e-01 4.5910e-01 1.5600e-01 1.7030e+00 +RP13-512J5.1 ENST00000438485 1.5818e-01 4.5883e-01 1.5600e-01 1.7030e+00 +CNBD1 ENST00000518476 4.4866e-18 1.2234e+00 8.8400e-01 1.7040e+00 +PPY ENST00000591228 1.1810e-02 7.4313e-01 3.3300e-01 1.7040e+00 +GKN1 ENST00000377938 1.1309e-06 1.0165e+00 6.1000e-01 1.7040e+00 +C5orf49 ENST00000399810 1.1792e-02 7.4365e-01 3.3300e-01 1.7040e+00 +C22orf34 ENST00000400023 1.3821e-04 9.1999e-01 5.0000e-01 1.7040e+00 +RP4-758J18.2 ENST00000448629 1.1799e-02 7.4345e-01 3.3300e-01 1.7040e+00 +MTHFSD ENST00000360900 6.5987e-12 1.1444e+00 7.7300e-01 1.7050e+00 +C2orf68 ENST00000306336 5.7612e-06 9.9040e-01 5.7800e-01 1.7050e+00 +C18orf56 ENST00000323813 1.5771e-01 4.6035e-01 1.5600e-01 1.7050e+00 +AGMO ENST00000342526 6.7791e-26 1.2877e+00 9.7800e-01 1.7050e+00 +CSN3 ENST00000304954 1.1763e-02 7.4449e-01 3.3300e-01 1.7050e+00 +PKIB ENST00000258014 4.6118e-02 6.3849e-01 2.5400e-01 1.7050e+00 +PYY ENST00000360085 1.1784e-02 7.4389e-01 3.3300e-01 1.7050e+00 +NKG2-E ENST00000539033 2.1937e-10 1.1165e+00 7.3500e-01 1.7050e+00 +TCTEX1D4 ENST00000372200 1.1783e-02 7.4390e-01 3.3300e-01 1.7050e+00 +APITD1 ENST00000602787 5.7500e-06 9.9071e-01 5.7800e-01 1.7060e+00 +APITD1-CORT ENST00000400900 5.7500e-06 9.9071e-01 5.7800e-01 1.7060e+00 +RCN3 ENST00000270645 3.8085e-11 1.1313e+00 7.5500e-01 1.7060e+00 +THEM6 ENST00000336138 4.6080e-02 6.3882e-01 2.5500e-01 1.7060e+00 +CPLX4 ENST00000299721 1.3620e-04 9.2302e-01 5.0100e-01 1.7070e+00 +GPR15 ENST00000284311 1.1106e-06 1.0191e+00 6.1100e-01 1.7070e+00 +OR2A14 ENST00000408899 1.3677e-04 9.2216e-01 5.0100e-01 1.7070e+00 +NKX1-2 ENST00000451024 2.7809e-03 8.2060e-01 3.9900e-01 1.7070e+00 +MZT1 ENST00000377818 4.5971e-02 6.3980e-01 2.5500e-01 1.7070e+00 +ZNF549 ENST00000376233 2.7791e-03 8.2079e-01 3.9900e-01 1.7070e+00 +GPR55 ENST00000392040 2.8503e-05 9.5966e-01 5.4200e-01 1.7070e+00 +ZNF700 ENST00000254321 2.7684e-03 8.2188e-01 4.0000e-01 1.7080e+00 +PLA2G7 ENST00000274793 5.3314e-22 1.2624e+00 9.3900e-01 1.7080e+00 +PRSS57 ENST00000329267 2.8309e-05 9.6089e-01 5.4300e-01 1.7080e+00 +SPAG16 ENST00000331683 1.4037e-34 1.3367e+00 1.0520e+00 1.7080e+00 +LIPT1 ENST00000393477 3.8254e-08 1.0657e+00 6.6800e-01 1.7080e+00 +XXcos-LUCA11.5 ENST00000606589 1.5663e-01 4.6383e-01 1.5700e-01 1.7090e+00 +HIST1H1D ENST00000244534 1.5610e-01 4.6559e-01 1.5800e-01 1.7100e+00 +ACTRT3 ENST00000330368 3.7565e-08 1.0679e+00 6.6900e-01 1.7100e+00 +CSNK2A3 ENST00000528848 2.1007e-10 1.1209e+00 7.3800e-01 1.7100e+00 +C16orf13 ENST00000397666 2.7974e-05 9.6306e-01 5.4400e-01 1.7100e+00 +GALR3 ENST00000249041 1.3455e-04 9.2556e-01 5.0300e-01 1.7100e+00 +WFDC11 ENST00000356562 2.7408e-03 8.2474e-01 4.0100e-01 1.7110e+00 +GAST ENST00000329402 2.7394e-03 8.2489e-01 4.0100e-01 1.7110e+00 +NEURL2 ENST00000372518 1.3395e-04 9.2650e-01 5.0300e-01 1.7110e+00 +CIDEA ENST00000320477 5.5761e-06 9.9564e-01 5.8100e-01 1.7110e+00 +AC005609.1 ENST00000502505 1.1550e-02 7.5066e-01 3.3600e-01 1.7110e+00 +TSSK1B ENST00000390666 1.3409e-04 9.2629e-01 5.0300e-01 1.7110e+00 +EFCAB4A ENST00000450448 3.6358e-11 1.1357e+00 7.5800e-01 1.7110e+00 +SPACA5 ENST00000304355 3.9716e-01 0.0000e+00 0.0000e+00 1.7120e+00 +CRYBB3 ENST00000215855 3.5766e-11 1.1373e+00 7.5900e-01 1.7120e+00 +GNA14 ENST00000341700 2.4256e-17 1.2225e+00 8.7800e-01 1.7120e+00 +GNG4 ENST00000391854 1.5575e-01 4.6675e-01 1.5800e-01 1.7120e+00 +RHBDD1 ENST00000392062 1.0582e-12 1.1628e+00 7.9400e-01 1.7120e+00 +IZUMO4 ENST00000395301 3.0023e-14 1.1865e+00 8.2600e-01 1.7130e+00 +AC132216.1 ENST00000330381 4.5338e-02 6.4553e-01 2.5700e-01 1.7130e+00 +HOXB13 ENST00000290295 3.6879e-08 1.0702e+00 6.7100e-01 1.7130e+00 +TMEM256 ENST00000302422 6.1452e-04 8.8306e-01 4.5700e-01 1.7130e+00 +IQCG ENST00000265239 3.0220e-21 1.2600e+00 9.3200e-01 1.7130e+00 +SLC16A13 ENST00000308027 3.5696e-11 1.1375e+00 7.5900e-01 1.7130e+00 +GTF2H5 ENST00000607778 4.5238e-02 6.4645e-01 2.5700e-01 1.7140e+00 +SMIM15 ENST00000339020 1.5518e-01 4.6867e-01 1.5800e-01 1.7140e+00 +CSN1S1 ENST00000246891 1.4185e-16 1.2156e+00 8.6700e-01 1.7140e+00 +GLYAT ENST00000344743 3.6418e-08 1.0717e+00 6.7200e-01 1.7140e+00 +PDZK1 ENST00000344770 1.1586e-09 1.1086e+00 7.1900e-01 1.7140e+00 +NDUFA6 ENST00000498737 1.3244e-04 9.2886e-01 5.0400e-01 1.7140e+00 +DEFB128 ENST00000334391 3.9598e-01 0.0000e+00 0.0000e+00 1.7150e+00 +LRRC3 ENST00000291592 2.7024e-03 8.2879e-01 4.0300e-01 1.7150e+00 +IL31 ENST00000377035 1.1445e-02 7.5379e-01 3.3700e-01 1.7150e+00 +C6orf100 ENST00000377186 3.9610e-01 0.0000e+00 0.0000e+00 1.7150e+00 +PTGDR2 ENST00000332539 2.7025e-03 8.2878e-01 4.0300e-01 1.7150e+00 +TCN1 ENST00000257264 2.3229e-17 1.2256e+00 8.8000e-01 1.7150e+00 +FADS6 ENST00000310226 1.1478e-09 1.1096e+00 7.2000e-01 1.7150e+00 +WFDC1 ENST00000219454 3.4678e-11 1.1403e+00 7.6100e-01 1.7160e+00 +C14orf64 ENST00000499006 2.6919e-03 8.2991e-01 4.0300e-01 1.7160e+00 +TRIM52 ENST00000327767 1.1417e-09 1.1101e+00 7.2000e-01 1.7160e+00 +OR8H3 ENST00000313472 1.1400e-02 7.5514e-01 3.3800e-01 1.7160e+00 +RARRES2 ENST00000466675 2.7160e-05 9.6845e-01 5.4700e-01 1.7160e+00 +ADM5 ENST00000420022 3.9555e-01 0.0000e+00 0.0000e+00 1.7160e+00 +C3orf65 ENST00000296270 3.9559e-01 0.0000e+00 0.0000e+00 1.7160e+00 +LCN2 ENST00000373017 1.1404e-09 1.1103e+00 7.2000e-01 1.7160e+00 +ZNF814 ENST00000435989 4.4817e-02 6.5037e-01 2.5900e-01 1.7170e+00 +TREML2 ENST00000483722 1.1362e-09 1.1107e+00 7.2100e-01 1.7170e+00 +LRRC10B ENST00000378075 4.4884e-02 6.4974e-01 2.5800e-01 1.7170e+00 +ZNF117 ENST00000282869 3.9531e-01 0.0000e+00 0.0000e+00 1.7170e+00 +MBL2 ENST00000373968 2.6836e-03 8.3080e-01 4.0400e-01 1.7170e+00 +ANKRD22 ENST00000371930 1.1192e-09 1.1123e+00 7.2200e-01 1.7180e+00 +CCDC107 ENST00000426546 6.3474e-09 1.0946e+00 6.9900e-01 1.7180e+00 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7.0000e-01 1.7200e+00 +TSSC4 ENST00000333256 4.4493e-02 6.5344e-01 2.6000e-01 1.7200e+00 +WFDC12 ENST00000372785 4.4550e-02 6.5290e-01 2.6000e-01 1.7200e+00 +MORN2 ENST00000410014 1.5342e-01 4.7467e-01 1.6000e-01 1.7200e+00 +RGPD3 ENST00000409886 1.4598e-50 1.4016e+00 1.1470e+00 1.7200e+00 +SCRG1 ENST00000296506 4.4451e-02 6.5384e-01 2.6000e-01 1.7210e+00 +XRCC3 ENST00000553264 1.9134e-10 1.1303e+00 7.4400e-01 1.7210e+00 +LEFTY1 ENST00000272134 9.6756e-13 1.1707e+00 7.9900e-01 1.7210e+00 +HCFC1R1 ENST00000248089 5.9302e-04 8.9179e-01 4.6100e-01 1.7220e+00 +OR5AK2 ENST00000326855 5.9331e-04 8.9167e-01 4.6100e-01 1.7220e+00 +MRPS34 ENST00000397375 2.6375e-03 8.3583e-01 4.0600e-01 1.7220e+00 +ACN9 ENST00000432641 2.6353e-03 8.3608e-01 4.0600e-01 1.7220e+00 +SSX4B ENST00000376884 1.5282e-01 4.7678e-01 1.6100e-01 1.7220e+00 +MAGEC3 ENST00000298296 7.6566e-16 1.2143e+00 8.5900e-01 1.7220e+00 +AMY2B ENST00000361355 5.8844e-30 1.3259e+00 1.0250e+00 1.7230e+00 +C21orf62 ENST00000536776 2.6248e-03 8.3724e-01 4.0700e-01 1.7230e+00 +OR2AE1 ENST00000316368 1.1172e-02 7.6215e-01 3.4100e-01 1.7230e+00 +PRR4 ENST00000228811 4.4222e-02 6.5605e-01 2.6100e-01 1.7230e+00 +HES2 ENST00000377834 2.6323e-03 8.3641e-01 4.0600e-01 1.7230e+00 +SLX1B ENST00000330181 4.4220e-02 6.5606e-01 2.6100e-01 1.7230e+00 +PROX2 ENST00000556084 5.5007e-12 1.1612e+00 7.8400e-01 1.7240e+00 +RGPD6 ENST00000329516 3.9245e-01 0.0000e+00 0.0000e+00 1.7240e+00 +SURF1 ENST00000371974 1.5883e-13 1.1851e+00 8.1700e-01 1.7240e+00 +C12orf71 ENST00000429849 2.6210e-03 8.3766e-01 4.0700e-01 1.7240e+00 +RP11-47I22.3 ENST00000556569 4.4082e-02 6.5740e-01 2.6100e-01 1.7240e+00 +CBWD6 ENST00000377457 9.8278e-07 1.0369e+00 6.2200e-01 1.7250e+00 +RP11-944C7.1 ENST00000550332 1.5197e-01 4.7978e-01 1.6200e-01 1.7250e+00 +APOL1 ENST00000319136 5.1357e-06 1.0090e+00 5.8800e-01 1.7250e+00 +NUDT16L1 ENST00000304301 1.2536e-04 9.4049e-01 5.1000e-01 1.7250e+00 +AP003774.4 ENST00000316124 3.9183e-01 0.0000e+00 0.0000e+00 1.7250e+00 +HSD17B2 ENST00000199936 1.8462e-10 1.1340e+00 7.4600e-01 1.7250e+00 +SSSCA1 ENST00000309328 1.8426e-07 1.0603e+00 6.5100e-01 1.7250e+00 +TEX13B ENST00000302917 1.1098e-02 7.6447e-01 3.4200e-01 1.7250e+00 +ZNF121 ENST00000320451 3.9211e-01 0.0000e+00 0.0000e+00 1.7250e+00 +FAM136A ENST00000037869 5.8595e-04 8.9476e-01 4.6200e-01 1.7250e+00 +SPANXN1 ENST00000370493 3.9191e-01 0.0000e+00 0.0000e+00 1.7250e+00 +LRRC14B ENST00000328278 1.0572e-09 1.1185e+00 7.2500e-01 1.7250e+00 +RD3 ENST00000367002 2.5702e-05 9.7863e-01 5.5200e-01 1.7260e+00 +UCN3 ENST00000380433 4.3878e-02 6.5939e-01 2.6200e-01 1.7260e+00 +S100B ENST00000291700 4.3870e-02 6.5948e-01 2.6200e-01 1.7260e+00 +SMR3A ENST00000226460 3.9147e-01 0.0000e+00 0.0000e+00 1.7260e+00 +VAMP5 ENST00000306384 1.1061e-02 7.6565e-01 3.4200e-01 1.7260e+00 +DNAJC4 ENST00000321685 1.8113e-10 1.1360e+00 7.4800e-01 1.7270e+00 +STOML3 ENST00000379631 2.5754e-14 1.1991e+00 8.3400e-01 1.7270e+00 +C9orf173 ENST00000388931 9.1242e-13 1.1759e+00 8.0300e-01 1.7270e+00 +TXN2 ENST00000216185 2.5584e-05 9.7949e-01 5.5300e-01 1.7270e+00 +C14orf79 ENST00000547315 5.3599e-12 1.1636e+00 7.8500e-01 1.7270e+00 +LYZL1 ENST00000375500 9.7227e-07 1.0385e+00 6.2200e-01 1.7270e+00 +IL17C ENST00000244241 1.2430e-04 9.4229e-01 5.1100e-01 1.7270e+00 +TMSB15A ENST00000289373 3.9053e-01 0.0000e+00 0.0000e+00 1.7280e+00 +SAPCD1 ENST00000415669 1.8051e-07 1.0630e+00 6.5200e-01 1.7280e+00 +DYNAP ENST00000321600 2.5806e-03 8.4222e-01 4.0900e-01 1.7280e+00 +SAC3D1 ENST00000398846 5.7480e-04 8.9954e-01 4.6500e-01 1.7290e+00 +CD1E ENST00000368167 3.2556e-18 1.2458e+00 9.0000e-01 1.7290e+00 +AC092675.3 ENST00000409490 1.0944e-02 7.6942e-01 3.4400e-01 1.7290e+00 +AC026407.1 ENST00000599823 1.5094e-01 4.8346e-01 1.6300e-01 1.7290e+00 +CDC42EP1 ENST00000249014 2.5355e-05 9.8117e-01 5.5400e-01 1.7290e+00 +IL37 ENST00000263326 1.2343e-04 9.4380e-01 5.1200e-01 1.7290e+00 +ZNF124 ENST00000340684 1.0911e-02 7.7046e-01 3.4400e-01 1.7300e+00 +IZUMO3 ENST00000543880 3.0367e-11 1.1533e+00 7.6900e-01 1.7300e+00 +PROZ ENST00000342783 1.1759e-16 1.2296e+00 8.7700e-01 1.7300e+00 +MRPS10 ENST00000053468 1.0138e-09 1.1230e+00 7.2800e-01 1.7300e+00 +CCDC96 ENST00000310085 1.9555e-17 1.2381e+00 8.8900e-01 1.7300e+00 +SLC22A18AS ENST00000533594 2.5627e-03 8.4428e-01 4.1000e-01 1.7300e+00 +AC009365.3 ENST00000332558 1.5063e-01 4.8462e-01 1.6300e-01 1.7300e+00 +SLC7A13 ENST00000297524 1.4830e-13 1.1910e+00 8.2100e-01 1.7300e+00 +POLR3G ENST00000399107 1.7611e-10 1.1389e+00 7.5000e-01 1.7300e+00 +VIPR1 ENST00000325123 7.4401e-27 1.3142e+00 1.0020e+00 1.7300e+00 +OR13G1 ENST00000359688 1.5033e-01 4.8573e-01 1.6300e-01 1.7310e+00 +PHLDA2 ENST00000314222 1.5046e-01 4.8522e-01 1.6300e-01 1.7310e+00 +DEPDC4 ENST00000416321 1.0075e-09 1.1237e+00 7.2900e-01 1.7310e+00 +KLRG2 ENST00000340940 5.1131e-12 1.1680e+00 7.8800e-01 1.7310e+00 +OR11A1 ENST00000377149 2.5494e-03 8.4582e-01 4.1100e-01 1.7320e+00 +RP11-180C1.1 ENST00000507759 1.5002e-01 4.8685e-01 1.6400e-01 1.7320e+00 +ART1 ENST00000250693 5.1026e-12 1.1682e+00 7.8800e-01 1.7320e+00 +C20orf141 ENST00000380589 4.3255e-02 6.6560e-01 2.6400e-01 1.7320e+00 +CHST13 ENST00000319340 1.2130e-04 9.4754e-01 5.1400e-01 1.7320e+00 +MRFAP1L1 ENST00000320848 2.5481e-03 8.4597e-01 4.1100e-01 1.7320e+00 +GRP ENST00000256857 2.5347e-03 8.4753e-01 4.1100e-01 1.7330e+00 +MS4A2 ENST00000278888 5.6048e-09 1.1090e+00 7.0800e-01 1.7330e+00 +KIR3DL3 ENST00000291860 1.2102e-04 9.4803e-01 5.1400e-01 1.7330e+00 +MFSD7 ENST00000322224 3.0952e-18 1.2494e+00 9.0300e-01 1.7330e+00 +SYCE1L ENST00000378644 2.4274e-14 1.2041e+00 8.3800e-01 1.7330e+00 +PF4 ENST00000296029 4.3062e-02 6.6756e-01 2.6500e-01 1.7330e+00 +RP11-661C8.3 ENST00000511936 3.8843e-01 0.0000e+00 0.0000e+00 1.7330e+00 +TMSB15B ENST00000436583 3.8882e-01 0.0000e+00 0.0000e+00 1.7330e+00 +UGT2B15 ENST00000338206 2.2864e-21 1.2777e+00 9.4500e-01 1.7330e+00 +PROL1 ENST00000399575 3.8851e-01 0.0000e+00 0.0000e+00 1.7330e+00 +C22orf24 ENST00000248984 1.4945e-01 4.8896e-01 1.6400e-01 1.7340e+00 +OR5W2 ENST00000344514 5.6247e-04 9.0498e-01 4.6700e-01 1.7340e+00 +DHRS1 ENST00000288111 3.9562e-15 1.2164e+00 8.5400e-01 1.7350e+00 +BCL2L10 ENST00000260442 1.0760e-02 7.7544e-01 3.4600e-01 1.7350e+00 +RFPL4A ENST00000434937 4.2929e-02 6.6892e-01 2.6500e-01 1.7350e+00 +PAEP ENST00000479141 3.1109e-08 1.0913e+00 6.8400e-01 1.7350e+00 +C12orf77 ENST00000549828 5.5995e-04 9.0611e-01 4.6800e-01 1.7350e+00 +OR56A1 ENST00000316650 5.5987e-04 9.0615e-01 4.6800e-01 1.7350e+00 +RPRM ENST00000325926 1.4925e-01 4.8972e-01 1.6400e-01 1.7350e+00 +C11orf94 ENST00000449465 4.2904e-02 6.6917e-01 2.6500e-01 1.7350e+00 +PPAPDC2 ENST00000381883 5.6067e-04 9.0579e-01 4.6800e-01 1.7350e+00 +FAM86B2 ENST00000262365 4.8114e-06 1.0198e+00 5.9400e-01 1.7360e+00 +PLA2G2E ENST00000375116 2.4363e-05 9.8866e-01 5.5800e-01 1.7360e+00 +NEIL2 ENST00000284503 2.8655e-11 1.1590e+00 7.7300e-01 1.7360e+00 +TACR3 ENST00000304883 1.8068e-17 1.2439e+00 8.9300e-01 1.7360e+00 +PATE2 ENST00000358524 5.5790e-04 9.0704e-01 4.6800e-01 1.7360e+00 +TUSC1 ENST00000358022 4.2737e-02 6.7090e-01 2.6600e-01 1.7360e+00 +TMEM158 ENST00000503771 1.4862e-01 4.9210e-01 1.6500e-01 1.7370e+00 +AC092964.1 ENST00000366261 3.8696e-01 0.0000e+00 0.0000e+00 1.7370e+00 +AC007204.1 ENST00000595282 1.4865e-01 4.9198e-01 1.6500e-01 1.7370e+00 +ASGR1 ENST00000269299 3.8718e-15 1.2182e+00 8.5500e-01 1.7370e+00 +LACRT ENST00000257867 1.1870e-04 9.5221e-01 5.1600e-01 1.7370e+00 +APH1B ENST00000261879 2.8377e-11 1.1600e+00 7.7300e-01 1.7370e+00 +UCP3 ENST00000314032 9.5517e-10 1.1296e+00 7.3200e-01 1.7370e+00 +HIST1H4J ENST00000355057 3.8683e-01 0.0000e+00 0.0000e+00 1.7370e+00 +ECHDC3 ENST00000379215 4.7572e-06 1.0217e+00 5.9500e-01 1.7370e+00 +RETNLB ENST00000295755 4.2650e-02 6.7180e-01 2.6600e-01 1.7370e+00 +IFI27 ENST00000555744 1.0698e-02 7.7752e-01 3.4700e-01 1.7370e+00 +MIIP ENST00000235332 1.3121e-20 1.2749e+00 9.3800e-01 1.7370e+00 +KRTAP10-4 ENST00000400374 8.1939e-13 1.1857e+00 8.0900e-01 1.7370e+00 +OR52D1 ENST00000322641 5.5635e-04 9.0775e-01 4.6900e-01 1.7370e+00 +SMR3B ENST00000304915 3.8712e-01 0.0000e+00 0.0000e+00 1.7370e+00 +LYPD1 ENST00000397463 5.5354e-04 9.0903e-01 4.6900e-01 1.7380e+00 +PSORS1C2 ENST00000259845 2.4913e-03 8.5270e-01 4.1400e-01 1.7380e+00 +LSM2 ENST00000375661 2.4045e-05 9.9114e-01 5.5900e-01 1.7380e+00 +IL36G ENST00000259205 1.1765e-04 9.5414e-01 5.1700e-01 1.7380e+00 +OST4 ENST00000456793 3.8665e-01 0.0000e+00 0.0000e+00 1.7380e+00 +SPATA6L ENST00000475086 1.0446e-16 1.2386e+00 8.8300e-01 1.7390e+00 +POTEB2 ENST00000454856 4.2457e-02 6.7382e-01 2.6700e-01 1.7390e+00 +ZNF229 ENST00000588931 8.9514e-07 1.0508e+00 6.3000e-01 1.7390e+00 +NTN5 ENST00000270235 3.7923e-15 1.2199e+00 8.5600e-01 1.7390e+00 +CRCP ENST00000395326 8.9725e-07 1.0505e+00 6.2900e-01 1.7390e+00 +RP11-497E19.2 ENST00000553678 1.4816e-01 4.9384e-01 1.6600e-01 1.7390e+00 +GJB4 ENST00000339480 5.5114e-04 9.1013e-01 4.7000e-01 1.7390e+00 +GJB6 ENST00000356192 1.6580e-07 1.0746e+00 6.5900e-01 1.7390e+00 +C2orf50 ENST00000381585 1.1749e-04 9.5443e-01 5.1800e-01 1.7390e+00 +ATG12 ENST00000509910 4.6926e-06 1.0240e+00 5.9700e-01 1.7400e+00 +RP11-343C2.9 ENST00000563634 2.3766e-05 9.9335e-01 5.6000e-01 1.7400e+00 +AC114783.1 ENST00000450035 8.9231e-07 1.0513e+00 6.3000e-01 1.7400e+00 +HYI ENST00000372425 2.2375e-14 1.2110e+00 8.4200e-01 1.7400e+00 +APOLD1 ENST00000326765 1.1689e-04 9.5556e-01 5.1800e-01 1.7400e+00 +FBXO36 ENST00000283946 8.9256e-07 1.0513e+00 6.3000e-01 1.7400e+00 +AC004076.7 ENST00000597410 3.8582e-01 0.0000e+00 0.0000e+00 1.7400e+00 +HTN1 ENST00000511674 4.2320e-02 6.7527e-01 2.6700e-01 1.7400e+00 +TMED5 ENST00000370282 5.2721e-09 1.1162e+00 7.1200e-01 1.7410e+00 +OR1A1 ENST00000304094 1.1603e-04 9.5716e-01 5.1900e-01 1.7410e+00 +RP11-166B2.1 ENST00000399147 2.9717e-08 1.0971e+00 6.8700e-01 1.7410e+00 +H2BFWT ENST00000217926 2.4619e-03 8.5626e-01 4.1500e-01 1.7410e+00 +NPPA ENST00000376480 5.4522e-04 9.1288e-01 4.7100e-01 1.7410e+00 +SENP8 ENST00000544411 5.4686e-04 9.1211e-01 4.7100e-01 1.7410e+00 +AC002472.13 ENST00000342608 6.2030e-16 1.2308e+00 8.7100e-01 1.7410e+00 +OR5C1 ENST00000373680 1.1562e-04 9.5794e-01 5.1900e-01 1.7420e+00 +OR6N1 ENST00000335094 1.1560e-04 9.5798e-01 5.1900e-01 1.7420e+00 +SULT1A4 ENST00000395400 3.8477e-01 0.0000e+00 0.0000e+00 1.7420e+00 +C11orf35 ENST00000329451 3.7854e-26 1.3197e+00 1.0030e+00 1.7420e+00 +LENG1 ENST00000222224 1.5816e-10 1.1502e+00 7.5700e-01 1.7420e+00 +SLCO1B7 ENST00000421593 3.8127e-26 1.3193e+00 1.0020e+00 1.7420e+00 +UGT1A10 ENST00000344644 4.5886e-19 1.2646e+00 9.2000e-01 1.7420e+00 +APIP ENST00000395787 2.6927e-11 1.1652e+00 7.7700e-01 1.7420e+00 +CTD-2203A3.1 ENST00000510583 1.4738e-01 4.9685e-01 1.6600e-01 1.7420e+00 +CEBPZ-AS1 ENST00000402297 1.0510e-02 7.8393e-01 3.4900e-01 1.7420e+00 +PPP1R1C ENST00000280295 2.3484e-05 9.9562e-01 5.6100e-01 1.7420e+00 +OR10H2 ENST00000305899 2.4515e-03 8.5755e-01 4.1600e-01 1.7420e+00 +CNTF ENST00000361987 2.3384e-05 9.9643e-01 5.6200e-01 1.7430e+00 +ZFP2 ENST00000361362 1.6618e-17 1.2501e+00 8.9700e-01 1.7430e+00 +SMIM2 ENST00000400419 4.1965e-02 6.7905e-01 2.6900e-01 1.7430e+00 +RP11-171N4.2 ENST00000511399 1.4697e-01 4.9849e-01 1.6700e-01 1.7430e+00 +ODF3L1 ENST00000332145 1.5657e-10 1.1512e+00 7.5700e-01 1.7430e+00 +SPATA31A2 ENST00000456183 3.8423e-01 0.0000e+00 0.0000e+00 1.7430e+00 +C8orf86 ENST00000358138 2.3242e-05 9.9759e-01 5.6300e-01 1.7440e+00 +CTF1 ENST00000279804 4.1899e-02 6.7977e-01 2.6900e-01 1.7440e+00 +MYADML2 ENST00000409745 1.1436e-04 9.6033e-01 5.2100e-01 1.7440e+00 +AC002365.1 ENST00000445307 2.3223e-05 9.9775e-01 5.6300e-01 1.7440e+00 +AC008686.1 ENST00000397557 4.1904e-02 6.7971e-01 2.6900e-01 1.7440e+00 +RP11-451M19.3 ENST00000369655 1.0446e-02 7.8618e-01 3.5000e-01 1.7440e+00 +ATXN7L3B ENST00000519948 1.4683e-01 4.9904e-01 1.6700e-01 1.7440e+00 +GSTO1 ENST00000369713 5.0916e-09 1.1204e+00 7.1500e-01 1.7450e+00 +PCDHB13 ENST00000341948 4.4828e-12 1.1806e+00 7.9700e-01 1.7450e+00 +RP11-706O15.1 ENST00000425492 1.4637e-01 5.0085e-01 1.6800e-01 1.7450e+00 +OSTN ENST00000339051 5.3727e-04 9.1663e-01 4.7300e-01 1.7450e+00 +GGTLC2 ENST00000480559 2.3206e-05 9.9789e-01 5.6300e-01 1.7450e+00 +AC093802.1 ENST00000407524 4.1827e-02 6.8054e-01 2.6900e-01 1.7450e+00 +MROH5 ENST00000521161 1.0417e-02 7.8720e-01 3.5100e-01 1.7450e+00 +CLC ENST00000221804 2.3026e-05 9.9938e-01 5.6300e-01 1.7460e+00 +ZNF222 ENST00000391960 5.3339e-04 9.1849e-01 4.7400e-01 1.7460e+00 +TRAPPC2 ENST00000458511 2.4140e-03 8.6222e-01 4.1800e-01 1.7460e+00 +TMEM27 ENST00000380342 1.1309e-04 9.6279e-01 5.2200e-01 1.7460e+00 +CD70 ENST00000245903 1.0394e-02 7.8799e-01 3.5100e-01 1.7460e+00 +CLDN23 ENST00000519106 2.2989e-05 9.9968e-01 5.6400e-01 1.7460e+00 +RP11-362K2.2 ENST00000546977 4.1623e-02 6.8276e-01 2.7000e-01 1.7460e+00 +SPANXN3 ENST00000370503 3.8315e-01 0.0000e+00 0.0000e+00 1.7460e+00 +LINC00998 ENST00000397764 3.8247e-01 0.0000e+00 0.0000e+00 1.7470e+00 +RESP18 ENST00000333527 8.7160e-10 1.1398e+00 7.3900e-01 1.7470e+00 +SIRPG ENST00000303415 3.4760e-15 1.2270e+00 8.6100e-01 1.7470e+00 +GLIPR1 ENST00000266659 2.0720e-14 1.2175e+00 8.4700e-01 1.7470e+00 +TMPRSS11B ENST00000332644 4.2885e-19 1.2694e+00 9.2300e-01 1.7470e+00 +TMEM37 ENST00000306406 2.3933e-03 8.6486e-01 4.1900e-01 1.7480e+00 +LILRA2 ENST00000251377 6.9073e-20 1.2779e+00 9.3500e-01 1.7480e+00 +C3orf55 ENST00000449199 2.3940e-03 8.6477e-01 4.1900e-01 1.7480e+00 +CCL8 ENST00000394620 4.1412e-02 6.8508e-01 2.7100e-01 1.7480e+00 +THAP2 ENST00000308086 1.5504e-07 1.0839e+00 6.6500e-01 1.7480e+00 +TMA7 ENST00000438607 2.3931e-03 8.6489e-01 4.1900e-01 1.7480e+00 +LGALS7 ENST00000378626 1.4567e-01 5.0365e-01 1.6800e-01 1.7480e+00 +OR2F1 ENST00000392899 2.2802e-05 1.0013e+00 5.6400e-01 1.7480e+00 +PSPN ENST00000245810 1.1172e-04 9.6548e-01 5.2300e-01 1.7490e+00 +KRTAP4-11 ENST00000391413 2.2612e-05 1.0029e+00 5.6500e-01 1.7490e+00 +KRTAP5-11 ENST00000398530 3.8177e-01 0.0000e+00 0.0000e+00 1.7490e+00 +C9orf57 ENST00000377024 1.1153e-04 9.6586e-01 5.2300e-01 1.7490e+00 +VMAC ENST00000339485 4.1351e-02 6.8575e-01 2.7100e-01 1.7490e+00 +OR6C76 ENST00000328314 2.3904e-03 8.6522e-01 4.1900e-01 1.7490e+00 +FKBP1C ENST00000370659 4.1342e-02 6.8585e-01 2.7100e-01 1.7490e+00 +SELK ENST00000495461 1.1124e-04 9.6643e-01 5.2400e-01 1.7490e+00 +C5orf66 ENST00000432382 5.2699e-04 9.2160e-01 4.7500e-01 1.7490e+00 +LNP1 ENST00000383693 4.4338e-06 1.0336e+00 6.0200e-01 1.7490e+00 +AC106876.2 ENST00000409905 1.0298e-02 7.9143e-01 3.5300e-01 1.7490e+00 +ANGPTL7 ENST00000376819 9.1680e-17 1.2487e+00 8.9000e-01 1.7500e+00 +ZNF582 ENST00000301310 5.2539e-04 9.2239e-01 4.7600e-01 1.7500e+00 +C11orf65 ENST00000393084 2.0163e-14 1.2199e+00 8.4900e-01 1.7500e+00 +LY86 ENST00000379953 2.2513e-05 1.0037e+00 5.6600e-01 1.7500e+00 +TUSC5 ENST00000333813 5.2419e-04 9.2299e-01 4.7600e-01 1.7500e+00 +GAL ENST00000265643 4.3885e-06 1.0353e+00 6.0300e-01 1.7500e+00 +CLDN14 ENST00000399137 1.1061e-04 9.6770e-01 5.2400e-01 1.7510e+00 +CCL11 ENST00000305869 1.0211e-02 7.9458e-01 3.5400e-01 1.7510e+00 +MYL2 ENST00000228841 2.7303e-08 1.1079e+00 6.9400e-01 1.7510e+00 +PGBD3 ENST00000374127 4.1167e-02 6.8781e-01 2.7200e-01 1.7510e+00 +RP11-1021N1.1 ENST00000568766 1.0224e-02 7.9410e-01 3.5400e-01 1.7510e+00 +ARHGAP8 ENST00000389773 8.5171e-28 1.3378e+00 1.0240e+00 1.7510e+00 +OR5J2 ENST00000312298 2.3661e-03 8.6837e-01 4.2100e-01 1.7510e+00 +CCL13 ENST00000225844 4.0987e-02 6.8983e-01 2.7300e-01 1.7520e+00 +NPY4R ENST00000374312 8.2144e-07 1.0639e+00 6.3700e-01 1.7520e+00 +CTD-2370N5.3 ENST00000578584 5.1939e-04 9.2537e-01 4.7700e-01 1.7520e+00 +OR6B1 ENST00000408922 4.3351e-06 1.0374e+00 6.0400e-01 1.7520e+00 +TMEM176B ENST00000447204 1.4172e-10 1.1619e+00 7.6400e-01 1.7530e+00 +C1orf115 ENST00000294889 4.0906e-02 6.9074e-01 2.7300e-01 1.7530e+00 +CCL14 ENST00000536149 1.0929e-04 9.7037e-01 5.2600e-01 1.7530e+00 +FAM166B ENST00000399742 8.2990e-10 1.1454e+00 7.4200e-01 1.7530e+00 +SNN ENST00000329565 1.4400e-01 5.1047e-01 1.7000e-01 1.7530e+00 +IL33 ENST00000381434 8.2925e-10 1.1455e+00 7.4200e-01 1.7530e+00 +OR5R1 ENST00000312253 5.1866e-04 9.2573e-01 4.7700e-01 1.7530e+00 +CCL26 ENST00000394905 1.0114e-02 7.9812e-01 3.5500e-01 1.7540e+00 +TTC23 ENST00000394132 7.3763e-24 1.3144e+00 9.8600e-01 1.7540e+00 +MMACHC ENST00000401061 1.1402e-13 1.2143e+00 8.3700e-01 1.7550e+00 +ZNF284 ENST00000421176 1.0802e-04 9.7296e-01 5.2700e-01 1.7550e+00 +ZNF30 ENST00000439785 2.3338e-03 8.7261e-01 4.2300e-01 1.7550e+00 +TRNP1 ENST00000522111 3.7880e-01 0.0000e+00 0.0000e+00 1.7550e+00 +C11orf24 ENST00000304271 2.3262e-03 8.7363e-01 4.2300e-01 1.7560e+00 +PRRG3 ENST00000370353 7.9468e-07 1.0690e+00 6.4000e-01 1.7560e+00 +RGS9BP ENST00000334176 2.3224e-03 8.7413e-01 4.2300e-01 1.7560e+00 +OIP5 ENST00000220514 1.4649e-07 1.0919e+00 6.6900e-01 1.7560e+00 +C1orf122 ENST00000373042 1.4325e-01 5.1361e-01 1.7100e-01 1.7560e+00 +ZNF714 ENST00000596143 4.0598e-02 6.9427e-01 2.7400e-01 1.7560e+00 +FAM109A ENST00000361483 1.0042e-02 8.0081e-01 3.5600e-01 1.7560e+00 +MYL12A ENST00000217652 5.1197e-04 9.2912e-01 4.7900e-01 1.7560e+00 +NCMAP ENST00000374392 4.0542e-02 6.9492e-01 2.7400e-01 1.7560e+00 +B3GALT5 ENST00000380620 2.1595e-05 1.0118e+00 5.7000e-01 1.7570e+00 +PINX1 ENST00000314787 4.5977e-09 1.1327e+00 7.2200e-01 1.7570e+00 +FBXO48 ENST00000377957 1.0680e-04 9.7550e-01 5.2800e-01 1.7570e+00 +TMEM196 ENST00000405764 4.2115e-06 1.0424e+00 6.0700e-01 1.7570e+00 +EFCAB9 ENST00000398186 1.0712e-04 9.7483e-01 5.2800e-01 1.7570e+00 +G0S2 ENST00000367029 3.7788e-01 0.0000e+00 0.0000e+00 1.7570e+00 +COX6A1 ENST00000229379 2.3136e-03 8.7532e-01 4.2400e-01 1.7570e+00 +C11orf44 ENST00000317019 2.3130e-03 8.7540e-01 4.2400e-01 1.7570e+00 +C11orf91 ENST00000379011 1.0029e-02 8.0131e-01 3.5600e-01 1.7570e+00 +RP11-343C2.12 ENST00000562949 2.3091e-03 8.7593e-01 4.2400e-01 1.7570e+00 +C17orf89 ENST00000431388 1.4285e-01 5.1531e-01 1.7100e-01 1.7570e+00 +CALML6 ENST00000307786 2.6089e-08 1.1138e+00 6.9700e-01 1.7570e+00 +C6orf223 ENST00000336600 5.0936e-04 9.3046e-01 4.8000e-01 1.7570e+00 +APOC3 ENST00000227667 1.0024e-02 8.0150e-01 3.5700e-01 1.7570e+00 +IGIP ENST00000333305 3.7789e-01 0.0000e+00 0.0000e+00 1.7570e+00 +BLVRB ENST00000263368 4.1869e-06 1.0434e+00 6.0800e-01 1.7580e+00 +SHISA8 ENST00000457093 3.7777e-01 0.0000e+00 0.0000e+00 1.7580e+00 +TMEM129 ENST00000382936 2.3074e-11 1.1810e+00 7.8700e-01 1.7580e+00 +HEBP1 ENST00000014930 4.1767e-06 1.0438e+00 6.0800e-01 1.7580e+00 +AL590708.2 ENST00000443493 3.7751e-01 0.0000e+00 0.0000e+00 1.7580e+00 +SPATA31A1 ENST00000377647 3.7761e-01 0.0000e+00 0.0000e+00 1.7580e+00 +PLD6 ENST00000321560 2.3012e-03 8.7700e-01 4.2400e-01 1.7580e+00 +AC110615.1 ENST00000599764 1.4254e-01 5.1664e-01 1.7200e-01 1.7580e+00 +GIPR ENST00000590918 1.9703e-29 1.3530e+00 1.0430e+00 1.7580e+00 +C22orf46 ENST00000402966 2.3074e-03 8.7615e-01 4.2400e-01 1.7580e+00 +PHGR1 ENST00000448599 1.4245e-01 5.1704e-01 1.7200e-01 1.7590e+00 +AC002553.1 ENST00000442828 1.4242e-01 5.1717e-01 1.7200e-01 1.7590e+00 +ZNF43 ENST00000354959 5.0468e-04 9.3288e-01 4.8100e-01 1.7590e+00 +ZNF254 ENST00000357002 5.0407e-04 9.3320e-01 4.8100e-01 1.7590e+00 +TRIQK ENST00000521988 9.9534e-03 8.0416e-01 3.5800e-01 1.7590e+00 +GEMIN6 ENST00000281950 1.0596e-04 9.7728e-01 5.2900e-01 1.7590e+00 +DEFB105A ENST00000334773 3.7719e-01 0.0000e+00 0.0000e+00 1.7590e+00 +AC135048.1 ENST00000602217 1.4211e-01 5.1852e-01 1.7200e-01 1.7600e+00 +FBXO27 ENST00000292853 2.2725e-11 1.1826e+00 7.8800e-01 1.7600e+00 +ZNF610 ENST00000403906 1.0546e-04 9.7834e-01 5.3000e-01 1.7600e+00 +AC023590.1 ENST00000366457 3.7657e-01 0.0000e+00 0.0000e+00 1.7600e+00 +CSH1 ENST00000316193 2.1264e-05 1.0148e+00 5.7200e-01 1.7600e+00 +TREML4 ENST00000341495 7.7513e-10 1.1532e+00 7.4700e-01 1.7600e+00 +TRIM61 ENST00000329314 1.0554e-04 9.7817e-01 5.3000e-01 1.7600e+00 +GIMAP6 ENST00000328902 1.4212e-01 5.1848e-01 1.7200e-01 1.7600e+00 +DDC8 ENST00000322630 3.7682e-01 0.0000e+00 0.0000e+00 1.7600e+00 +SLC25A52 ENST00000269205 5.0170e-04 9.3444e-01 4.8200e-01 1.7600e+00 +CRIP1 ENST00000330233 4.9848e-04 9.3614e-01 4.8200e-01 1.7610e+00 +MS4A14 ENST00000531783 7.7109e-07 1.0737e+00 6.4300e-01 1.7610e+00 +OR2G6 ENST00000343414 4.9951e-04 9.3559e-01 4.8200e-01 1.7610e+00 +MMP8 ENST00000236826 1.0661e-24 1.3269e+00 1.0000e+00 1.7610e+00 +SPDYE2B ENST00000507450 3.7648e-01 0.0000e+00 0.0000e+00 1.7610e+00 +PKIA ENST00000396418 1.4180e-01 5.1985e-01 1.7300e-01 1.7610e+00 +OR4F17 ENST00000585993 3.7614e-01 0.0000e+00 0.0000e+00 1.7610e+00 +UQCR10 ENST00000330029 1.4162e-01 5.2064e-01 1.7300e-01 1.7610e+00 +PGLYRP4 ENST00000359650 2.9387e-15 1.2411e+00 8.7100e-01 1.7610e+00 +RNF224 ENST00000445101 3.9980e-02 7.0150e-01 2.7700e-01 1.7610e+00 +PRKRIP1 ENST00000496391 2.2336e-11 1.1843e+00 7.8900e-01 1.7610e+00 +NPVF ENST00000222674 1.0444e-04 9.8053e-01 5.3100e-01 1.7620e+00 +ATPIF1 ENST00000335514 1.0367e-04 9.8221e-01 5.3200e-01 1.7630e+00 +PKD1L2 ENST00000527937 2.0902e-05 1.0182e+00 5.7300e-01 1.7630e+00 +CNPY4 ENST00000262932 1.0277e-13 1.2237e+00 8.4300e-01 1.7640e+00 +METTL20 ENST00000357721 4.2985e-09 1.1409e+00 7.2700e-01 1.7640e+00 +LHB ENST00000221421 2.2475e-03 8.8442e-01 4.2800e-01 1.7640e+00 +TOMM7 ENST00000358435 9.7668e-03 8.1138e-01 3.6000e-01 1.7640e+00 +DLEU2L ENST00000371086 3.7476e-01 0.0000e+00 0.0000e+00 1.7640e+00 +C4orf46 ENST00000379205 3.9595e-02 7.0613e-01 2.7800e-01 1.7640e+00 +WFDC9 ENST00000326000 9.7671e-03 8.1136e-01 3.6000e-01 1.7640e+00 +SCO2 ENST00000543927 7.5473e-07 1.0771e+00 6.4500e-01 1.7640e+00 +LY6G6C ENST00000375819 4.9312e-04 9.3900e-01 4.8400e-01 1.7640e+00 +A3GALT2 ENST00000442999 1.2823e-10 1.1727e+00 7.7100e-01 1.7640e+00 +ST20 ENST00000478497 3.7485e-01 0.0000e+00 0.0000e+00 1.7640e+00 +RP1-228P16.5 ENST00000547602 3.9518e-02 7.0707e-01 2.7800e-01 1.7650e+00 +TRIM73 ENST00000323819 1.0272e-04 9.8430e-01 5.3300e-01 1.7650e+00 +SNTN ENST00000343837 1.0257e-04 9.8463e-01 5.3300e-01 1.7650e+00 +C1orf194 ENST00000369949 3.9833e-06 1.0521e+00 6.1200e-01 1.7650e+00 +KRTAP29-1 ENST00000391353 4.2651e-09 1.1419e+00 7.2800e-01 1.7650e+00 +CLNK ENST00000226951 1.7251e-29 1.3601e+00 1.0480e+00 1.7660e+00 +PGAM2 ENST00000297283 1.3574e-07 1.1027e+00 6.7600e-01 1.7660e+00 +COMMD8 ENST00000381571 7.3184e-10 1.1598e+00 7.5100e-01 1.7660e+00 +LPAR4 ENST00000435339 2.2346e-03 8.8624e-01 4.2900e-01 1.7660e+00 +ZNF443 ENST00000301547 4.8827e-04 9.4163e-01 4.8500e-01 1.7660e+00 +C1orf68 ENST00000368775 1.3581e-07 1.1027e+00 6.7600e-01 1.7660e+00 +LSM3 ENST00000306024 3.9529e-06 1.0534e+00 6.1300e-01 1.7660e+00 +TYW1B ENST00000438904 5.4289e-20 1.2947e+00 9.4700e-01 1.7660e+00 +BPIFA3 ENST00000375454 5.9419e-13 1.2158e+00 8.2900e-01 1.7670e+00 +RP11-849H4.2 ENST00000528511 2.4042e-08 1.1246e+00 7.0400e-01 1.7670e+00 +OR2W3 ENST00000537741 1.0132e-04 9.8741e-01 5.3400e-01 1.7670e+00 +CDC42EP2 ENST00000544348 3.9267e-02 7.1015e-01 2.7900e-01 1.7670e+00 +LSMEM2 ENST00000316436 7.3629e-07 1.0810e+00 6.4700e-01 1.7670e+00 +CTXN3 ENST00000379445 1.3992e-01 5.2819e-01 1.7500e-01 1.7670e+00 +MPV17L ENST00000396385 7.3866e-07 1.0804e+00 6.4600e-01 1.7670e+00 +AL031590.1 ENST00000456974 3.7335e-01 0.0000e+00 0.0000e+00 1.7670e+00 +AC018867.2 ENST00000595956 3.7315e-01 0.0000e+00 0.0000e+00 1.7680e+00 +C19orf69 ENST00000378187 3.9196e-02 7.1103e-01 2.8000e-01 1.7680e+00 +HNRNPCL1 ENST00000317869 3.7278e-01 0.0000e+00 0.0000e+00 1.7680e+00 +TNFRSF6B ENST00000369996 3.8740e-06 1.0569e+00 6.1500e-01 1.7690e+00 +TEDDM1 ENST00000367565 2.2029e-03 8.9079e-01 4.3100e-01 1.7690e+00 +C8orf22 ENST00000303202 1.0013e-04 9.9013e-01 5.3600e-01 1.7690e+00 +LGALS16 ENST00000392051 1.0017e-04 9.9003e-01 5.3600e-01 1.7690e+00 +MTNR1A ENST00000307161 7.2327e-07 1.0838e+00 6.4800e-01 1.7690e+00 +CLPS ENST00000259938 9.5685e-03 8.1932e-01 3.6400e-01 1.7700e+00 +CYSLTR2 ENST00000282018 9.9817e-05 9.9083e-01 5.3600e-01 1.7700e+00 +METTL23 ENST00000341249 1.3147e-07 1.1073e+00 6.7900e-01 1.7700e+00 +MRP63 ENST00000309594 1.3887e-01 5.3304e-01 1.7600e-01 1.7700e+00 +C22orf39 ENST00000399562 1.9976e-05 1.0271e+00 5.7800e-01 1.7700e+00 +SPRR4 ENST00000328051 3.8928e-02 7.1438e-01 2.8100e-01 1.7700e+00 +AURKAIP1 ENST00000338370 9.9678e-05 9.9115e-01 5.3600e-01 1.7700e+00 +OGFOD2 ENST00000397389 3.4370e-12 1.2068e+00 8.1400e-01 1.7700e+00 +OR4K5 ENST00000315915 9.9425e-05 9.9174e-01 5.3600e-01 1.7710e+00 +HOGA1 ENST00000370646 1.5812e-14 1.2412e+00 8.6300e-01 1.7710e+00 +C9orf47 ENST00000334490 9.9199e-05 9.9226e-01 5.3700e-01 1.7710e+00 +SPINK13 ENST00000512953 4.7605e-04 9.4842e-01 4.8800e-01 1.7710e+00 +LAMTOR5 ENST00000256644 3.8329e-06 1.0588e+00 6.1600e-01 1.7710e+00 +KCTD14 ENST00000353172 2.1830e-03 8.9370e-01 4.3200e-01 1.7710e+00 +FBXO17 ENST00000292852 5.6825e-13 1.2201e+00 8.3200e-01 1.7710e+00 +AMH ENST00000221496 3.3974e-12 1.2079e+00 8.1500e-01 1.7710e+00 +NDUFA13 ENST00000507754 3.8049e-06 1.0601e+00 6.1700e-01 1.7720e+00 +NIT2 ENST00000394140 1.1471e-17 1.2784e+00 9.1700e-01 1.7720e+00 +ACSF3 ENST00000317447 2.3246e-26 1.3477e+00 1.0240e+00 1.7720e+00 +C22orf26 ENST00000396008 3.8713e-02 7.1710e-01 2.8200e-01 1.7720e+00 +OR1Q1 ENST00000297913 4.7324e-04 9.5001e-01 4.8900e-01 1.7720e+00 +GZMH ENST00000216338 1.2818e-07 1.1110e+00 6.8100e-01 1.7730e+00 +SIRT4 ENST00000202967 6.8625e-10 1.1674e+00 7.5600e-01 1.7730e+00 +ZNF728 ENST00000594710 4.7070e-04 9.5147e-01 4.9000e-01 1.7730e+00 +PCP4 ENST00000328619 2.1696e-03 8.9569e-01 4.3300e-01 1.7730e+00 +FAM26F ENST00000368605 9.4610e-03 8.2374e-01 3.6500e-01 1.7730e+00 +REG3G ENST00000272324 1.2831e-07 1.1109e+00 6.8100e-01 1.7730e+00 +C10orf131 ENST00000423344 3.7440e-06 1.0630e+00 6.1800e-01 1.7740e+00 +S100A8 ENST00000368733 1.3761e-01 5.3897e-01 1.7800e-01 1.7740e+00 +MAGEB16 ENST00000399989 3.7021e-01 0.0000e+00 0.0000e+00 1.7740e+00 +RP11-1085N6.3 ENST00000556696 3.7027e-01 0.0000e+00 0.0000e+00 1.7740e+00 +RIPPLY1 ENST00000276173 9.4433e-03 8.2448e-01 3.6600e-01 1.7740e+00 +PDHA2 ENST00000295266 3.9282e-09 1.1521e+00 7.3400e-01 1.7740e+00 +C22orf43 ENST00000317749 2.9283e-19 1.2970e+00 9.4300e-01 1.7750e+00 +TNFAIP8L2 ENST00000368910 3.8364e-02 7.2158e-01 2.8300e-01 1.7750e+00 +C19orf35 ENST00000342063 2.1505e-03 8.9854e-01 4.3400e-01 1.7750e+00 +RP11-712L6.5 ENST00000524964 3.6961e-01 0.0000e+00 0.0000e+00 1.7750e+00 +TAS2R3 ENST00000247879 4.6636e-04 9.5398e-01 4.9100e-01 1.7750e+00 +RP11-187E13.1 ENST00000553330 1.3718e-01 5.4104e-01 1.7800e-01 1.7760e+00 +RP11-321F6.1 ENST00000558797 9.3616e-03 8.2791e-01 3.6700e-01 1.7760e+00 +C19orf45 ENST00000361664 1.0898e-17 1.2824e+00 9.2000e-01 1.7760e+00 +BOLA1 ENST00000369153 3.8160e-02 7.2424e-01 2.8400e-01 1.7770e+00 +CLDND2 ENST00000291715 3.6610e-06 1.0670e+00 6.2000e-01 1.7770e+00 +ORAI1 ENST00000330079 1.9068e-05 1.0365e+00 5.8300e-01 1.7770e+00 +TCTA ENST00000273590 4.6337e-04 9.5572e-01 4.9200e-01 1.7770e+00 +AC136604.1 ENST00000425471 3.6879e-01 0.0000e+00 0.0000e+00 1.7770e+00 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1.8000e-01 1.7790e+00 +TEX12 ENST00000280358 4.5664e-04 9.5971e-01 4.9400e-01 1.7790e+00 +KPRP ENST00000368773 3.0815e-12 1.2179e+00 8.2100e-01 1.7800e+00 +CCDC70 ENST00000242819 9.2427e-03 8.3300e-01 3.6900e-01 1.7800e+00 +CPO ENST00000272852 7.2710e-21 1.3152e+00 9.6700e-01 1.7800e+00 +COX16 ENST00000389912 1.8748e-05 1.0399e+00 5.8500e-01 1.7800e+00 +KRTAP26-1 ENST00000360542 1.3581e-01 5.4770e-01 1.8000e-01 1.7800e+00 +AC010336.1 ENST00000539278 3.5917e-06 1.0704e+00 6.2200e-01 1.7800e+00 +CCDC115 ENST00000259229 1.2061e-07 1.1199e+00 6.8600e-01 1.7800e+00 +AGAP7 ENST00000374095 3.7798e-02 7.2905e-01 2.8600e-01 1.7800e+00 +BSND ENST00000371265 1.0949e-10 1.1903e+00 7.8200e-01 1.7800e+00 +OPN1MW ENST00000369935 3.7781e-02 7.2927e-01 2.8600e-01 1.7800e+00 +TNFAIP8L3 ENST00000327536 1.8707e-05 1.0403e+00 5.8500e-01 1.7800e+00 +KRTAP10-9 ENST00000397911 1.8729e-05 1.0401e+00 5.8500e-01 1.7800e+00 +OR52L1 ENST00000332249 1.8725e-05 1.0401e+00 5.8500e-01 1.7800e+00 +UPK3A ENST00000216211 1.0773e-10 1.1921e+00 7.8300e-01 1.7810e+00 +IFITM1 ENST00000408968 1.3569e-01 5.4832e-01 1.8000e-01 1.7810e+00 +FRG2 ENST00000378763 3.6635e-01 0.0000e+00 0.0000e+00 1.7810e+00 +RP11-571M6.15 ENST00000546504 1.8659e-05 1.0409e+00 5.8500e-01 1.7810e+00 +RP11-10J21.3 ENST00000518520 1.3543e-01 5.4962e-01 1.8100e-01 1.7810e+00 +CCL18 ENST00000004921 9.1743e-03 8.3598e-01 3.7000e-01 1.7820e+00 +KIR3DL1 ENST00000391728 8.3578e-14 1.2429e+00 8.5600e-01 1.7820e+00 +FGF3 ENST00000334134 9.3139e-05 1.0069e+00 5.4400e-01 1.7820e+00 +MRAP ENST00000399784 2.0810e-03 9.0928e-01 4.3900e-01 1.7820e+00 +TNP1 ENST00000236979 3.7552e-02 7.3236e-01 2.8700e-01 1.7820e+00 +TNP2 ENST00000312693 9.1467e-03 8.3719e-01 3.7100e-01 1.7820e+00 +NPBWR2 ENST00000369768 9.2479e-05 1.0086e+00 5.4500e-01 1.7830e+00 +POP7 ENST00000303151 3.7473e-02 7.3343e-01 2.8700e-01 1.7830e+00 +OR9G1 ENST00000312153 4.4763e-04 9.6520e-01 4.9600e-01 1.7830e+00 +ZNF594 ENST00000399604 9.2635e-05 1.0082e+00 5.4500e-01 1.7830e+00 +MGMT ENST00000306010 1.1756e-07 1.1237e+00 6.8800e-01 1.7830e+00 +ZNF556 ENST00000307635 9.2480e-05 1.0086e+00 5.4500e-01 1.7830e+00 +TLDC1 ENST00000343629 9.7663e-18 1.2911e+00 9.2600e-01 1.7840e+00 +C8orf12 ENST00000284481 3.7394e-02 7.3451e-01 2.8800e-01 1.7840e+00 +SCN4B ENST00000324727 6.4529e-07 1.1021e+00 6.5900e-01 1.7840e+00 +CCDC179 ENST00000532798 9.0890e-03 8.3975e-01 3.7200e-01 1.7840e+00 +ZBED2 ENST00000317012 4.4529e-04 9.6664e-01 4.9700e-01 1.7840e+00 +C20orf85 ENST00000371168 1.8292e-05 1.0449e+00 5.8800e-01 1.7840e+00 +AL049829.1 ENST00000594872 1.3466e-01 5.5351e-01 1.8200e-01 1.7840e+00 +MRPL14 ENST00000372014 9.2387e-05 1.0088e+00 5.4500e-01 1.7840e+00 +FAM86A ENST00000427587 2.1924e-15 1.2664e+00 8.8800e-01 1.7850e+00 +KHDC1 ENST00000370384 6.1330e-10 1.1807e+00 7.6400e-01 1.7850e+00 +HINT3 ENST00000229633 3.4813e-06 1.0760e+00 6.2500e-01 1.7850e+00 +PROKR1 ENST00000303786 1.1631e-07 1.1253e+00 6.8900e-01 1.7850e+00 +PROSER2 ENST00000277570 1.1594e-07 1.1258e+00 6.8900e-01 1.7850e+00 +XCL2 ENST00000367819 9.0664e-03 8.4076e-01 3.7200e-01 1.7850e+00 +ZNF727 ENST00000550760 2.0573e-03 9.1306e-01 4.4000e-01 1.7850e+00 +CYYR1 ENST00000299340 4.4425e-04 9.6729e-01 4.9700e-01 1.7850e+00 +ZNF844 ENST00000439326 2.0558e-03 9.1330e-01 4.4000e-01 1.7850e+00 +C22orf42 ENST00000382097 8.1231e-14 1.2456e+00 8.5800e-01 1.7850e+00 +ATP5EP2 ENST00000381026 3.6391e-01 0.0000e+00 0.0000e+00 1.7860e+00 +KB-1507C5.2 ENST00000522939 3.6430e-01 0.0000e+00 0.0000e+00 1.7860e+00 +PLA2G2D ENST00000375105 1.8079e-05 1.0473e+00 5.8900e-01 1.7860e+00 +FCRL6 ENST00000368106 2.7809e-23 1.3401e+00 1.0000e+00 1.7860e+00 +HTR5A-AS1 ENST00000543018 9.1314e-05 1.0115e+00 5.4600e-01 1.7860e+00 +ZCCHC16 ENST00000340433 3.4473e-06 1.0778e+00 6.2600e-01 1.7860e+00 +HCST ENST00000246551 2.0464e-03 9.1483e-01 4.4100e-01 1.7860e+00 +AC103809.2 ENST00000599136 3.7079e-02 7.3887e-01 2.8900e-01 1.7860e+00 +C7orf50 ENST00000397098 3.4242e-06 1.0790e+00 6.2700e-01 1.7870e+00 +MS4A12 ENST00000016913 3.4953e-09 1.1670e+00 7.4300e-01 1.7870e+00 +PGLYRP1 ENST00000008938 1.7919e-05 1.0491e+00 5.9000e-01 1.7870e+00 +C5orf28 ENST00000500337 1.1396e-07 1.1283e+00 6.9100e-01 1.7870e+00 +LYZ ENST00000261267 3.4114e-06 1.0797e+00 6.2700e-01 1.7870e+00 +DAND5 ENST00000317060 2.0422e-03 9.1550e-01 4.4100e-01 1.7870e+00 +AP5S1 ENST00000246041 9.0339e-05 1.0141e+00 5.4800e-01 1.7870e+00 +UCP1 ENST00000262999 1.6903e-11 1.2140e+00 8.0800e-01 1.7880e+00 +FAM109B ENST00000321753 3.3928e-06 1.0807e+00 6.2800e-01 1.7880e+00 +ZNF479 ENST00000331162 9.0123e-05 1.0147e+00 5.4800e-01 1.7880e+00 +ZSCAN5D ENST00000600684 6.2931e-07 1.1062e+00 6.6100e-01 1.7880e+00 +APOL3 ENST00000349314 4.3634e-04 9.7228e-01 5.0000e-01 1.7880e+00 +RP6-24A23.6 ENST00000563887 3.6317e-01 0.0000e+00 0.0000e+00 1.7880e+00 +CCDC78 ENST00000293889 2.9690e-31 1.3893e+00 1.0770e+00 1.7880e+00 +SULT1A3 ENST00000395137 3.6251e-01 0.0000e+00 0.0000e+00 1.7890e+00 +NMBR ENST00000258042 1.9761e-08 1.1512e+00 7.2000e-01 1.7890e+00 +ANKRD20A1 ENST00000377477 3.3618e-06 1.0824e+00 6.2900e-01 1.7890e+00 +LYZL2 ENST00000375318 1.1221e-07 1.1306e+00 6.9200e-01 1.7890e+00 +C2orf53 ENST00000335524 6.1868e-07 1.1090e+00 6.6300e-01 1.7900e+00 +AQP12B ENST00000407834 2.0112e-03 9.2062e-01 4.4400e-01 1.7900e+00 +SMPDL3A ENST00000368440 6.2788e-21 1.3256e+00 9.7500e-01 1.7900e+00 +ATP5E ENST00000243997 8.8748e-03 8.4950e-01 3.7500e-01 1.7900e+00 +SMIM5 ENST00000537494 1.3265e-01 5.6400e-01 1.8400e-01 1.7900e+00 +LEMD1 ENST00000367153 3.3433e-06 1.0834e+00 6.2900e-01 1.7900e+00 +CTD-2014B16.3 ENST00000554907 3.6562e-02 7.4620e-01 2.9100e-01 1.7910e+00 +ZNF586 ENST00000396154 3.6539e-02 7.4654e-01 2.9200e-01 1.7910e+00 +GTSF1L ENST00000373003 1.9965e-03 9.2309e-01 4.4500e-01 1.7910e+00 +RETN ENST00000221515 3.6545e-02 7.4645e-01 2.9200e-01 1.7910e+00 +CDNF ENST00000465530 6.1335e-07 1.1104e+00 6.6300e-01 1.7910e+00 +OR2A5 ENST00000408906 1.7421e-05 1.0549e+00 5.9300e-01 1.7910e+00 +ADIRF ENST00000372013 3.6481e-02 7.4736e-01 2.9200e-01 1.7910e+00 +C12orf23 ENST00000280756 8.8522e-03 8.5056e-01 3.7600e-01 1.7910e+00 +GAL3ST3 ENST00000312006 1.9296e-08 1.1545e+00 7.2200e-01 1.7920e+00 +TMEM155 ENST00000337677 3.6443e-02 7.4792e-01 2.9200e-01 1.7920e+00 +SFTA2 ENST00000359086 3.6441e-02 7.4794e-01 2.9200e-01 1.7920e+00 +AC111200.1 ENST00000441903 3.6087e-01 0.0000e+00 0.0000e+00 1.7920e+00 +B3GNT9 ENST00000449549 1.7363e-05 1.0556e+00 5.9300e-01 1.7920e+00 +MPV17 ENST00000380044 9.6582e-11 1.2046e+00 7.9100e-01 1.7920e+00 +TREM2 ENST00000373113 3.2892e-09 1.1748e+00 7.4800e-01 1.7930e+00 +ECSCR ENST00000515823 4.2521e-04 9.7954e-01 5.0300e-01 1.7930e+00 +TMEM167A ENST00000502346 4.2515e-04 9.7958e-01 5.0300e-01 1.7930e+00 +NAT2 ENST00000286479 3.2744e-06 1.0872e+00 6.3100e-01 1.7930e+00 +HRK ENST00000257572 3.6033e-01 0.0000e+00 0.0000e+00 1.7930e+00 +WFDC10B ENST00000335769 3.6238e-02 7.5090e-01 2.9300e-01 1.7930e+00 +CGB1 ENST00000301407 3.6312e-02 7.4983e-01 2.9300e-01 1.7930e+00 +CAPS ENST00000222125 1.7206e-05 1.0575e+00 5.9400e-01 1.7930e+00 +CDCP2 ENST00000371330 9.4718e-11 1.2069e+00 7.9300e-01 1.7940e+00 +PRM3 ENST00000327157 3.5959e-01 0.0000e+00 0.0000e+00 1.7940e+00 +PDGFRL ENST00000541323 1.1787e-14 1.2679e+00 8.8100e-01 1.7950e+00 +RNASE10 ENST00000328444 1.9671e-03 9.2812e-01 4.4700e-01 1.7950e+00 +ENPP7 ENST00000328313 1.1797e-14 1.2679e+00 8.8100e-01 1.7950e+00 +TPRX1 ENST00000322175 3.5947e-01 0.0000e+00 0.0000e+00 1.7950e+00 +RNF181 ENST00000306368 3.2390e-09 1.1768e+00 7.4900e-01 1.7950e+00 +B3GNTL1 ENST00000320865 4.0733e-28 1.3793e+00 1.0550e+00 1.7950e+00 +C17orf100 ENST00000391428 1.3110e-01 5.7241e-01 1.8600e-01 1.7950e+00 +C3orf52 ENST00000431717 8.6244e-05 1.0252e+00 5.5300e-01 1.7950e+00 +RDH14 ENST00000381249 1.7034e-05 1.0596e+00 5.9500e-01 1.7950e+00 +ANKRD66 ENST00000565422 1.6946e-05 1.0607e+00 5.9600e-01 1.7950e+00 +C8orf4 ENST00000315792 8.6883e-03 8.5834e-01 3.7900e-01 1.7960e+00 +AGAP10 ENST00000413193 3.5899e-01 0.0000e+00 0.0000e+00 1.7960e+00 +RP13-672B3.2 ENST00000537262 4.1945e-04 9.8339e-01 5.0500e-01 1.7960e+00 +KRT32 ENST00000225899 1.3564e-18 1.3113e+00 9.4700e-01 1.7960e+00 +FAM174A ENST00000312637 8.5833e-05 1.0263e+00 5.5400e-01 1.7960e+00 +AC006538.4 ENST00000586572 1.3057e-01 5.7535e-01 1.8700e-01 1.7960e+00 +NAT14 ENST00000205194 8.6687e-03 8.5929e-01 3.7900e-01 1.7960e+00 +HIST1H4F ENST00000377745 1.3072e-01 5.7451e-01 1.8700e-01 1.7960e+00 +OR5T3 ENST00000303059 4.1970e-04 9.8323e-01 5.0500e-01 1.7960e+00 +C9orf169 ENST00000359069 8.6287e-03 8.6123e-01 3.8000e-01 1.7970e+00 +OR10A4 ENST00000379829 1.6786e-05 1.0627e+00 5.9700e-01 1.7970e+00 +TMEM212 ENST00000334567 1.8330e-08 1.1617e+00 7.2600e-01 1.7970e+00 +FAM72C ENST00000369175 3.5833e-01 0.0000e+00 0.0000e+00 1.7970e+00 +LAPTM4B ENST00000445593 4.2764e-13 1.2481e+00 8.5000e-01 1.7970e+00 +LL22NC03-75H12.2 ENST00000405369 3.5827e-02 7.5700e-01 2.9500e-01 1.7970e+00 +PAGE3 ENST00000519203 8.6303e-03 8.6115e-01 3.8000e-01 1.7970e+00 +KLRK1 ENST00000240618 6.9812e-14 1.2602e+00 8.6700e-01 1.7970e+00 +TIMM8B ENST00000541231 8.6544e-03 8.5998e-01 3.7900e-01 1.7970e+00 +ZNF665 ENST00000396424 8.6277e-03 8.6128e-01 3.8000e-01 1.7970e+00 +SLC31A2 ENST00000259392 8.5199e-05 1.0281e+00 5.5500e-01 1.7970e+00 +C2CD4D ENST00000454109 1.3012e-01 5.7788e-01 1.8800e-01 1.7980e+00 +CER1 ENST00000380911 1.6674e-05 1.0641e+00 5.9800e-01 1.7980e+00 +PCDHB7 ENST00000231137 8.0848e-18 1.3063e+00 9.3700e-01 1.7980e+00 +GPR18 ENST00000340807 5.3465e-10 1.1975e+00 7.7500e-01 1.7980e+00 +POTED ENST00000299443 4.1359e-04 9.8740e-01 5.0700e-01 1.7980e+00 +ZNF737 ENST00000427401 4.1409e-04 9.8705e-01 5.0600e-01 1.7980e+00 +TNFRSF10C ENST00000356864 3.1588e-06 1.0938e+00 6.3500e-01 1.7980e+00 +AP002956.1 ENST00000599663 3.5763e-01 0.0000e+00 0.0000e+00 1.7980e+00 +AC064874.1 ENST00000440101 3.5541e-02 7.6135e-01 2.9600e-01 1.7990e+00 +COX14 ENST00000550487 3.5730e-01 0.0000e+00 0.0000e+00 1.7990e+00 +PIR ENST00000380421 5.3402e-10 1.1976e+00 7.7500e-01 1.7990e+00 +OR4N2 ENST00000315947 4.1111e-04 9.8912e-01 5.0700e-01 1.7990e+00 +C10orf67 ENST00000323327 1.7976e-08 1.1644e+00 7.2700e-01 1.7990e+00 +MCCD1 ENST00000376191 1.9319e-03 9.3429e-01 4.4900e-01 1.7990e+00 +INCA1 ENST00000396829 1.5015e-11 1.2270e+00 8.1700e-01 1.7990e+00 +GYPB ENST00000502664 8.3815e-05 1.0321e+00 5.5700e-01 1.8000e+00 +PSG11 ENST00000401740 4.8498e-17 1.3003e+00 9.2600e-01 1.8000e+00 +PRSS58 ENST00000552471 3.0681e-09 1.1839e+00 7.5300e-01 1.8010e+00 +ZNF487 ENST00000437590 3.5261e-02 7.6567e-01 2.9800e-01 1.8010e+00 +AAED1 ENST00000375234 1.0063e-07 1.1471e+00 7.0200e-01 1.8010e+00 +PPP1R27 ENST00000330261 8.3279e-05 1.0337e+00 5.5700e-01 1.8010e+00 +G6PC2 ENST00000375363 2.9565e-16 1.2925e+00 9.1300e-01 1.8010e+00 +OR5M1 ENST00000526538 1.9124e-03 9.3778e-01 4.5100e-01 1.8010e+00 +CTXN2 ENST00000417307 3.5215e-02 7.6638e-01 2.9800e-01 1.8020e+00 +OR1B1 ENST00000304833 1.6150e-05 1.0708e+00 6.0100e-01 1.8020e+00 +OR51T1 ENST00000380378 1.6162e-05 1.0707e+00 6.0100e-01 1.8020e+00 +S100A11 ENST00000271638 8.4662e-03 8.6931e-01 3.8300e-01 1.8020e+00 +RP11-113D6.10 ENST00000340135 3.5174e-02 7.6701e-01 2.9800e-01 1.8020e+00 +ACP1 ENST00000272067 1.7531e-08 1.1680e+00 7.3000e-01 1.8020e+00 +OMP ENST00000529803 4.0499e-04 9.9342e-01 5.0900e-01 1.8020e+00 +HIST1H3I ENST00000328488 8.4746e-03 8.6888e-01 3.8300e-01 1.8020e+00 +OR6M1 ENST00000309154 8.2424e-05 1.0362e+00 5.5900e-01 1.8020e+00 +ZNHIT3 ENST00000225410 5.5408e-07 1.1273e+00 6.7300e-01 1.8030e+00 +AP001631.10 ENST00000433840 3.5520e-01 0.0000e+00 0.0000e+00 1.8030e+00 +ACKR4 ENST00000249887 2.9962e-09 1.1871e+00 7.5500e-01 1.8030e+00 +POU5F2 ENST00000510627 4.0316e-04 9.9472e-01 5.1000e-01 1.8030e+00 +RP1-32I10.10 ENST00000406912 1.2851e-01 5.8721e-01 1.9000e-01 1.8030e+00 +C7orf33 ENST00000307003 1.6048e-05 1.0722e+00 6.0200e-01 1.8030e+00 +AL035588.1 ENST00000597468 3.5496e-01 0.0000e+00 0.0000e+00 1.8030e+00 +C3orf14 ENST00000494481 1.5981e-05 1.0731e+00 6.0200e-01 1.8040e+00 +CCL22 ENST00000219235 8.4014e-03 8.7260e-01 3.8400e-01 1.8040e+00 +CBR3 ENST00000290354 3.0158e-06 1.1025e+00 6.4000e-01 1.8040e+00 +AC005008.2 ENST00000431501 3.0161e-06 1.1025e+00 6.4000e-01 1.8040e+00 +GAGE2C ENST00000381708 3.5460e-01 0.0000e+00 0.0000e+00 1.8040e+00 +TSHB ENST00000256592 8.3588e-03 8.7479e-01 3.8500e-01 1.8050e+00 +C16orf95 ENST00000567970 8.4064e-11 1.2208e+00 8.0100e-01 1.8050e+00 +SPATC1L ENST00000291672 1.7055e-08 1.1719e+00 7.3200e-01 1.8050e+00 +CLRN1 ENST00000328863 1.7074e-08 1.1717e+00 7.3200e-01 1.8050e+00 +RNASE12 ENST00000556526 8.3516e-03 8.7517e-01 3.8500e-01 1.8050e+00 +NUDT8 ENST00000376693 8.0897e-05 1.0408e+00 5.6100e-01 1.8050e+00 +HIGD1C ENST00000398455 3.9609e-04 9.9985e-01 5.1200e-01 1.8060e+00 +S100A14 ENST00000368702 1.8638e-03 9.4674e-01 4.5500e-01 1.8060e+00 +SLC10A5 ENST00000518568 9.6960e-08 1.1529e+00 7.0500e-01 1.8060e+00 +PSMG4 ENST00000419065 1.8651e-03 9.4649e-01 4.5500e-01 1.8060e+00 +ZNF587B ENST00000442832 3.8024e-13 1.2601e+00 8.5800e-01 1.8060e+00 +C6orf99 ENST00000367072 1.2728e-01 5.9457e-01 1.9200e-01 1.8060e+00 +KRTAP21-1 ENST00000335093 3.5324e-01 0.0000e+00 0.0000e+00 1.8060e+00 +OR5K3 ENST00000383695 8.0434e-05 1.0422e+00 5.6200e-01 1.8060e+00 +LAGE3 ENST00000357360 1.2721e-01 5.9501e-01 1.9200e-01 1.8060e+00 +FAM154B ENST00000339465 8.3284e-11 1.2219e+00 8.0200e-01 1.8060e+00 +POTEB ENST00000439682 3.5277e-01 0.0000e+00 0.0000e+00 1.8070e+00 +RP11-315D16.2 ENST00000562767 1.8580e-03 9.4783e-01 4.5500e-01 1.8070e+00 +KLRC2 ENST00000381902 4.8735e-10 1.2090e+00 7.8200e-01 1.8070e+00 +CKLF-CMTM1 ENST00000527729 3.4621e-02 7.7583e-01 3.0100e-01 1.8070e+00 +TMEM258 ENST00000537328 1.8504e-03 9.4927e-01 4.5600e-01 1.8070e+00 +GOLGA8A ENST00000360553 3.9454e-04 1.0010e+00 5.1300e-01 1.8070e+00 +PRKCDBP ENST00000303927 7.9971e-05 1.0436e+00 5.6200e-01 1.8070e+00 +AL031666.2 ENST00000599904 1.8503e-03 9.4928e-01 4.5600e-01 1.8070e+00 +PDE6H ENST00000266395 8.2921e-03 8.7827e-01 3.8600e-01 1.8070e+00 +AC011308.1 ENST00000601086 3.5252e-01 0.0000e+00 0.0000e+00 1.8070e+00 +RAX2 ENST00000555633 8.2874e-03 8.7851e-01 3.8600e-01 1.8070e+00 +SPANXN4 ENST00000446864 3.5242e-01 0.0000e+00 0.0000e+00 1.8070e+00 +TIMM23B ENST00000374098 1.2671e-01 5.9810e-01 1.9300e-01 1.8080e+00 +NIPSNAP3A ENST00000374767 2.2722e-12 1.2499e+00 8.4200e-01 1.8080e+00 +STATH ENST00000246895 7.9792e-05 1.0442e+00 5.6300e-01 1.8080e+00 +AMTN ENST00000339336 8.1348e-11 1.2247e+00 8.0400e-01 1.8080e+00 +C10orf126 ENST00000375520 1.8470e-03 9.4992e-01 4.5600e-01 1.8080e+00 +BLOC1S5 ENST00000397457 2.8546e-09 1.1935e+00 7.5900e-01 1.8080e+00 +AC025287.1 ENST00000538623 3.9239e-04 1.0026e+00 5.1400e-01 1.8080e+00 +SDSL ENST00000403593 1.3641e-11 1.2378e+00 8.2300e-01 1.8080e+00 +OPTC ENST00000367222 4.8162e-10 1.2105e+00 7.8300e-01 1.8090e+00 +ZNF93 ENST00000343769 3.9048e-04 1.0040e+00 5.1400e-01 1.8090e+00 +OR51Q1 ENST00000300778 7.9022e-05 1.0466e+00 5.6400e-01 1.8090e+00 +CST11 ENST00000377009 7.8838e-05 1.0471e+00 5.6400e-01 1.8090e+00 +JMJD8 ENST00000412368 6.0633e-14 1.2740e+00 8.7700e-01 1.8090e+00 +RDH13 ENST00000415061 6.0402e-14 1.2744e+00 8.7700e-01 1.8090e+00 +RP11-113D6.6 ENST00000527671 3.8877e-04 1.0053e+00 5.1500e-01 1.8090e+00 +C12orf36 ENST00000318426 3.4360e-02 7.8008e-01 3.0200e-01 1.8090e+00 +C20orf202 ENST00000400633 3.4298e-02 7.8111e-01 3.0300e-01 1.8090e+00 +KRTAP10-2 ENST00000391621 3.5103e-01 0.0000e+00 0.0000e+00 1.8100e+00 +HINT1 ENST00000304043 1.8235e-03 9.5443e-01 4.5800e-01 1.8100e+00 +GPR39 ENST00000329321 2.8069e-09 1.1958e+00 7.6100e-01 1.8100e+00 +PRAMEF2 ENST00000240189 4.7446e-10 1.2124e+00 7.8400e-01 1.8100e+00 +HAMP ENST00000598398 8.1797e-03 8.8423e-01 3.8900e-01 1.8100e+00 +TCEAL2 ENST00000372780 3.5082e-01 0.0000e+00 0.0000e+00 1.8100e+00 +C19orf40 ENST00000588258 9.2129e-08 1.1608e+00 7.0900e-01 1.8110e+00 +SFR1 ENST00000369727 4.7059e-10 1.2134e+00 7.8500e-01 1.8110e+00 +AF165138.7 ENST00000400562 5.2132e-07 1.1377e+00 6.7900e-01 1.8110e+00 +TBC1D28 ENST00000345096 1.6133e-08 1.1799e+00 7.3700e-01 1.8110e+00 +SLC22A31 ENST00000562855 7.9100e-11 1.2281e+00 8.0600e-01 1.8110e+00 +HSF2BP ENST00000291560 2.5257e-16 1.3064e+00 9.2300e-01 1.8120e+00 +TMEM223 ENST00000307366 1.5027e-05 1.0863e+00 6.0900e-01 1.8120e+00 +SDHAF2 ENST00000301761 2.8312e-06 1.1145e+00 6.4600e-01 1.8120e+00 +C17orf102 ENST00000357754 8.1248e-03 8.8720e-01 3.9000e-01 1.8120e+00 +AL354993.1 ENST00000439873 3.3998e-02 7.8610e-01 3.0400e-01 1.8120e+00 +TMIE ENST00000326431 7.7490e-05 1.0514e+00 5.6600e-01 1.8120e+00 +PABPC1L2A ENST00000373519 3.5004e-01 0.0000e+00 0.0000e+00 1.8120e+00 +ZNF547 ENST00000282282 8.0575e-03 8.9089e-01 3.9100e-01 1.8130e+00 +KRTAP4-6 ENST00000345847 3.7950e-04 1.0124e+00 5.1800e-01 1.8130e+00 +AC131097.4 ENST00000452112 8.0869e-03 8.8927e-01 3.9100e-01 1.8130e+00 +COMMD5 ENST00000450361 1.4970e-05 1.0871e+00 6.0900e-01 1.8130e+00 +GINS2 ENST00000253462 1.5745e-08 1.1834e+00 7.3900e-01 1.8130e+00 +C2orf27A ENST00000355171 3.4910e-01 0.0000e+00 0.0000e+00 1.8130e+00 +RSAD2 ENST00000382040 9.4432e-15 1.2889e+00 8.9500e-01 1.8130e+00 +AC003002.4 ENST00000597658 8.0575e-03 8.9089e-01 3.9100e-01 1.8130e+00 +KRTAP5-2 ENST00000412090 8.0469e-03 8.9147e-01 3.9100e-01 1.8140e+00 +TMEM45B ENST00000281441 1.2660e-11 1.2463e+00 8.2900e-01 1.8140e+00 +OR1N2 ENST00000373688 1.4852e-05 1.0888e+00 6.1000e-01 1.8140e+00 +TAAR2 ENST00000367931 7.6400e-11 1.2323e+00 8.0900e-01 1.8140e+00 +BRI3 ENST00000297290 3.3766e-02 7.9005e-01 3.0600e-01 1.8140e+00 +C21orf37 ENST00000440664 3.3685e-02 7.9144e-01 3.0600e-01 1.8140e+00 +OR5T2 ENST00000313264 3.7811e-04 1.0135e+00 5.1900e-01 1.8140e+00 +AC106873.4 ENST00000420664 1.2431e-01 6.1335e-01 1.9600e-01 1.8150e+00 +C1orf185 ENST00000371759 5.0044e-07 1.1448e+00 6.8300e-01 1.8150e+00 +FCN1 ENST00000371806 3.9675e-17 1.3175e+00 9.3800e-01 1.8150e+00 +MANBAL ENST00000373605 3.3539e-02 7.9397e-01 3.0700e-01 1.8150e+00 +OTOL1 ENST00000327928 1.4999e-15 1.3007e+00 9.1100e-01 1.8150e+00 +LRRC66 ENST00000343457 4.5037e-10 1.2190e+00 7.8800e-01 1.8150e+00 +DNAJC24 ENST00000465995 5.0103e-07 1.1446e+00 6.8200e-01 1.8150e+00 +ZNF616 ENST00000600228 8.0095e-03 8.9355e-01 3.9200e-01 1.8150e+00 +CCL1 ENST00000225842 7.9669e-03 8.9594e-01 3.9300e-01 1.8160e+00 +CDRT15L2 ENST00000399044 1.7737e-03 9.6434e-01 4.6200e-01 1.8160e+00 +CTD-2600O9.1 ENST00000564282 3.4754e-01 0.0000e+00 0.0000e+00 1.8160e+00 +LINC01098 ENST00000507870 3.7385e-04 1.0169e+00 5.2000e-01 1.8160e+00 +PQLC3 ENST00000295083 4.4278e-10 1.2212e+00 7.8900e-01 1.8160e+00 +RP11-167N24.6 ENST00000549961 3.4753e-01 0.0000e+00 0.0000e+00 1.8160e+00 +RP11-215A19.2 ENST00000509111 1.2380e-01 6.1676e-01 1.9700e-01 1.8160e+00 +AC068987.1 ENST00000599343 1.2376e-01 6.1701e-01 1.9700e-01 1.8160e+00 +MRPL20 ENST00000344843 2.7079e-06 1.1230e+00 6.5100e-01 1.8170e+00 +C20ORF135 ENST00000601296 1.2342e-01 6.1928e-01 1.9800e-01 1.8170e+00 +OR10Q1 ENST00000316770 7.5216e-05 1.0589e+00 5.7000e-01 1.8170e+00 +PLA2G2F ENST00000375102 2.7094e-06 1.1229e+00 6.5100e-01 1.8170e+00 +C7orf71 ENST00000409974 3.7182e-04 1.0185e+00 5.2100e-01 1.8170e+00 +C14orf182 ENST00000399206 7.5190e-05 1.0590e+00 5.7000e-01 1.8170e+00 +TRIM49 ENST00000329758 4.9111e-07 1.1480e+00 6.8400e-01 1.8170e+00 +OR4K17 ENST00000315543 1.7626e-03 9.6660e-01 4.6300e-01 1.8170e+00 +S100A3 ENST00000368713 7.9273e-03 8.9818e-01 3.9400e-01 1.8170e+00 +RP4-576H24.4 ENST00000567028 1.7506e-03 9.6907e-01 4.6400e-01 1.8180e+00 +CCL5 ENST00000293272 1.7516e-03 9.6886e-01 4.6400e-01 1.8180e+00 +CFHR2 ENST00000367415 1.5063e-08 1.1899e+00 7.4200e-01 1.8180e+00 +RP11-126K1.2 ENST00000447795 1.2305e-01 6.2178e-01 1.9800e-01 1.8180e+00 +C12orf68 ENST00000316554 1.7497e-03 9.6926e-01 4.6400e-01 1.8180e+00 +C8orf59 ENST00000417663 7.8980e-03 8.9985e-01 3.9400e-01 1.8180e+00 +CRYGA ENST00000304502 4.3304e-10 1.2241e+00 7.9100e-01 1.8180e+00 +TMEM114 ENST00000568335 3.3213e-02 7.9968e-01 3.0900e-01 1.8180e+00 +CITED4 ENST00000372638 3.4638e-01 0.0000e+00 0.0000e+00 1.8180e+00 +GPR78 ENST00000382487 2.6834e-06 1.1248e+00 6.5200e-01 1.8180e+00 +S100P ENST00000296370 3.3257e-02 7.9892e-01 3.0800e-01 1.8180e+00 +SSX7 ENST00000298181 2.6848e-06 1.1247e+00 6.5200e-01 1.8180e+00 +AP000708.1 ENST00000527818 1.2270e-01 6.2417e-01 1.9900e-01 1.8190e+00 +OR12D3 ENST00000396806 7.8534e-03 9.0242e-01 3.9500e-01 1.8190e+00 +IL18BP ENST00000404792 1.4840e-08 1.1921e+00 7.4400e-01 1.8190e+00 +TSPAN19 ENST00000532498 1.9829e-12 1.2647e+00 8.5100e-01 1.8190e+00 +RP11-17M16.1 ENST00000532511 3.4567e-01 0.0000e+00 0.0000e+00 1.8190e+00 +ASCL2 ENST00000331289 3.4557e-01 0.0000e+00 0.0000e+00 1.8190e+00 +CEA ENST00000598976 4.8616e-07 1.1498e+00 6.8500e-01 1.8190e+00 +CACNG1 ENST00000226021 1.4908e-08 1.1914e+00 7.4300e-01 1.8190e+00 +FAM69C ENST00000343998 4.8312e-07 1.1509e+00 6.8600e-01 1.8190e+00 +PTER ENST00000378000 3.2773e-13 1.2756e+00 8.6800e-01 1.8190e+00 +COMMD2 ENST00000473414 2.5421e-09 1.2093e+00 7.6900e-01 1.8190e+00 +FAM187B ENST00000324675 2.5120e-09 1.2109e+00 7.7000e-01 1.8200e+00 +ZNF559 ENST00000393883 1.4172e-05 1.0991e+00 6.1600e-01 1.8200e+00 +C19orf84 ENST00000574814 3.4514e-01 0.0000e+00 0.0000e+00 1.8200e+00 +OR1G1 ENST00000328890 3.6576e-04 1.0234e+00 5.2300e-01 1.8200e+00 +C16orf98 ENST00000561916 3.4493e-01 0.0000e+00 0.0000e+00 1.8200e+00 +C1orf162 ENST00000343534 1.4202e-05 1.0986e+00 6.1500e-01 1.8200e+00 +SMIM1 ENST00000444870 3.2962e-02 8.0418e-01 3.1000e-01 1.8200e+00 +MAGEE2 ENST00000373359 1.9687e-12 1.2655e+00 8.5200e-01 1.8200e+00 +GAGE12H ENST00000381722 3.4494e-01 0.0000e+00 0.0000e+00 1.8200e+00 +WBP5 ENST00000372661 1.2214e-01 6.2801e-01 2.0000e-01 1.8210e+00 +FAM72A ENST00000367128 3.2815e-02 8.0684e-01 3.1100e-01 1.8210e+00 +GPR111 ENST00000296862 2.5133e-24 1.3838e+00 1.0370e+00 1.8210e+00 +VCX ENST00000381059 3.4444e-01 0.0000e+00 0.0000e+00 1.8210e+00 +LSMEM1 ENST00000312849 3.6247e-04 1.0261e+00 5.2400e-01 1.8210e+00 +STARD4 ENST00000296632 6.9854e-11 1.2431e+00 8.1500e-01 1.8220e+00 +TXNL4A ENST00000269601 7.2309e-05 1.0690e+00 5.7500e-01 1.8220e+00 +AC017028.1 ENST00000396489 7.7214e-03 9.1017e-01 3.9800e-01 1.8230e+00 +P2RY11 ENST00000321826 7.7062e-03 9.1107e-01 3.9900e-01 1.8230e+00 +PET100 ENST00000594797 3.5883e-04 1.0292e+00 5.2600e-01 1.8230e+00 +CHST6 ENST00000332272 2.4495e-09 1.2144e+00 7.7200e-01 1.8230e+00 +RP11-386G21.2 ENST00000522559 3.4302e-01 0.0000e+00 0.0000e+00 1.8230e+00 +AL035406.1 ENST00000594544 3.4347e-01 0.0000e+00 0.0000e+00 1.8230e+00 +ZFP41 ENST00000330701 3.5717e-04 1.0306e+00 5.2600e-01 1.8230e+00 +ZFP41 ENST00000522452 3.5717e-04 1.0306e+00 5.2600e-01 1.8230e+00 +MS4A10 ENST00000308287 1.1360e-11 1.2588e+00 8.3700e-01 1.8230e+00 +RP11-1396O13.13 ENST00000508324 3.5770e-04 1.0302e+00 5.2600e-01 1.8230e+00 +CRYGB ENST00000260988 8.1381e-08 1.1806e+00 7.2100e-01 1.8240e+00 +C21orf54 ENST00000451980 3.5513e-04 1.0324e+00 5.2700e-01 1.8240e+00 +C14orf142 ENST00000306954 7.6870e-03 9.1222e-01 3.9900e-01 1.8240e+00 +NACA2 ENST00000521764 3.2413e-02 8.1428e-01 3.1300e-01 1.8240e+00 +C1orf234 ENST00000566855 7.6505e-03 9.1443e-01 4.0000e-01 1.8250e+00 +CTD-2583A14.10 ENST00000598031 7.6389e-03 9.1513e-01 4.0000e-01 1.8250e+00 +OR5AS1 ENST00000313555 1.6835e-03 9.8343e-01 4.7000e-01 1.8250e+00 +AKR1CL1 ENST00000488756 1.3656e-05 1.1073e+00 6.2000e-01 1.8250e+00 +GJB5 ENST00000338513 1.3704e-05 1.1066e+00 6.1900e-01 1.8250e+00 +C11orf83 ENST00000531323 3.2331e-02 8.1582e-01 3.1300e-01 1.8250e+00 +HIST1H2AE ENST00000303910 3.2343e-02 8.1559e-01 3.1300e-01 1.8250e+00 +CCL3L1 ENST00000422211 1.2057e-01 6.3918e-01 2.0200e-01 1.8250e+00 +MT1G ENST00000444837 3.2173e-02 8.1881e-01 3.1400e-01 1.8260e+00 +MUSTN1 ENST00000446157 7.0616e-05 1.0751e+00 5.7800e-01 1.8260e+00 +C9orf153 ENST00000376001 7.6085e-03 9.1699e-01 4.0100e-01 1.8260e+00 +EIF5AL1 ENST00000520547 3.4147e-01 0.0000e+00 0.0000e+00 1.8260e+00 +CLLU1 ENST00000378485 1.6736e-03 9.8562e-01 4.7100e-01 1.8260e+00 +TMEM218 ENST00000455225 1.6754e-03 9.8522e-01 4.7100e-01 1.8260e+00 +TP53TG3D ENST00000398664 7.5995e-03 9.1753e-01 4.0100e-01 1.8260e+00 +CLDN4 ENST00000435050 6.9789e-05 1.0781e+00 5.7900e-01 1.8270e+00 +NBPF12 ENST00000442909 1.2675e-15 1.3166e+00 9.2200e-01 1.8270e+00 +ZNF519 ENST00000590202 7.5723e-03 9.1921e-01 4.0200e-01 1.8270e+00 +CIB3 ENST00000269878 2.3448e-09 1.2204e+00 7.7500e-01 1.8270e+00 +C19orf82 ENST00000587536 1.6695e-03 9.8654e-01 4.7100e-01 1.8270e+00 +PET117 ENST00000432901 3.2067e-02 8.2083e-01 3.1500e-01 1.8270e+00 +C7orf69 ENST00000258776 1.6636e-03 9.8784e-01 4.7200e-01 1.8270e+00 +UBE2Q2L ENST00000558195 3.4005e-01 0.0000e+00 0.0000e+00 1.8280e+00 +C1orf233 ENST00000422725 1.1948e-01 6.4725e-01 2.0400e-01 1.8280e+00 +GAGE10 ENST00000407599 1.6612e-03 9.8839e-01 4.7200e-01 1.8280e+00 +CYB5D1 ENST00000332439 3.9032e-10 1.2376e+00 7.9900e-01 1.8280e+00 +SULT2A1 ENST00000222002 1.2523e-15 1.3177e+00 9.2300e-01 1.8280e+00 +AL162407.1 ENST00000451472 3.3991e-01 0.0000e+00 0.0000e+00 1.8280e+00 +SLC34A1 ENST00000324417 8.9128e-27 1.4064e+00 1.0670e+00 1.8280e+00 +BTN2A1 ENST00000312541 3.3959e-21 1.3710e+00 1.0070e+00 1.8290e+00 +ZNF670 ENST00000366503 3.4522e-04 1.0411e+00 5.3100e-01 1.8290e+00 +EIF4EBP3 ENST00000310331 3.4389e-04 1.0422e+00 5.3200e-01 1.8290e+00 +CFHR5 ENST00000256785 2.1117e-32 1.4363e+00 1.1160e+00 1.8290e+00 +PRSS48 ENST00000455694 1.0574e-11 1.2672e+00 8.4200e-01 1.8290e+00 +TCTE3 ENST00000366774 2.2780e-09 1.2245e+00 7.7800e-01 1.8290e+00 +C22orf23 ENST00000249079 4.6831e-14 1.3002e+00 8.9400e-01 1.8290e+00 +RP11-770J1.5 ENST00000534438 1.1927e-01 6.4885e-01 2.0400e-01 1.8290e+00 +LCN1 ENST00000263598 1.3298e-08 1.2084e+00 7.5300e-01 1.8300e+00 +OR1J1 ENST00000259357 6.8342e-05 1.0836e+00 5.8200e-01 1.8300e+00 +RP11-219B4.6 ENST00000551479 1.1869e-01 6.5323e-01 2.0500e-01 1.8300e+00 +PSMB11 ENST00000408907 2.4272e-06 1.1446e+00 6.6200e-01 1.8300e+00 +CTRB1 ENST00000361017 2.4233e-06 1.1449e+00 6.6200e-01 1.8300e+00 +SIGLECL1 ENST00000316401 7.6919e-08 1.1897e+00 7.2600e-01 1.8300e+00 +APCS ENST00000255040 3.1714e-02 8.2771e-01 3.1700e-01 1.8300e+00 +AC013468.1 ENST00000424876 3.3869e-01 0.0000e+00 0.0000e+00 1.8300e+00 +CELA2A ENST00000359621 1.9736e-16 1.3288e+00 9.3800e-01 1.8300e+00 +OR2A4 ENST00000315453 1.1869e-01 6.5326e-01 2.0500e-01 1.8300e+00 +FAM174B ENST00000327355 1.6376e-03 9.9377e-01 4.7400e-01 1.8300e+00 +ASCL4 ENST00000342331 1.6311e-03 9.9528e-01 4.7500e-01 1.8310e+00 +ZNF28 ENST00000457749 7.4328e-03 9.2797e-01 4.0500e-01 1.8310e+00 +ZNF576 ENST00000336564 1.6326e-03 9.9492e-01 4.7500e-01 1.8310e+00 +KCNE1L ENST00000372101 1.1854e-01 6.5440e-01 2.0500e-01 1.8310e+00 +HRASLS2 ENST00000255695 6.7817e-05 1.0856e+00 5.8300e-01 1.8310e+00 +CD3EAP ENST00000309424 3.1626e-02 8.2943e-01 3.1800e-01 1.8310e+00 +C15orf56 ENST00000319503 3.1586e-02 8.3024e-01 3.1800e-01 1.8310e+00 +ZNF530 ENST00000332854 7.4390e-03 9.2757e-01 4.0500e-01 1.8310e+00 +AC007956.1 ENST00000338772 7.4157e-03 9.2907e-01 4.0500e-01 1.8310e+00 +PNRC2 ENST00000334351 3.3763e-01 0.0000e+00 0.0000e+00 1.8320e+00 +MNDA ENST00000368141 3.0917e-17 1.3395e+00 9.5300e-01 1.8320e+00 +C1orf204 ENST00000368102 1.2953e-08 1.2124e+00 7.5500e-01 1.8320e+00 +SMIM9 ENST00000369529 7.3927e-03 9.3055e-01 4.0600e-01 1.8320e+00 +C16orf91 ENST00000310355 1.6879e-12 1.2827e+00 8.6300e-01 1.8320e+00 +CTD-2210P24.4 ENST00000378779 1.1792e-01 6.5922e-01 2.0700e-01 1.8320e+00 +TRIM40 ENST00000307859 6.1659e-11 1.2586e+00 8.2500e-01 1.8320e+00 +RP11-463J10.2 ENST00000556834 3.1374e-02 8.3448e-01 3.1900e-01 1.8320e+00 +ID4 ENST00000378700 3.1243e-02 8.3713e-01 3.2000e-01 1.8330e+00 +MT1E ENST00000306061 3.1344e-02 8.3509e-01 3.1900e-01 1.8330e+00 +PGBD4 ENST00000397766 3.3709e-01 0.0000e+00 0.0000e+00 1.8330e+00 +AL136218.1 ENST00000400396 3.3675e-04 1.0488e+00 5.3400e-01 1.8330e+00 +AL138815.1 ENST00000400553 1.1764e-01 6.6142e-01 2.0700e-01 1.8330e+00 +AL929472.1 ENST00000448796 3.3693e-01 0.0000e+00 0.0000e+00 1.8330e+00 +HIST1H2BJ ENST00000607124 3.1259e-02 8.3681e-01 3.2000e-01 1.8330e+00 +OR5M11 ENST00000528616 3.3488e-04 1.0505e+00 5.3500e-01 1.8330e+00 +RNASE9 ENST00000404716 3.3655e-01 0.0000e+00 0.0000e+00 1.8330e+00 +CDKN2B ENST00000276925 7.3369e-03 9.3417e-01 4.0700e-01 1.8330e+00 +OR51B6 ENST00000380219 6.6815e-05 1.0895e+00 5.8400e-01 1.8330e+00 +OR13F1 ENST00000334726 1.2757e-05 1.1227e+00 6.2800e-01 1.8330e+00 +LYG2 ENST00000333017 2.1715e-09 1.2313e+00 7.8200e-01 1.8330e+00 +VCX3B ENST00000381032 3.3685e-01 0.0000e+00 0.0000e+00 1.8330e+00 +CARD17 ENST00000375707 6.6679e-05 1.0901e+00 5.8500e-01 1.8330e+00 +MR1 ENST00000367580 4.9023e-18 1.3483e+00 9.6600e-01 1.8330e+00 +RP11-77K12.1 ENST00000567194 1.2828e-05 1.1214e+00 6.2700e-01 1.8330e+00 +C2orf66 ENST00000342506 7.3036e-03 9.3636e-01 4.0800e-01 1.8340e+00 +MMP23B ENST00000356026 1.1732e-01 6.6399e-01 2.0800e-01 1.8340e+00 +C10orf10 ENST00000298295 3.3608e-01 0.0000e+00 0.0000e+00 1.8340e+00 +CLDN17 ENST00000286808 3.3411e-04 1.0512e+00 5.3600e-01 1.8340e+00 +TAF9 ENST00000328663 4.2231e-07 1.1748e+00 6.9900e-01 1.8340e+00 +APOL2 ENST00000249066 7.3139e-03 9.3568e-01 4.0800e-01 1.8340e+00 +SSNA1 ENST00000322310 3.3383e-04 1.0515e+00 5.3600e-01 1.8340e+00 +PCBD1 ENST00000299299 3.3216e-04 1.0531e+00 5.3600e-01 1.8350e+00 +C1orf63 ENST00000243189 4.3086e-14 1.3088e+00 8.9900e-01 1.8350e+00 +C10orf91 ENST00000392630 3.1044e-02 8.4123e-01 3.2100e-01 1.8350e+00 +ARL17B ENST00000450673 3.3578e-01 0.0000e+00 0.0000e+00 1.8350e+00 +NDUFA7 ENST00000301457 6.6032e-05 1.0927e+00 5.8600e-01 1.8350e+00 +CCL4L1 ENST00000444414 3.3576e-01 0.0000e+00 0.0000e+00 1.8350e+00 +DGCR6 ENST00000331444 9.8176e-12 1.2761e+00 8.4800e-01 1.8350e+00 +HHLA3 ENST00000370940 7.2792e-03 9.3797e-01 4.0800e-01 1.8350e+00 +MAGIX ENST00000412696 6.6022e-05 1.0927e+00 5.8600e-01 1.8350e+00 +AC112205.1 ENST00000599797 3.3575e-01 0.0000e+00 0.0000e+00 1.8350e+00 +ACYP2 ENST00000394666 6.5331e-05 1.0955e+00 5.8700e-01 1.8360e+00 +PSG6 ENST00000292125 4.8204e-22 1.3857e+00 1.0230e+00 1.8360e+00 +OR51F2 ENST00000322110 4.1263e-07 1.1790e+00 7.0100e-01 1.8360e+00 +RNASE7 ENST00000298690 1.1606e-01 6.7418e-01 2.1000e-01 1.8370e+00 +C5orf64 ENST00000505642 7.1986e-03 9.4337e-01 4.1000e-01 1.8370e+00 +COX8A ENST00000314133 1.1606e-01 6.7418e-01 2.1000e-01 1.8370e+00 +MEIG1 ENST00000407572 3.2669e-04 1.0583e+00 5.3900e-01 1.8370e+00 +CHAC2 ENST00000295304 2.2869e-06 1.1566e+00 6.6800e-01 1.8370e+00 +TREML1 ENST00000426005 1.5671e-12 1.2912e+00 8.6800e-01 1.8370e+00 +MC5R ENST00000324750 6.5130e-05 1.0963e+00 5.8800e-01 1.8370e+00 +DDTL ENST00000215770 3.3439e-01 0.0000e+00 0.0000e+00 1.8370e+00 +OR4S1 ENST00000319988 1.5718e-03 1.0094e+00 4.8100e-01 1.8370e+00 +C8orf33 ENST00000331434 2.0873e-09 1.2369e+00 7.8500e-01 1.8370e+00 +OR2T33 ENST00000318021 1.1612e-01 6.7374e-01 2.1000e-01 1.8370e+00 +ANXA8L1 ENST00000359178 3.3439e-01 0.0000e+00 0.0000e+00 1.8370e+00 +ECI1 ENST00000301729 1.5853e-12 1.2899e+00 8.6700e-01 1.8370e+00 +RP11-830F9.6 ENST00000378347 3.3439e-01 0.0000e+00 0.0000e+00 1.8370e+00 +AC003006.7 ENST00000594684 7.1661e-03 9.4558e-01 4.1100e-01 1.8380e+00 +PHPT1 ENST00000247665 6.4270e-05 1.0999e+00 5.8900e-01 1.8380e+00 +AAMDC ENST00000526415 2.2702e-06 1.1581e+00 6.6900e-01 1.8380e+00 +ATP2C2 ENST00000262429 5.0246e-60 1.5302e+00 1.2680e+00 1.8380e+00 +C17orf64 ENST00000269127 1.5580e-12 1.2919e+00 8.6900e-01 1.8380e+00 +LCE2A ENST00000368779 7.1716e-03 9.4520e-01 4.1100e-01 1.8380e+00 +SCP2D1 ENST00000377428 7.1644e-03 9.4569e-01 4.1100e-01 1.8380e+00 +OR1L1 ENST00000309623 3.3258e-01 0.0000e+00 0.0000e+00 1.8390e+00 +C14orf177 ENST00000325812 3.0533e-02 8.5199e-01 3.2400e-01 1.8390e+00 +IFITM3 ENST00000399808 3.0466e-02 8.5341e-01 3.2500e-01 1.8390e+00 +AMY1A ENST00000370083 3.2325e-04 1.0617e+00 5.4000e-01 1.8390e+00 +PSG3 ENST00000327495 2.9137e-25 1.4101e+00 1.0610e+00 1.8390e+00 +AC011500.1 ENST00000396843 1.5552e-03 1.0136e+00 4.8200e-01 1.8390e+00 +SCGB3A1 ENST00000292641 3.0493e-02 8.5284e-01 3.2500e-01 1.8390e+00 +SPINK8 ENST00000434006 6.3692e-05 1.1023e+00 5.9100e-01 1.8390e+00 +AC009802.1 ENST00000599868 3.3190e-01 0.0000e+00 0.0000e+00 1.8400e+00 +OR4F5 ENST00000335137 3.0354e-02 8.5584e-01 3.2500e-01 1.8400e+00 +CCL24 ENST00000416943 7.0888e-03 9.5091e-01 4.1300e-01 1.8400e+00 +MTMR8 ENST00000374852 7.0105e-19 1.3653e+00 9.8400e-01 1.8400e+00 +ZNF730 ENST00000597761 6.3597e-05 1.1027e+00 5.9100e-01 1.8400e+00 +CRYGN ENST00000337323 3.9735e-07 1.1860e+00 7.0500e-01 1.8400e+00 +GDPGP1 ENST00000558017 1.1916e-08 1.2252e+00 7.6300e-01 1.8400e+00 +CGB2 ENST00000359342 3.0408e-02 8.5468e-01 3.2500e-01 1.8400e+00 +RP1-127H14.3 ENST00000535109 1.5489e-03 1.0151e+00 4.8300e-01 1.8400e+00 +AC015987.2 ENST00000416501 1.1503e-01 6.8286e-01 2.1200e-01 1.8400e+00 +AC015989.1 ENST00000400312 3.3245e-01 0.0000e+00 0.0000e+00 1.8400e+00 +CLEC2A ENST00000455827 2.1910e-06 1.1653e+00 6.7300e-01 1.8410e+00 +DEFB104B ENST00000316169 3.3176e-01 0.0000e+00 0.0000e+00 1.8410e+00 +DKFZP779J2370 ENST00000378904 3.0253e-02 8.5806e-01 3.2600e-01 1.8410e+00 +RP11-368I7.4 ENST00000567544 3.1840e-04 1.0665e+00 5.4200e-01 1.8410e+00 +S100G ENST00000380200 1.1469e-01 6.8581e-01 2.1200e-01 1.8410e+00 +RPAIN ENST00000405578 5.5657e-11 1.2716e+00 8.3300e-01 1.8410e+00 +VCPKMT ENST00000395860 5.5498e-11 1.2720e+00 8.3300e-01 1.8410e+00 +UBD ENST00000377050 7.0467e-03 9.5386e-01 4.1400e-01 1.8410e+00 +RP11-80A15.1 ENST00000555109 1.1481e-01 6.8480e-01 2.1200e-01 1.8410e+00 +RP11-9B6.1 ENST00000504213 3.3142e-01 0.0000e+00 0.0000e+00 1.8410e+00 +ZNF92 ENST00000328747 6.2887e-05 1.1057e+00 5.9200e-01 1.8410e+00 +GPR148 ENST00000309926 6.2587e-05 1.1070e+00 5.9300e-01 1.8420e+00 +PRAMEF7 ENST00000361079 3.3075e-01 0.0000e+00 0.0000e+00 1.8420e+00 +OR10R2 ENST00000368152 3.1480e-04 1.0702e+00 5.4400e-01 1.8420e+00 +IGFALS ENST00000415638 5.4379e-11 1.2746e+00 8.3500e-01 1.8420e+00 +DYNLRB2 ENST00000305904 6.1715e-05 1.1108e+00 5.9500e-01 1.8430e+00 +UBL4B ENST00000334179 3.0024e-02 8.6311e-01 3.2800e-01 1.8430e+00 +ZNF736 ENST00000423484 3.1345e-04 1.0716e+00 5.4500e-01 1.8430e+00 +LCE1B ENST00000360090 3.0040e-02 8.6275e-01 3.2800e-01 1.8430e+00 +TRIM65 ENST00000269383 2.7066e-21 1.3885e+00 1.0190e+00 1.8430e+00 +FAM86B1 ENST00000448228 3.8216e-07 1.1932e+00 7.0900e-01 1.8440e+00 +AC096644.1 ENST00000416839 1.1357e-01 6.9567e-01 2.1400e-01 1.8440e+00 +KRTAP2-3 ENST00000391418 6.9368e-03 9.6171e-01 4.1700e-01 1.8440e+00 +FAM72D ENST00000400889 2.9905e-02 8.6578e-01 3.2800e-01 1.8440e+00 +PRAMEF15 ENST00000330087 3.2928e-01 0.0000e+00 0.0000e+00 1.8440e+00 +C1orf200 ENST00000377320 2.9774e-02 8.6874e-01 3.2900e-01 1.8440e+00 +LRP5L ENST00000402859 5.3205e-11 1.2774e+00 8.3600e-01 1.8440e+00 +DDT ENST00000398344 3.2959e-01 0.0000e+00 0.0000e+00 1.8440e+00 +AC006486.1 ENST00000378108 1.1351e-01 6.9621e-01 2.1400e-01 1.8440e+00 +GAGE13 ENST00000381751 3.2958e-01 0.0000e+00 0.0000e+00 1.8440e+00 +DEFB124 ENST00000317676 1.1330e-01 6.9810e-01 2.1500e-01 1.8440e+00 +RNF183 ENST00000478815 1.5130e-03 1.0244e+00 4.8700e-01 1.8440e+00 +VMO1 ENST00000328739 2.1183e-06 1.1723e+00 6.7700e-01 1.8450e+00 +MMP28 ENST00000250144 6.0903e-05 1.1145e+00 5.9600e-01 1.8450e+00 +ID1 ENST00000376112 3.1026e-04 1.0749e+00 5.4600e-01 1.8450e+00 +HSPB3 ENST00000302005 6.0944e-05 1.1143e+00 5.9600e-01 1.8450e+00 +UPK3BL ENST00000340457 1.1302e-01 7.0056e-01 2.1500e-01 1.8450e+00 +LCE5A ENST00000334269 2.9651e-02 8.7156e-01 3.3000e-01 1.8450e+00 +TMEM61 ENST00000371268 6.0832e-05 1.1148e+00 5.9600e-01 1.8450e+00 +SLC22A16 ENST00000368919 6.3118e-27 1.4287e+00 1.0840e+00 1.8460e+00 +CHURC1 ENST00000607599 2.0933e-06 1.1748e+00 6.7800e-01 1.8460e+00 +OR4F6 ENST00000328882 1.1444e-05 1.1480e+00 6.4000e-01 1.8460e+00 +MC2R ENST00000327606 3.0712e-04 1.0782e+00 5.4700e-01 1.8460e+00 +HIST1H2AI ENST00000358739 2.9517e-02 8.7465e-01 3.3100e-01 1.8460e+00 +RP11-10A14.4 ENST00000518496 2.9508e-02 8.7488e-01 3.3100e-01 1.8460e+00 +C1orf145 ENST00000295012 2.9398e-02 8.7744e-01 3.3200e-01 1.8470e+00 +CXorf66 ENST00000370540 2.9379e-02 8.7787e-01 3.3200e-01 1.8470e+00 +PEX12 ENST00000225873 9.4838e-16 1.3448e+00 9.4100e-01 1.8470e+00 +POM121L2 ENST00000444565 3.2747e-01 0.0000e+00 0.0000e+00 1.8470e+00 +TIMM10 ENST00000257245 1.4821e-03 1.0326e+00 4.9000e-01 1.8470e+00 +C11orf1 ENST00000260276 1.8467e-09 1.2547e+00 7.9500e-01 1.8470e+00 +ZNF695 ENST00000339986 3.0547e-04 1.0799e+00 5.4800e-01 1.8470e+00 +TRAPPC2P1 ENST00000543226 2.9497e-02 8.7513e-01 3.3100e-01 1.8470e+00 +OR10X1 ENST00000368150 3.0581e-04 1.0796e+00 5.4800e-01 1.8470e+00 +AC003101.1 ENST00000412403 3.0547e-04 1.0799e+00 5.4800e-01 1.8470e+00 +CXCL3 ENST00000296026 3.0234e-04 1.0833e+00 5.5000e-01 1.8480e+00 +RP11-664D7.4 ENST00000512294 1.4724e-03 1.0352e+00 4.9100e-01 1.8480e+00 +PMAIP1 ENST00000316660 1.1182e-01 7.1177e-01 2.1800e-01 1.8480e+00 +OR56B3P ENST00000316517 1.1268e-05 1.1516e+00 6.4200e-01 1.8480e+00 +TMEM221 ENST00000341130 6.7947e-03 9.7222e-01 4.2100e-01 1.8480e+00 +C1orf134 ENST00000375605 3.2626e-01 0.0000e+00 0.0000e+00 1.8480e+00 +CXorf31 ENST00000377879 1.1186e-01 7.1137e-01 2.1700e-01 1.8480e+00 +DEFB107A ENST00000335021 3.2633e-01 0.0000e+00 0.0000e+00 1.8480e+00 +ULBP2 ENST00000367351 1.8392e-09 1.2553e+00 7.9600e-01 1.8480e+00 +CTC-236F12.4 ENST00000506836 6.7819e-03 9.7318e-01 4.2100e-01 1.8480e+00 +VTCN1 ENST00000369458 1.3669e-12 1.3071e+00 8.7800e-01 1.8480e+00 +GNG5P2 ENST00000372054 3.2594e-01 0.0000e+00 0.0000e+00 1.8490e+00 +RP11-45H22.3 ENST00000505950 1.1161e-01 7.1374e-01 2.1800e-01 1.8490e+00 +RP11-738G5.2 ENST00000520800 2.9157e-02 8.8313e-01 3.3300e-01 1.8490e+00 +ZG16B ENST00000382280 2.9994e-04 1.0859e+00 5.5100e-01 1.8490e+00 +ZNF550 ENST00000506609 3.6166e-07 1.2035e+00 7.1500e-01 1.8490e+00 +OR5AN1 ENST00000313940 5.9253e-05 1.1220e+00 6.0000e-01 1.8490e+00 +OR6P1 ENST00000334632 5.8864e-05 1.1238e+00 6.0100e-01 1.8490e+00 +CLDN24 ENST00000541814 2.0392e-06 1.1803e+00 6.8100e-01 1.8490e+00 +FBXL22 ENST00000360587 1.4582e-03 1.0391e+00 4.9300e-01 1.8490e+00 +HLA-DRB5 ENST00000374975 3.6359e-07 1.2025e+00 7.1400e-01 1.8490e+00 +RPS17 ENST00000330339 3.2566e-01 0.0000e+00 0.0000e+00 1.8490e+00 +SVIP ENST00000354193 3.0038e-04 1.0855e+00 5.5100e-01 1.8490e+00 +ZNF417 ENST00000312026 6.7514e-03 9.7550e-01 4.2200e-01 1.8490e+00 +PSG9 ENST00000270077 3.8689e-22 1.4025e+00 1.0350e+00 1.8490e+00 +FAM150A ENST00000358543 5.9081e-05 1.1228e+00 6.0000e-01 1.8490e+00 +VSTM5 ENST00000409977 6.2537e-08 1.2245e+00 7.4500e-01 1.8490e+00 +C9orf129 ENST00000375419 2.9845e-04 1.0876e+00 5.5200e-01 1.8500e+00 +C21orf90 ENST00000330490 2.8961e-02 8.8785e-01 3.3500e-01 1.8500e+00 +HLA-DOA ENST00000229829 2.9776e-10 1.2742e+00 8.2100e-01 1.8500e+00 +TPSD1 ENST00000211076 8.0398e-12 1.3005e+00 8.6300e-01 1.8500e+00 +AC012313.1 ENST00000601382 2.8998e-02 8.8696e-01 3.3400e-01 1.8500e+00 +IL1F10 ENST00000393197 2.0230e-06 1.1820e+00 6.8200e-01 1.8500e+00 +ZNF114 ENST00000595607 6.7173e-03 9.7811e-01 4.2300e-01 1.8500e+00 +FOXI2 ENST00000388920 2.9852e-04 1.0875e+00 5.5200e-01 1.8500e+00 +KRT6C ENST00000252250 3.8079e-22 1.4037e+00 1.0360e+00 1.8500e+00 +HBA1 ENST00000320868 6.7313e-03 9.7704e-01 4.2200e-01 1.8500e+00 +NMNAT3 ENST00000406164 6.2389e-08 1.2249e+00 7.4600e-01 1.8500e+00 +AC104667.3 ENST00000452801 6.7205e-03 9.7786e-01 4.2200e-01 1.8500e+00 +IQCD ENST00000299732 1.7712e-09 1.2608e+00 7.9900e-01 1.8510e+00 +ARGFX ENST00000334384 2.9585e-04 1.0905e+00 5.5300e-01 1.8510e+00 +TLR1 ENST00000308979 5.8704e-23 1.4112e+00 1.0470e+00 1.8510e+00 +AC018816.3 ENST00000449914 5.7938e-05 1.1282e+00 6.0300e-01 1.8510e+00 +NXPE1 ENST00000251921 1.3061e-12 1.3125e+00 8.8200e-01 1.8510e+00 +RFPL2 ENST00000400237 3.5388e-07 1.2076e+00 7.1700e-01 1.8510e+00 +SSX5 ENST00000311798 1.0514e-08 1.2449e+00 7.7400e-01 1.8510e+00 +MFSD3 ENST00000301327 7.8565e-12 1.3034e+00 8.6500e-01 1.8520e+00 +MAGED4 ENST00000375626 3.2367e-01 0.0000e+00 0.0000e+00 1.8520e+00 +HCRT ENST00000293330 2.8774e-02 8.9242e-01 3.3600e-01 1.8520e+00 +OR10G7 ENST00000330487 2.9385e-04 1.0927e+00 5.5400e-01 1.8520e+00 +RP11-131H24.4 ENST00000557646 2.8802e-02 8.9174e-01 3.3600e-01 1.8520e+00 +FAM154A ENST00000380534 2.3001e-21 1.4014e+00 1.0280e+00 1.8520e+00 +OR10A3 ENST00000360759 3.5206e-07 1.2086e+00 7.1700e-01 1.8520e+00 +BHLHA15 ENST00000609256 6.5801e-03 9.8888e-01 4.2600e-01 1.8530e+00 +AL359736.1 ENST00000422229 3.2290e-01 0.0000e+00 0.0000e+00 1.8530e+00 +HIST1H3F ENST00000446824 6.5896e-03 9.8812e-01 4.2600e-01 1.8530e+00 +ULBP3 ENST00000367339 4.7366e-11 1.2926e+00 8.4600e-01 1.8530e+00 +C1orf61 ENST00000368243 1.0714e-05 1.1637e+00 6.4800e-01 1.8530e+00 +CYTL1 ENST00000307746 1.0733e-05 1.1633e+00 6.4800e-01 1.8530e+00 +OR5K2 ENST00000427338 2.9208e-04 1.0948e+00 5.5500e-01 1.8530e+00 +NPIPA1 ENST00000328085 3.2248e-01 0.0000e+00 0.0000e+00 1.8530e+00 +PATE4 ENST00000457514 1.4234e-03 1.0490e+00 4.9600e-01 1.8530e+00 +POU5F1B ENST00000465342 2.9118e-04 1.0958e+00 5.5500e-01 1.8530e+00 +MAGEB18 ENST00000325250 5.6883e-05 1.1334e+00 6.0500e-01 1.8530e+00 +TMEM262 ENST00000530719 2.9110e-04 1.0959e+00 5.5500e-01 1.8530e+00 +RCVRN ENST00000226193 1.7064e-09 1.2664e+00 8.0200e-01 1.8540e+00 +COX8C ENST00000342144 1.0931e-01 7.3650e-01 2.2200e-01 1.8540e+00 +CARD18 ENST00000530950 1.4150e-03 1.0514e+00 4.9700e-01 1.8540e+00 +KRTAP4-4 ENST00000390661 3.2211e-01 0.0000e+00 0.0000e+00 1.8540e+00 +CSTB ENST00000291568 6.5562e-03 9.9079e-01 4.2700e-01 1.8540e+00 +CYS1 ENST00000381813 1.0934e-01 7.3619e-01 2.2200e-01 1.8540e+00 +FAM47E-STBD1 ENST00000237642 7.6594e-12 1.3066e+00 8.6700e-01 1.8540e+00 +C1orf53 ENST00000367393 5.6149e-05 1.1371e+00 6.0700e-01 1.8550e+00 +C1orf64 ENST00000329454 1.0907e-01 7.3891e-01 2.2300e-01 1.8550e+00 +PABPC1L2B ENST00000373521 3.2142e-01 0.0000e+00 0.0000e+00 1.8550e+00 +SLMO1 ENST00000440960 1.6682e-09 1.2698e+00 8.0400e-01 1.8550e+00 +NT5M ENST00000389022 1.0052e-08 1.2521e+00 7.7800e-01 1.8550e+00 +RLN1 ENST00000223862 6.5226e-03 9.9352e-01 4.2800e-01 1.8550e+00 +CDC42EP5 ENST00000301200 3.2109e-01 0.0000e+00 0.0000e+00 1.8550e+00 +ZNF208 ENST00000397126 5.6261e-05 1.1365e+00 6.0700e-01 1.8550e+00 +ZNF776 ENST00000317178 6.5070e-03 9.9478e-01 4.2800e-01 1.8550e+00 +NDUFB2 ENST00000476279 1.0531e-05 1.1679e+00 6.5000e-01 1.8550e+00 +RP11-834C11.12 ENST00000513209 2.8771e-04 1.0998e+00 5.5700e-01 1.8550e+00 +OTUB2 ENST00000203664 4.5366e-11 1.2983e+00 8.4900e-01 1.8560e+00 +ZNF708 ENST00000356929 5.5534e-05 1.1402e+00 6.0800e-01 1.8560e+00 +ZNF709 ENST00000397732 2.8372e-04 1.1045e+00 5.5900e-01 1.8560e+00 +SERPINB3 ENST00000283752 8.2146e-16 1.3592e+00 9.5000e-01 1.8560e+00 +C7orf65 ENST00000408988 6.5023e-03 9.9517e-01 4.2800e-01 1.8560e+00 +C12orf42 ENST00000378113 2.7519e-10 1.2852e+00 8.2800e-01 1.8560e+00 +ZCCHC13 ENST00000339534 1.3939e-03 1.0576e+00 5.0000e-01 1.8560e+00 +C15orf48 ENST00000344300 5.5498e-05 1.1404e+00 6.0800e-01 1.8560e+00 +AC121757.1 ENST00000594763 1.0845e-01 7.4546e-01 2.2400e-01 1.8560e+00 +CLLU1OS ENST00000378487 2.8369e-04 1.1046e+00 5.5900e-01 1.8560e+00 +OR13C8 ENST00000335040 5.5814e-05 1.1387e+00 6.0800e-01 1.8560e+00 +LRRC30 ENST00000383467 1.8966e-06 1.1957e+00 6.8900e-01 1.8560e+00 +FAM72B ENST00000369390 1.3854e-03 1.0602e+00 5.0100e-01 1.8570e+00 +AC023469.1 ENST00000409243 2.8236e-04 1.1062e+00 5.6000e-01 1.8570e+00 +NPIPA5 ENST00000360151 1.0805e-01 7.4973e-01 2.2500e-01 1.8570e+00 +LUZP4 ENST00000371920 1.3873e-03 1.0596e+00 5.0100e-01 1.8570e+00 +HMGN4 ENST00000377575 3.1986e-01 0.0000e+00 0.0000e+00 1.8570e+00 +GNLY ENST00000263863 9.6899e-09 1.2580e+00 7.8200e-01 1.8570e+00 +TMSB4Y ENST00000284856 3.1923e-01 0.0000e+00 0.0000e+00 1.8580e+00 +ZNF347 ENST00000452676 5.4610e-05 1.1450e+00 6.1000e-01 1.8580e+00 +OR10H1 ENST00000334920 5.4696e-05 1.1445e+00 6.1000e-01 1.8580e+00 +LCE1C ENST00000368768 2.7961e-02 9.1315e-01 3.4200e-01 1.8580e+00 +ANAPC13 ENST00000510994 1.3703e-03 1.0648e+00 5.0300e-01 1.8580e+00 +OR9G4 ENST00000302957 1.8533e-06 1.2007e+00 6.9100e-01 1.8580e+00 +PRLH ENST00000165524 1.0769e-01 7.5355e-01 2.2600e-01 1.8580e+00 +RNF222 ENST00000399398 2.8079e-04 1.1081e+00 5.6000e-01 1.8580e+00 +ZCCHC5 ENST00000321110 4.4007e-11 1.3024e+00 8.5200e-01 1.8580e+00 +RP11-625H11.1 ENST00000558940 1.3759e-03 1.0631e+00 5.0200e-01 1.8580e+00 +SPAG11B ENST00000398462 2.7751e-02 9.1872e-01 3.4300e-01 1.8590e+00 +C1orf213 ENST00000335648 2.7702e-02 9.2005e-01 3.4400e-01 1.8590e+00 +KLHDC4 ENST00000270583 4.5566e-31 1.4658e+00 1.1310e+00 1.8590e+00 +AC090616.2 ENST00000398832 3.1750e-01 0.0000e+00 0.0000e+00 1.8600e+00 +DRD4 ENST00000176183 9.3362e-09 1.2641e+00 7.8500e-01 1.8600e+00 +C19orf71 ENST00000329493 9.3436e-09 1.2640e+00 7.8500e-01 1.8600e+00 +OR2L8 ENST00000357191 3.1779e-01 0.0000e+00 0.0000e+00 1.8600e+00 +MT1H ENST00000332374 6.3432e-03 1.0085e+00 4.3300e-01 1.8600e+00 +PLA2G16 ENST00000323646 1.8145e-06 1.2053e+00 6.9400e-01 1.8600e+00 +AC120194.1 ENST00000391684 3.1775e-01 0.0000e+00 0.0000e+00 1.8600e+00 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1.1837e+00 6.5800e-01 1.8620e+00 +MRPS2 ENST00000371785 3.1326e-07 1.2312e+00 7.2900e-01 1.8620e+00 +RP11-1026M7.2 ENST00000502515 3.1617e-01 0.0000e+00 0.0000e+00 1.8620e+00 +CTD-2021H9.3 ENST00000549357 6.2598e-03 1.0157e+00 4.3500e-01 1.8620e+00 +OR52N5 ENST00000317093 5.2840e-05 1.1544e+00 6.1500e-01 1.8620e+00 +OR7A17 ENST00000327462 3.1571e-01 0.0000e+00 0.0000e+00 1.8620e+00 +RP11-366L20.2 ENST00000356215 9.7977e-06 1.1857e+00 6.5900e-01 1.8620e+00 +RP11-404L6.2 ENST00000520762 3.1577e-01 0.0000e+00 0.0000e+00 1.8620e+00 +CCL3L3 ENST00000378354 3.1517e-01 0.0000e+00 0.0000e+00 1.8630e+00 +TSPAN10 ENST00000328585 9.7125e-06 1.1879e+00 6.6000e-01 1.8630e+00 +KRTAP9-2 ENST00000377721 3.1515e-01 0.0000e+00 0.0000e+00 1.8630e+00 +OR2AJ1 ENST00000318244 6.2212e-03 1.0191e+00 4.3700e-01 1.8630e+00 +TDRP ENST00000523656 1.5111e-09 1.2849e+00 8.1300e-01 1.8630e+00 +PRSS1 ENST00000311737 4.1384e-11 1.3107e+00 8.5700e-01 1.8630e+00 +CCDC74A ENST00000295171 4.7184e-19 1.3999e+00 1.0080e+00 1.8630e+00 +ERP27 ENST00000266397 1.0936e-12 1.3339e+00 8.9500e-01 1.8630e+00 +C11orf31 ENST00000388857 1.3219e-03 1.0801e+00 5.0900e-01 1.8630e+00 +C12orf57 ENST00000229281 5.2408e-05 1.1568e+00 6.1600e-01 1.8630e+00 +ENHO ENST00000399775 1.0526e-01 7.8112e-01 2.3100e-01 1.8640e+00 +RAET1L ENST00000367341 2.4837e-10 1.2999e+00 8.3700e-01 1.8640e+00 +FABP4 ENST00000256104 5.1764e-05 1.1604e+00 6.1700e-01 1.8640e+00 +ZNF709 ENST00000428311 2.6774e-04 1.1245e+00 5.6700e-01 1.8640e+00 +MPZL2 ENST00000278937 1.0755e-12 1.3360e+00 8.9600e-01 1.8640e+00 +NPIPB9 ENST00000550983 1.0514e-01 7.8257e-01 2.3100e-01 1.8640e+00 +NNMT ENST00000535401 5.2791e-08 1.2543e+00 7.6200e-01 1.8640e+00 +S100A4 ENST00000368716 6.1838e-03 1.0225e+00 4.3800e-01 1.8640e+00 +UFSP1 ENST00000388761 2.7072e-02 9.3751e-01 3.4800e-01 1.8640e+00 +RP11-872D17.8 ENST00000529411 9.6353e-06 1.1899e+00 6.6100e-01 1.8640e+00 +RAB40AL ENST00000218249 3.1342e-01 0.0000e+00 0.0000e+00 1.8650e+00 +PSORS1C1 ENST00000259881 2.6534e-04 1.1276e+00 5.6900e-01 1.8650e+00 +ZNF578 ENST00000421239 1.3064e-03 1.0852e+00 5.1100e-01 1.8650e+00 +AL592284.1 ENST00000538264 3.1339e-01 0.0000e+00 0.0000e+00 1.8650e+00 +AC140481.2 ENST00000409982 1.0469e-01 7.8798e-01 2.3200e-01 1.8650e+00 +RP11-1105G2.3 ENST00000551941 3.1322e-01 0.0000e+00 0.0000e+00 1.8650e+00 +GDF15 ENST00000252809 3.0133e-07 1.2389e+00 7.3300e-01 1.8650e+00 +OR4N4 ENST00000328795 5.1332e-05 1.1629e+00 6.1900e-01 1.8650e+00 +CTAG2 ENST00000247306 1.0495e-01 7.8480e-01 2.3200e-01 1.8650e+00 +DNAJC25-GNG10 ENST00000374294 1.3097e-03 1.0841e+00 5.1000e-01 1.8650e+00 +FAM159A ENST00000517870 5.1161e-05 1.1638e+00 6.1900e-01 1.8650e+00 +CXCR1 ENST00000295683 3.0337e-07 1.2375e+00 7.3300e-01 1.8650e+00 +RP11-826N14.2 ENST00000512675 3.1333e-01 0.0000e+00 0.0000e+00 1.8650e+00 +SCGB3A2 ENST00000296694 6.1075e-03 1.0294e+00 4.4000e-01 1.8660e+00 +GOLGA6L4 ENST00000510439 6.0938e-03 1.0307e+00 4.4000e-01 1.8660e+00 +PRM1 ENST00000312511 2.6770e-02 9.4621e-01 3.5100e-01 1.8660e+00 +NDUFV3 ENST00000354250 2.8018e-18 1.3987e+00 1.0000e+00 1.8660e+00 +ZNF69 ENST00000340180 5.1561e-08 1.2586e+00 7.6400e-01 1.8660e+00 +TRAPPC6A ENST00000006275 5.1450e-08 1.2590e+00 7.6400e-01 1.8660e+00 +XAGE5 ENST00000351072 1.7076e-06 1.2186e+00 7.0000e-01 1.8660e+00 +XCL1 ENST00000367818 1.2982e-03 1.0879e+00 5.1200e-01 1.8660e+00 +COMMD10 ENST00000274458 6.4803e-12 1.3279e+00 8.8000e-01 1.8660e+00 +AC009041.2 ENST00000601510 3.1271e-01 0.0000e+00 0.0000e+00 1.8660e+00 +RP11-293M10.1 ENST00000553510 1.0374e-01 7.9959e-01 2.3400e-01 1.8670e+00 +CTD-3203P2.2 ENST00000566854 2.6580e-02 9.5184e-01 3.5200e-01 1.8670e+00 +ARL16 ENST00000397498 1.6932e-06 1.2205e+00 7.0100e-01 1.8670e+00 +OR8I2 ENST00000302124 9.3688e-06 1.1970e+00 6.6400e-01 1.8670e+00 +SPACA5B ENST00000304270 3.1210e-01 0.0000e+00 0.0000e+00 1.8670e+00 +DNAJB7 ENST00000307221 8.5920e-09 1.2779e+00 7.9300e-01 1.8670e+00 +SPRR1A ENST00000307122 6.0385e-03 1.0358e+00 4.4200e-01 1.8670e+00 +RP11-1102P16.1 ENST00000523987 1.0386e-01 7.9808e-01 2.3400e-01 1.8670e+00 +AC110781.3 ENST00000402221 1.0378e-01 7.9907e-01 2.3400e-01 1.8670e+00 +OR2A1 ENST00000408951 2.5996e-04 1.1348e+00 5.7200e-01 1.8670e+00 +KRTAP5-6 ENST00000382160 1.0396e-01 7.9692e-01 2.3400e-01 1.8670e+00 +RNF223 ENST00000453464 2.6565e-02 9.5227e-01 3.5200e-01 1.8670e+00 +CARHSP1 ENST00000396593 5.0284e-05 1.1689e+00 6.2100e-01 1.8670e+00 +TMEM31 ENST00000319560 1.2864e-03 1.0919e+00 5.1300e-01 1.8670e+00 +C10orf115 ENST00000376501 1.2785e-03 1.0946e+00 5.1400e-01 1.8680e+00 +S100A1 ENST00000292169 6.0044e-03 1.0391e+00 4.4300e-01 1.8680e+00 +AC017104.2 ENST00000370380 6.0024e-03 1.0393e+00 4.4300e-01 1.8680e+00 +AL162431.1 ENST00000457152 3.1086e-01 0.0000e+00 0.0000e+00 1.8680e+00 +RP4-583P15.14 ENST00000467211 1.0325e-01 8.0580e-01 2.3500e-01 1.8680e+00 +ZNF766 ENST00000439461 9.2466e-06 1.2003e+00 6.6600e-01 1.8680e+00 +LYRM2 ENST00000523377 2.5796e-04 1.1376e+00 5.7300e-01 1.8680e+00 +IFNL2 ENST00000331982 4.9903e-08 1.2645e+00 7.6700e-01 1.8680e+00 +SMN2 ENST00000380743 1.0337e-01 8.0431e-01 2.3500e-01 1.8680e+00 +C7orf34 ENST00000409607 2.5816e-04 1.1373e+00 5.7300e-01 1.8680e+00 +IL9R ENST00000244174 2.6805e-22 1.4313e+00 1.0550e+00 1.8680e+00 +RP11-683L23.1 ENST00000308911 2.5890e-04 1.1363e+00 5.7200e-01 1.8680e+00 +HIST1H2BA ENST00000274764 1.0308e-01 8.0798e-01 2.3600e-01 1.8690e+00 +LEAP2 ENST00000296877 1.2684e-03 1.0981e+00 5.1500e-01 1.8690e+00 +AL390778.1 ENST00000593613 3.0974e-01 0.0000e+00 0.0000e+00 1.8690e+00 +THEM5 ENST00000368817 3.7917e-11 1.3227e+00 8.6400e-01 1.8690e+00 +KCNMB3 ENST00000314235 8.2989e-09 1.2837e+00 7.9600e-01 1.8690e+00 +RXFP3 ENST00000330120 1.6003e-13 1.3559e+00 9.2000e-01 1.8690e+00 +ZSCAN5B ENST00000586855 1.0007e-12 1.3449e+00 9.0200e-01 1.8690e+00 +TSPY1 ENST00000451548 3.0999e-01 0.0000e+00 0.0000e+00 1.8690e+00 +AC005082.1 ENST00000366347 1.0283e-01 8.1119e-01 2.3600e-01 1.8690e+00 +VCX3A ENST00000381089 3.0958e-01 0.0000e+00 0.0000e+00 1.8700e+00 +KRTAP8-1 ENST00000329621 1.0270e-01 8.1295e-01 2.3700e-01 1.8700e+00 +PRR24 ENST00000552360 3.0901e-01 0.0000e+00 0.0000e+00 1.8700e+00 +SIGLEC15 ENST00000389474 8.2148e-09 1.2854e+00 7.9700e-01 1.8700e+00 +C2ORF15 ENST00000302513 2.5278e-04 1.1448e+00 5.7600e-01 1.8700e+00 +USP50 ENST00000532404 2.6279e-18 1.4047e+00 1.0040e+00 1.8700e+00 +AP001024.2 ENST00000447610 2.6211e-02 9.6299e-01 3.5500e-01 1.8700e+00 +OR10J3 ENST00000332217 2.5309e-04 1.1444e+00 5.7600e-01 1.8700e+00 +OR10S1 ENST00000531945 4.8947e-05 1.1769e+00 6.2500e-01 1.8700e+00 +TMEM211 ENST00000407886 2.6107e-02 9.6624e-01 3.5600e-01 1.8700e+00 +KIR3DL2 ENST00000326321 6.0804e-12 1.3362e+00 8.8500e-01 1.8700e+00 +KRTAP13-4 ENST00000334068 3.0876e-01 0.0000e+00 0.0000e+00 1.8700e+00 +OR4D5 ENST00000307033 9.0283e-06 1.2064e+00 6.6900e-01 1.8700e+00 +KBTBD13 ENST00000432196 2.2574e-10 1.3138e+00 8.4500e-01 1.8700e+00 +SELM ENST00000402395 1.6327e-06 1.2287e+00 7.0500e-01 1.8700e+00 +CYP2C19 ENST00000371321 6.4882e-20 1.4187e+00 1.0280e+00 1.8710e+00 +AL365202.1 ENST00000366116 3.0835e-01 0.0000e+00 0.0000e+00 1.8710e+00 +CYP4A22 ENST00000371891 1.4246e-29 1.4756e+00 1.1310e+00 1.8710e+00 +LY6D ENST00000301263 2.6045e-02 9.6814e-01 3.5700e-01 1.8710e+00 +ZNF321P ENST00000391777 1.2443e-03 1.1067e+00 5.1900e-01 1.8710e+00 +GRAPL ENST00000344415 3.0873e-01 0.0000e+00 0.0000e+00 1.8710e+00 +FAM163B ENST00000496132 2.5948e-02 9.7121e-01 3.5700e-01 1.8710e+00 +PABPN1L ENST00000419291 1.0122e-16 1.3934e+00 9.8100e-01 1.8720e+00 +TTLL2 ENST00000239587 5.8508e-03 1.0540e+00 4.4800e-01 1.8720e+00 +AC073569.1 ENST00000598624 3.0784e-01 0.0000e+00 0.0000e+00 1.8720e+00 +HSPB1 ENST00000248553 2.7797e-07 1.2551e+00 7.4200e-01 1.8720e+00 +AC005549.3 ENST00000601918 3.0741e-01 0.0000e+00 0.0000e+00 1.8720e+00 +OR4F4 ENST00000326183 3.0741e-01 0.0000e+00 0.0000e+00 1.8720e+00 +CGREF1 ENST00000402394 4.7425e-08 1.2739e+00 7.7200e-01 1.8720e+00 +AC104057.1 ENST00000593865 3.0714e-01 0.0000e+00 0.0000e+00 1.8720e+00 +BLOC1S4 ENST00000320776 1.0151e-01 8.2878e-01 2.3900e-01 1.8720e+00 +TMEM234 ENST00000309777 4.7801e-08 1.2725e+00 7.7100e-01 1.8720e+00 +GOLGA8B ENST00000267731 4.7959e-05 1.1831e+00 6.2800e-01 1.8720e+00 +CTB-54O9.9 ENST00000586012 5.8012e-03 1.0591e+00 4.5000e-01 1.8730e+00 +GAGE2A ENST00000362097 1.0091e-01 8.3703e-01 2.4100e-01 1.8730e+00 +MRPL21 ENST00000362034 2.4125e-14 1.3725e+00 9.4000e-01 1.8730e+00 +AL136376.1 ENST00000598661 2.5680e-02 9.7977e-01 3.6000e-01 1.8730e+00 +OR6V1 ENST00000418316 2.4770e-04 1.1521e+00 5.7900e-01 1.8730e+00 +ZNF85 ENST00000328178 4.7300e-05 1.1872e+00 6.3000e-01 1.8730e+00 +VEGFB ENST00000309422 1.3114e-09 1.3070e+00 8.2600e-01 1.8730e+00 +GAPT ENST00000396776 3.0619e-01 0.0000e+00 0.0000e+00 1.8730e+00 +TCF24 ENST00000563496 2.5682e-02 9.7972e-01 3.6000e-01 1.8730e+00 +RAB19 ENST00000537763 1.5787e-06 1.2363e+00 7.0900e-01 1.8730e+00 +SFT2D3 ENST00000310981 1.0130e-01 8.3165e-01 2.4000e-01 1.8730e+00 +DNLZ ENST00000371738 2.4737e-04 1.1526e+00 5.7900e-01 1.8730e+00 +C15orf54 ENST00000318578 2.5572e-02 9.8328e-01 3.6100e-01 1.8740e+00 +OR5B3 ENST00000309403 4.7001e-05 1.1892e+00 6.3000e-01 1.8740e+00 +OR5H1 ENST00000354565 4.6874e-05 1.1900e+00 6.3100e-01 1.8740e+00 +ZNF780A ENST00000455521 1.5554e-06 1.2397e+00 7.1100e-01 1.8740e+00 +TMEM171 ENST00000454765 7.7679e-09 1.2950e+00 8.0200e-01 1.8740e+00 +PGA4 ENST00000378149 3.0546e-01 0.0000e+00 0.0000e+00 1.8740e+00 +PLGRKT ENST00000223864 4.6040e-08 1.2794e+00 7.7500e-01 1.8740e+00 +RNASE1 ENST00000397967 2.5608e-02 9.8213e-01 3.6000e-01 1.8740e+00 +FAM90A1 ENST00000538603 1.5557e-06 1.2396e+00 7.1100e-01 1.8740e+00 +OR1S2 ENST00000302592 8.7248e-06 1.2153e+00 6.7300e-01 1.8740e+00 +AL590714.1 ENST00000594609 3.0518e-01 0.0000e+00 0.0000e+00 1.8750e+00 +HIST1H3H ENST00000369163 5.7387e-03 1.0655e+00 4.5200e-01 1.8750e+00 +ANKRD33 ENST00000301190 1.4957e-17 1.4078e+00 9.9900e-01 1.8750e+00 +CCL20 ENST00000358813 2.4242e-04 1.1600e+00 5.8200e-01 1.8750e+00 +PAGE2B ENST00000374971 1.2072e-03 1.1203e+00 5.2400e-01 1.8750e+00 +P2RY6 ENST00000393590 1.5307e-06 1.2434e+00 7.1300e-01 1.8750e+00 +MRPS28 ENST00000276585 4.6621e-05 1.1916e+00 6.3200e-01 1.8750e+00 +MRPL11 ENST00000310999 1.5371e-06 1.2424e+00 7.1200e-01 1.8750e+00 +CGB5 ENST00000301408 2.5362e-02 9.9025e-01 3.6200e-01 1.8750e+00 +CT45A6 ENST00000491002 3.0472e-01 0.0000e+00 0.0000e+00 1.8750e+00 +PRAMEF18 ENST00000376126 3.0430e-01 0.0000e+00 0.0000e+00 1.8760e+00 +CMA1 ENST00000250378 7.5861e-09 1.2991e+00 8.0400e-01 1.8760e+00 +PAPPA-AS1 ENST00000445861 3.0349e-01 0.0000e+00 0.0000e+00 1.8760e+00 +SLC39A11 ENST00000542342 2.3522e-18 1.4152e+00 1.0110e+00 1.8760e+00 +ZNF705B ENST00000443676 2.3945e-04 1.1645e+00 5.8400e-01 1.8760e+00 +AC108868.1 ENST00000596204 3.0351e-01 0.0000e+00 0.0000e+00 1.8760e+00 +CLEC7A ENST00000304084 5.5087e-12 1.3493e+00 8.9300e-01 1.8760e+00 +FGF5 ENST00000312465 2.0811e-10 1.3259e+00 8.5200e-01 1.8760e+00 +C6orf226 ENST00000408925 3.0419e-01 0.0000e+00 0.0000e+00 1.8760e+00 +OR2T29 ENST00000328570 9.9777e-02 8.5324e-01 2.4300e-01 1.8760e+00 +PLGLB2 ENST00000359481 3.0421e-01 0.0000e+00 0.0000e+00 1.8760e+00 +C20orf201 ENST00000308906 2.5208e-02 9.9541e-01 3.6400e-01 1.8760e+00 +TMEM257 ENST00000408967 9.9640e-02 8.5524e-01 2.4400e-01 1.8760e+00 +DDIT4L ENST00000273990 1.5197e-06 1.2450e+00 7.1400e-01 1.8760e+00 +CTD-2547L24.3 ENST00000554096 2.5230e-02 9.9467e-01 3.6300e-01 1.8760e+00 +TMEM134 ENST00000308022 2.0372e-10 1.3292e+00 8.5400e-01 1.8770e+00 +KRTAP4-1 ENST00000398472 5.6309e-03 1.0769e+00 4.5500e-01 1.8770e+00 +EQTN ENST00000380032 5.4219e-12 1.3515e+00 8.9400e-01 1.8770e+00 +AL163636.6 ENST00000553909 9.9062e-02 8.6386e-01 2.4500e-01 1.8770e+00 +FFAR3 ENST00000327809 2.3758e-04 1.1674e+00 5.8500e-01 1.8770e+00 +LAIR2 ENST00000301202 2.5967e-07 1.2691e+00 7.4900e-01 1.8770e+00 +MRAP2 ENST00000257776 2.5633e-07 1.2718e+00 7.5000e-01 1.8780e+00 +NPB ENST00000333383 9.8900e-02 8.6630e-01 2.4500e-01 1.8780e+00 +OR5H2 ENST00000355273 2.3505e-04 1.1714e+00 5.8700e-01 1.8780e+00 +AEN ENST00000332810 2.0092e-10 1.3312e+00 8.5500e-01 1.8780e+00 +KIR2DL1 ENST00000336077 3.5684e-15 1.3898e+00 9.6100e-01 1.8780e+00 +ANKRD23 ENST00000318357 3.5366e-19 1.4263e+00 1.0260e+00 1.8780e+00 +CTB-60B18.6 ENST00000591656 3.0206e-01 0.0000e+00 0.0000e+00 1.8780e+00 +GUCA1C ENST00000261047 2.5694e-07 1.2713e+00 7.5000e-01 1.8780e+00 +GOLGA8J ENST00000567927 8.9595e-17 1.4059e+00 9.8900e-01 1.8780e+00 +CGB ENST00000357383 9.8257e-02 8.7618e-01 2.4700e-01 1.8790e+00 +PRAMEF1 ENST00000332296 3.2165e-11 1.3458e+00 8.7800e-01 1.8790e+00 +SYCN ENST00000318438 4.4492e-05 1.2060e+00 6.3800e-01 1.8790e+00 +OR8H2 ENST00000313503 1.1661e-03 1.1363e+00 5.3000e-01 1.8790e+00 +SERPINB4 ENST00000341074 8.7622e-17 1.4082e+00 9.9100e-01 1.8790e+00 +KRTAP9-7 ENST00000391354 3.0156e-01 0.0000e+00 0.0000e+00 1.8790e+00 +SMIM8 ENST00000392863 5.5617e-03 1.0844e+00 4.5800e-01 1.8790e+00 +POLR2K ENST00000353107 1.1708e-03 1.1345e+00 5.2900e-01 1.8790e+00 +PMM2 ENST00000268261 1.4072e-17 1.4139e+00 1.0030e+00 1.8790e+00 +C12orf73 ENST00000378090 2.4774e-02 1.0105e+00 3.6700e-01 1.8790e+00 +FAM111B ENST00000343597 9.8549e-02 8.7166e-01 2.4600e-01 1.8790e+00 +GOLGA6L10 ENST00000439287 1.1700e-03 1.1348e+00 5.2900e-01 1.8790e+00 +TNFRSF18 ENST00000328596 1.4516e-06 1.2557e+00 7.1900e-01 1.8800e+00 +NBPF24 ENST00000369228 5.5357e-03 1.0873e+00 4.5900e-01 1.8800e+00 +LCE2B ENST00000368780 9.7851e-02 8.8256e-01 2.4800e-01 1.8800e+00 +OR8S1 ENST00000310194 1.4449e-06 1.2568e+00 7.1900e-01 1.8800e+00 +ZNF256 ENST00000282308 5.5297e-03 1.0879e+00 4.5900e-01 1.8800e+00 +CT45A1 ENST00000497301 3.0048e-01 0.0000e+00 0.0000e+00 1.8800e+00 +ZBED6CL ENST00000343855 1.1628e-03 1.1377e+00 5.3000e-01 1.8800e+00 +SERF1B ENST00000380750 3.0017e-01 0.0000e+00 0.0000e+00 1.8800e+00 +PRSS55 ENST00000328655 3.1731e-11 1.3478e+00 8.7900e-01 1.8800e+00 +OR56B4 ENST00000316529 8.0533e-06 1.2364e+00 6.8300e-01 1.8810e+00 +OR4A16 ENST00000314721 2.2787e-04 1.1830e+00 5.9200e-01 1.8810e+00 +ZNF671 ENST00000317398 4.2147e-08 1.2961e+00 7.8400e-01 1.8810e+00 +MOAP1 ENST00000556883 1.1736e-09 1.3249e+00 8.3600e-01 1.8810e+00 +IL3RA ENST00000331035 2.9891e-27 1.4798e+00 1.1210e+00 1.8810e+00 +DUPD1 ENST00000338487 2.4781e-07 1.2789e+00 7.5400e-01 1.8810e+00 +SEPT12 ENST00000268231 3.3500e-19 1.4313e+00 1.0290e+00 1.8810e+00 +FAM162B ENST00000368557 4.2377e-08 1.2951e+00 7.8400e-01 1.8810e+00 +PIGY ENST00000527353 9.7240e-02 8.9237e-01 2.5000e-01 1.8810e+00 +MANSC4 ENST00000381273 4.3796e-05 1.2109e+00 6.4000e-01 1.8810e+00 +SPIN2A ENST00000374908 1.1466e-03 1.1443e+00 5.3300e-01 1.8810e+00 +DEFB118 ENST00000253381 9.6825e-02 8.9919e-01 2.5100e-01 1.8820e+00 +DEFB119 ENST00000376315 9.6676e-02 9.0166e-01 2.5100e-01 1.8820e+00 +DEFB129 ENST00000246105 9.7066e-02 8.9521e-01 2.5000e-01 1.8820e+00 +DAPL1 ENST00000309950 4.2949e-05 1.2171e+00 6.4300e-01 1.8820e+00 +C2orf57 ENST00000313965 9.7049e-02 8.9549e-01 2.5000e-01 1.8820e+00 +LCNL1 ENST00000408973 1.1448e-03 1.1450e+00 5.3300e-01 1.8820e+00 +PRAMEF16 ENST00000376121 2.9790e-01 0.0000e+00 0.0000e+00 1.8820e+00 +CXorf40B ENST00000370406 2.4390e-02 1.0243e+00 3.7100e-01 1.8820e+00 +OR11G2 ENST00000357366 1.4116e-06 1.2622e+00 7.2200e-01 1.8820e+00 +AC187652.1 ENST00000599994 9.6431e-02 9.0577e-01 2.5200e-01 1.8830e+00 +KBTBD4 ENST00000450908 2.9725e-01 0.0000e+00 0.0000e+00 1.8830e+00 +OR10A6 ENST00000309838 6.8327e-09 1.3174e+00 8.1400e-01 1.8830e+00 +VPREB1 ENST00000403807 9.6491e-02 9.0475e-01 2.5100e-01 1.8830e+00 +HIST1H3D ENST00000377831 1.1300e-03 1.1512e+00 5.3500e-01 1.8830e+00 +CYP2C8 ENST00000371270 1.9759e-22 1.4563e+00 1.0730e+00 1.8830e+00 +GIMAP5 ENST00000358647 9.6506e-02 9.0450e-01 2.5100e-01 1.8830e+00 +OR6K2 ENST00000359610 2.4185e-07 1.2840e+00 7.5700e-01 1.8830e+00 +DEFB121 ENST00000376314 9.6502e-02 9.0457e-01 2.5100e-01 1.8830e+00 +AP000688.1 ENST00000600312 2.9757e-01 0.0000e+00 0.0000e+00 1.8830e+00 +ZNF716 ENST00000420713 1.3942e-06 1.2652e+00 7.2400e-01 1.8830e+00 +LST1 ENST00000376093 1.1303e-03 1.1511e+00 5.3500e-01 1.8830e+00 +OTOP1 ENST00000296358 4.8437e-24 1.4657e+00 1.0910e+00 1.8830e+00 +PP13004 ENST00000381493 9.6611e-02 9.0274e-01 2.5100e-01 1.8830e+00 +CCDC23 ENST00000372521 1.1348e-03 1.1492e+00 5.3400e-01 1.8830e+00 +TMEM261 ENST00000358227 5.4207e-03 1.1003e+00 4.6300e-01 1.8830e+00 +MT1B ENST00000334346 5.3775e-03 1.1054e+00 4.6400e-01 1.8840e+00 +SYNGR4 ENST00000344846 1.1085e-09 1.3343e+00 8.4100e-01 1.8840e+00 +OR2D2 ENST00000299459 4.0212e-08 1.3052e+00 7.8900e-01 1.8840e+00 +C9orf141 ENST00000371629 1.1229e-03 1.1542e+00 5.3600e-01 1.8840e+00 +AC090427.1 ENST00000596056 2.9639e-01 0.0000e+00 0.0000e+00 1.8840e+00 +C1orf143 ENST00000443836 9.5863e-02 9.1547e-01 2.5300e-01 1.8840e+00 +RBMY1F ENST00000303766 2.9637e-01 0.0000e+00 0.0000e+00 1.8840e+00 +CDRT4 ENST00000312177 9.5789e-02 9.1675e-01 2.5300e-01 1.8840e+00 +APOL6 ENST00000409652 9.6029e-02 9.1261e-01 2.5300e-01 1.8840e+00 +TNFRSF17 ENST00000053243 1.3715e-06 1.2691e+00 7.2500e-01 1.8840e+00 +CTB-134H23.2 ENST00000424293 9.6089e-02 9.1158e-01 2.5200e-01 1.8840e+00 +EMP2 ENST00000359543 2.3873e-07 1.2868e+00 7.5800e-01 1.8840e+00 +DEFB130 ENST00000437818 2.9563e-01 0.0000e+00 0.0000e+00 1.8850e+00 +OR1S1 ENST00000309433 4.1578e-05 1.2274e+00 6.4700e-01 1.8850e+00 +SPATA31A3 ENST00000356699 2.9526e-01 0.0000e+00 0.0000e+00 1.8850e+00 +TSPY2 ENST00000320701 9.5282e-02 9.2564e-01 2.5500e-01 1.8850e+00 +NBPF11 ENST00000605317 1.1126e-03 1.1587e+00 5.3800e-01 1.8850e+00 +BHLHA9 ENST00000391429 2.9590e-01 0.0000e+00 0.0000e+00 1.8850e+00 +C9orf66 ENST00000382387 2.3936e-02 1.0415e+00 3.7500e-01 1.8850e+00 +LRG1 ENST00000306390 9.5143e-02 9.2811e-01 2.5500e-01 1.8850e+00 +AC112721.1 ENST00000409162 2.9560e-01 0.0000e+00 0.0000e+00 1.8850e+00 +B3GNT6 ENST00000533140 1.0930e-09 1.3366e+00 8.4200e-01 1.8850e+00 +MBD3L4 ENST00000381394 2.9496e-01 0.0000e+00 0.0000e+00 1.8850e+00 +GAL3ST2 ENST00000192314 2.9341e-11 1.3591e+00 8.8500e-01 1.8850e+00 +HTN3 ENST00000530128 4.1066e-05 1.2314e+00 6.4900e-01 1.8860e+00 +RHOXF2 ENST00000371388 2.1767e-04 1.2006e+00 5.9900e-01 1.8860e+00 +DMRTC1 ENST00000373529 2.3698e-02 1.0508e+00 3.7700e-01 1.8860e+00 +ARL11 ENST00000282026 5.2678e-03 1.1186e+00 4.6800e-01 1.8860e+00 +NEUROG1 ENST00000314744 2.1722e-04 1.2014e+00 5.9900e-01 1.8860e+00 +CGB7 ENST00000597853 5.2599e-03 1.1196e+00 4.6900e-01 1.8860e+00 +HIST1H2AJ ENST00000333151 2.3700e-02 1.0507e+00 3.7700e-01 1.8860e+00 +RP11-210M15.2 ENST00000559008 2.3659e-02 1.0523e+00 3.7800e-01 1.8860e+00 +C6orf48 ENST00000375640 2.3621e-02 1.0539e+00 3.7800e-01 1.8860e+00 +KRTAP5-8 ENST00000398534 9.5069e-02 9.2944e-01 2.5500e-01 1.8860e+00 +OR2T6 ENST00000355728 4.1385e-05 1.2289e+00 6.4800e-01 1.8860e+00 +NAT1 ENST00000545197 1.9294e-14 1.3987e+00 9.5700e-01 1.8860e+00 +AL161784.1 ENST00000594963 9.4750e-02 9.3518e-01 2.5600e-01 1.8860e+00 +WFDC6 ENST00000372670 1.0970e-03 1.1655e+00 5.4000e-01 1.8860e+00 +SERPINA9 ENST00000337425 1.2106e-13 1.3899e+00 9.4100e-01 1.8860e+00 +C1orf111 ENST00000367935 1.7676e-10 1.3509e+00 8.6600e-01 1.8860e+00 +ZNF721 ENST00000511833 9.4789e-02 9.3448e-01 2.5600e-01 1.8860e+00 +SPG20OS ENST00000379848 2.3665e-02 1.0521e+00 3.7800e-01 1.8860e+00 +RP11-386G21.1 ENST00000522186 2.3775e-02 1.0477e+00 3.7600e-01 1.8860e+00 +SIRPD ENST00000381623 3.9148e-08 1.3104e+00 7.9200e-01 1.8860e+00 +TEX38 ENST00000334122 2.2724e-07 1.2974e+00 7.6400e-01 1.8870e+00 +ZNF726 ENST00000594466 7.4752e-06 1.2567e+00 6.9200e-01 1.8870e+00 +VPREB3 ENST00000248948 9.4588e-02 9.3814e-01 2.5600e-01 1.8870e+00 +SPRN ENST00000541506 2.9377e-01 0.0000e+00 0.0000e+00 1.8870e+00 +C10orf32 ENST00000339834 2.2921e-07 1.2955e+00 7.6300e-01 1.8870e+00 +C4orf19 ENST00000284437 9.4310e-02 9.4326e-01 2.5700e-01 1.8870e+00 +CBWD3 ENST00000360171 1.3260e-06 1.2772e+00 7.2900e-01 1.8870e+00 +AC022400.2 ENST00000595757 2.9318e-01 0.0000e+00 0.0000e+00 1.8870e+00 +TSPY8 ENST00000330628 2.9328e-01 0.0000e+00 0.0000e+00 1.8870e+00 +C1orf180 ENST00000370624 9.4516e-02 9.3947e-01 2.5700e-01 1.8870e+00 +TMEM238 ENST00000444469 2.9387e-01 0.0000e+00 0.0000e+00 1.8870e+00 +CST9 ENST00000376971 1.0911e-03 1.1681e+00 5.4100e-01 1.8870e+00 +C8orf31 ENST00000395172 3.8618e-08 1.3131e+00 7.9300e-01 1.8870e+00 +DEFB113 ENST00000398718 9.4090e-02 9.4736e-01 2.5800e-01 1.8880e+00 +ANKRD34B ENST00000338682 1.8309e-14 1.4050e+00 9.6100e-01 1.8880e+00 +TRIB3 ENST00000217233 1.1597e-13 1.3953e+00 9.4400e-01 1.8880e+00 +KRTAP3-1 ENST00000391588 2.3316e-02 1.0663e+00 3.8100e-01 1.8880e+00 +DEFB104A ENST00000314265 9.3748e-02 9.5383e-01 2.5900e-01 1.8880e+00 +AC009403.2 ENST00000401694 2.3373e-02 1.0639e+00 3.8000e-01 1.8880e+00 +AC012360.1 ENST00000595481 2.9230e-01 0.0000e+00 0.0000e+00 1.8880e+00 +AL161450.1 ENST00000601793 2.9230e-01 0.0000e+00 0.0000e+00 1.8880e+00 +ZNF429 ENST00000358491 4.0549e-05 1.2355e+00 6.5100e-01 1.8880e+00 +DNAJC15 ENST00000379221 1.6820e-10 1.3587e+00 8.7100e-01 1.8890e+00 +RPUSD1 ENST00000561734 1.6742e-10 1.3594e+00 8.7100e-01 1.8890e+00 +OR1J2 ENST00000335302 9.3349e-02 9.6152e-01 2.6000e-01 1.8890e+00 +OR4C6 ENST00000314259 5.1290e-03 1.1361e+00 4.7400e-01 1.8890e+00 +PRAMEF13 ENST00000376132 2.9184e-01 0.0000e+00 0.0000e+00 1.8890e+00 +TFF2 ENST00000291526 2.2197e-07 1.3024e+00 7.6600e-01 1.8890e+00 +CDRT15 ENST00000420162 1.2820e-06 1.2854e+00 7.3300e-01 1.8890e+00 +DEFB105B ENST00000335510 2.9184e-01 0.0000e+00 0.0000e+00 1.8890e+00 +TYRP1 ENST00000388918 6.5570e-25 1.4813e+00 1.1070e+00 1.8890e+00 +URAD ENST00000332715 5.1396e-03 1.1347e+00 4.7300e-01 1.8890e+00 +OVCA2 ENST00000572195 1.2811e-06 1.2855e+00 7.3300e-01 1.8890e+00 +CLIC3 ENST00000494426 6.2316e-09 1.3339e+00 8.2300e-01 1.8890e+00 +IFITM2 ENST00000399817 5.1529e-03 1.1330e+00 4.7300e-01 1.8890e+00 +MBD3L3 ENST00000333843 2.9097e-01 0.0000e+00 0.0000e+00 1.8890e+00 +CTD-2215E18.1 ENST00000509481 2.0994e-04 1.2148e+00 6.0400e-01 1.8890e+00 +ZNF534 ENST00000332323 1.2886e-06 1.2841e+00 7.3300e-01 1.8890e+00 +PPP3R2 ENST00000374806 1.0651e-03 1.1801e+00 5.4500e-01 1.8890e+00 +RP11-998D10.1 ENST00000531638 5.1512e-03 1.1332e+00 4.7300e-01 1.8890e+00 +PRAMEF14 ENST00000334600 2.9026e-01 0.0000e+00 0.0000e+00 1.8900e+00 +OR9Q2 ENST00000311591 6.1559e-09 1.3361e+00 8.2500e-01 1.8900e+00 +HCG27 ENST00000383331 2.3063e-02 1.0769e+00 3.8300e-01 1.8900e+00 +MS4A4E ENST00000425663 1.0614e-03 1.1818e+00 5.4600e-01 1.8900e+00 +SCGB2B2 ENST00000601241 1.0603e-03 1.1823e+00 5.4600e-01 1.8900e+00 +S100A16 ENST00000368704 1.0573e-03 1.1837e+00 5.4700e-01 1.8900e+00 +TRIM49D1 ENST00000530311 2.9086e-01 0.0000e+00 0.0000e+00 1.8900e+00 +OR6K3 ENST00000368145 9.2932e-02 9.6967e-01 2.6100e-01 1.8900e+00 +RBMY1A1 ENST00000382707 2.9035e-01 0.0000e+00 0.0000e+00 1.8900e+00 +RBMY1E ENST00000382659 2.9054e-01 0.0000e+00 0.0000e+00 1.8900e+00 +C7orf66 ENST00000379007 9.2294e-02 9.8252e-01 2.6300e-01 1.8910e+00 +HIGD1B ENST00000253410 3.9132e-05 1.2471e+00 6.5600e-01 1.8910e+00 +KRTAP9-9 ENST00000394008 2.8956e-01 0.0000e+00 0.0000e+00 1.8910e+00 +MGARP ENST00000398955 3.8778e-05 1.2501e+00 6.5700e-01 1.8910e+00 +OR4K2 ENST00000298642 3.8826e-05 1.2497e+00 6.5700e-01 1.8910e+00 +ZNF846 ENST00000397902 1.2532e-06 1.2909e+00 7.3600e-01 1.8910e+00 +DEFB136 ENST00000382209 9.2480e-02 9.7872e-01 2.6200e-01 1.8910e+00 +KLLN ENST00000445946 5.0546e-03 1.1458e+00 4.7700e-01 1.8910e+00 +AL121963.1 ENST00000430695 2.0649e-04 1.2213e+00 6.0700e-01 1.8910e+00 +OR5AU1 ENST00000304418 1.2459e-06 1.2924e+00 7.3700e-01 1.8910e+00 +ARL14 ENST00000320767 1.2351e-06 1.2945e+00 7.3800e-01 1.8920e+00 +GPX1 ENST00000419783 3.8518e-05 1.2523e+00 6.5800e-01 1.8920e+00 +MRPS12 ENST00000407800 2.0409e-04 1.2260e+00 6.0900e-01 1.8920e+00 +DEFB114 ENST00000322066 9.1552e-02 9.9794e-01 2.6500e-01 1.8920e+00 +DAZ2 ENST00000382440 2.8800e-01 0.0000e+00 0.0000e+00 1.8920e+00 +SPP2 ENST00000168148 1.6930e-14 1.4145e+00 9.6700e-01 1.8920e+00 +SNAPC5 ENST00000316634 2.0115e-04 1.2319e+00 6.1100e-01 1.8930e+00 +ANG ENST00000336811 2.8738e-01 0.0000e+00 0.0000e+00 1.8930e+00 +KAAG1 ENST00000274766 2.8715e-01 0.0000e+00 0.0000e+00 1.8930e+00 +KCNG4 ENST00000308251 4.2136e-16 1.4305e+00 9.9600e-01 1.8930e+00 +OR4C12 ENST00000335238 3.7877e-05 1.2579e+00 6.6000e-01 1.8930e+00 +CST5 ENST00000304710 6.8894e-06 1.2795e+00 7.0300e-01 1.8930e+00 +SLN ENST00000531293 2.8701e-01 0.0000e+00 0.0000e+00 1.8930e+00 +AVPI1 ENST00000370626 3.8026e-05 1.2566e+00 6.6000e-01 1.8930e+00 +SPON2 ENST00000290902 2.6609e-15 1.4233e+00 9.8200e-01 1.8930e+00 +FGFBP3 ENST00000311575 1.0279e-03 1.1980e+00 5.5200e-01 1.8930e+00 +OR8K3 ENST00000312711 1.2144e-06 1.2987e+00 7.4000e-01 1.8930e+00 +LCE1F ENST00000334371 4.9674e-03 1.1577e+00 4.8000e-01 1.8930e+00 +RBMY1J ENST00000250831 2.8682e-01 0.0000e+00 0.0000e+00 1.8930e+00 +FAM90A26 ENST00000512047 2.8656e-01 0.0000e+00 0.0000e+00 1.8940e+00 +KRTAP5-7 ENST00000398536 9.0951e-02 1.0109e+00 2.6600e-01 1.8940e+00 +SPANXN2 ENST00000370498 9.0812e-02 1.0139e+00 2.6700e-01 1.8940e+00 +PRAMEF3 ENST00000376173 2.8624e-01 0.0000e+00 0.0000e+00 1.8940e+00 +ZNF486 ENST00000335117 6.7949e-06 1.2834e+00 7.0400e-01 1.8940e+00 +DEFA3 ENST00000327857 9.0546e-02 1.0198e+00 2.6800e-01 1.8940e+00 +RP11-763F8.1 ENST00000502368 1.0216e-03 1.2011e+00 5.5300e-01 1.8940e+00 +AC026369.1 ENST00000594563 2.8615e-01 0.0000e+00 0.0000e+00 1.8940e+00 +OR10H4 ENST00000322107 4.8912e-03 1.1683e+00 4.8300e-01 1.8950e+00 +COX7A1 ENST00000292907 3.7270e-05 1.2633e+00 6.6300e-01 1.8950e+00 +PYCARD ENST00000247470 1.9768e-04 1.2389e+00 6.1400e-01 1.8950e+00 +RNASE11 ENST00000555283 2.2247e-02 1.1133e+00 3.9200e-01 1.8950e+00 +OTUD6A ENST00000338352 2.8466e-01 0.0000e+00 0.0000e+00 1.8950e+00 +CLDN20 ENST00000367165 4.8881e-03 1.1688e+00 4.8300e-01 1.8950e+00 +AC009065.1 ENST00000454671 6.7438e-06 1.2856e+00 7.0500e-01 1.8950e+00 +CHCHD1 ENST00000372833 6.7411e-06 1.2857e+00 7.0500e-01 1.8950e+00 +IL36RN ENST00000393200 3.3941e-08 1.3388e+00 8.0600e-01 1.8950e+00 +AC011239.1 ENST00000430988 2.2220e-02 1.1145e+00 3.9200e-01 1.8950e+00 +HIST4H4 ENST00000539745 2.2279e-02 1.1118e+00 3.9100e-01 1.8950e+00 +NPFF ENST00000267017 3.6460e-05 1.2707e+00 6.6600e-01 1.8960e+00 +IFNK ENST00000276943 9.0615e-10 1.3685e+00 8.6000e-01 1.8960e+00 +C12orf74 ENST00000397833 1.1533e-06 1.3116e+00 7.4600e-01 1.8960e+00 +KRTAP9-6 ENST00000391355 2.8406e-01 0.0000e+00 0.0000e+00 1.8960e+00 +TSPY10 ENST00000428845 2.8371e-01 0.0000e+00 0.0000e+00 1.8960e+00 +FOXD4 ENST00000382500 6.6406e-06 1.2900e+00 7.0700e-01 1.8960e+00 +SKA2 ENST00000330137 1.9960e-07 1.3259e+00 7.7800e-01 1.8960e+00 +C8orf82 ENST00000524821 3.6066e-05 1.2744e+00 6.6700e-01 1.8970e+00 +C11orf86 ENST00000308963 6.5689e-06 1.2932e+00 7.0900e-01 1.8970e+00 +CENPBD1 ENST00000314994 2.8303e-01 0.0000e+00 0.0000e+00 1.8970e+00 +LINC00632 ENST00000370535 8.9251e-02 1.0496e+00 2.7100e-01 1.8970e+00 +AC019206.1 ENST00000599032 2.8267e-01 0.0000e+00 0.0000e+00 1.8970e+00 +AL355390.1 ENST00000325811 8.9110e-02 1.0530e+00 2.7200e-01 1.8970e+00 +DEFB133 ENST00000398721 2.8270e-01 0.0000e+00 0.0000e+00 1.8970e+00 +NDUFB1 ENST00000329559 3.5908e-05 1.2759e+00 6.6800e-01 1.8970e+00 +C17orf67 ENST00000397861 6.5469e-06 1.2941e+00 7.0900e-01 1.8970e+00 +SPACA4 ENST00000321762 2.8303e-01 0.0000e+00 0.0000e+00 1.8970e+00 +COX7A2L ENST00000378669 1.1516e-06 1.3120e+00 7.4600e-01 1.8970e+00 +KLHL35 ENST00000539798 2.3745e-15 1.4368e+00 9.9100e-01 1.8980e+00 +TPSB2 ENST00000430512 5.3313e-09 1.3629e+00 8.3900e-01 1.8980e+00 +C10orf120 ENST00000329446 3.5549e-05 1.2794e+00 6.6900e-01 1.8980e+00 +CCL4L2 ENST00000394465 8.8586e-02 1.0658e+00 2.7300e-01 1.8980e+00 +RP11-404P21.8 ENST00000553811 4.7505e-03 1.1890e+00 4.8900e-01 1.8980e+00 +FAM25C ENST00000342763 8.8745e-02 1.0619e+00 2.7300e-01 1.8980e+00 +PSG5 ENST00000366175 8.8239e-22 1.4823e+00 1.0840e+00 1.8980e+00 +SLC38A8 ENST00000299709 3.3217e-24 1.4960e+00 1.1120e+00 1.8980e+00 +AL591025.1 ENST00000397897 2.1752e-02 1.1371e+00 3.9700e-01 1.8980e+00 +OR6B3 ENST00000319423 1.9086e-04 1.2534e+00 6.1900e-01 1.8980e+00 +OR13J1 ENST00000377981 6.3322e-06 1.3039e+00 7.1300e-01 1.8990e+00 +KRTAP6-2 ENST00000334897 2.1487e-02 1.1505e+00 4.0000e-01 1.8990e+00 +C10orf95 ENST00000239125 4.7379e-03 1.1909e+00 4.9000e-01 1.8990e+00 +CLDN9 ENST00000445369 6.3138e-06 1.3047e+00 7.1400e-01 1.8990e+00 +OR8K5 ENST00000313447 1.1097e-06 1.3214e+00 7.5000e-01 1.8990e+00 +LRRC18 ENST00000374160 3.5136e-05 1.2834e+00 6.7100e-01 1.8990e+00 +RP11-379H8.1 ENST00000568285 2.1480e-02 1.1509e+00 4.0000e-01 1.8990e+00 +FAM24B ENST00000368898 8.8274e-02 1.0735e+00 2.7400e-01 1.8990e+00 +OR4X1 ENST00000320048 6.3135e-06 1.3047e+00 7.1400e-01 1.8990e+00 +AC026202.1 ENST00000600805 9.6777e-04 1.2294e+00 5.6200e-01 1.8990e+00 +ZNF658 ENST00000602553 9.0413e-14 1.4274e+00 9.6300e-01 1.9000e+00 +OR10G9 ENST00000375024 3.4945e-05 1.2853e+00 6.7200e-01 1.9000e+00 +C17orf50 ENST00000285023 1.1002e-06 1.3236e+00 7.5100e-01 1.9000e+00 +PRSS3 ENST00000361005 3.5636e-12 1.4103e+00 9.2900e-01 1.9000e+00 +RP11-410N8.4 ENST00000375670 2.1323e-02 1.1590e+00 4.0200e-01 1.9000e+00 +RP11-867G23.8 ENST00000531602 2.1441e-02 1.1528e+00 4.0000e-01 1.9000e+00 +ZNF845 ENST00000458035 9.5913e-04 1.2342e+00 5.6400e-01 1.9000e+00 +NUDT16 ENST00000502852 4.6241e-03 1.2086e+00 4.9500e-01 1.9010e+00 +PROK1 ENST00000271331 6.1702e-06 1.3115e+00 7.1700e-01 1.9010e+00 +SDHAF1 ENST00000378887 8.7043e-02 1.1056e+00 2.7800e-01 1.9010e+00 +ZNF107 ENST00000395391 2.1156e-02 1.1678e+00 4.0300e-01 1.9010e+00 +C4orf36 ENST00000473559 1.8365e-04 1.2697e+00 6.2500e-01 1.9010e+00 +FAM182B ENST00000376403 8.7202e-02 1.1013e+00 2.7800e-01 1.9010e+00 +HIST2H2BF ENST00000545683 4.6330e-03 1.2071e+00 4.9400e-01 1.9010e+00 +OR52N2 ENST00000317037 1.8247e-04 1.2724e+00 6.2600e-01 1.9020e+00 +FCGR1B ENST00000369384 1.3372e-10 1.3958e+00 8.9100e-01 1.9020e+00 +TMEM107 ENST00000316425 3.0521e-08 1.3607e+00 8.1800e-01 1.9020e+00 +CXorf64 ENST00000371125 4.5812e-03 1.2155e+00 4.9700e-01 1.9020e+00 +MT1X ENST00000394485 9.3353e-04 1.2489e+00 5.6900e-01 1.9020e+00 +RGPD4 ENST00000408999 8.5288e-62 1.6104e+00 1.3350e+00 1.9020e+00 +SERPINA3 ENST00000467132 8.8330e-14 1.4304e+00 9.6500e-01 1.9020e+00 +C11orf40 ENST00000307616 1.0628e-06 1.3326e+00 7.5600e-01 1.9020e+00 +KRTAP1-1 ENST00000306271 5.9686e-06 1.3214e+00 7.2100e-01 1.9030e+00 +GJD3 ENST00000578689 3.3471e-05 1.3004e+00 6.7800e-01 1.9030e+00 +DNAH10OS ENST00000514254 1.7857e-04 1.2817e+00 6.3000e-01 1.9030e+00 +TMEM243 ENST00000433078 1.0471e-06 1.3365e+00 7.5700e-01 1.9030e+00 +HTATIP2 ENST00000419348 5.3767e-13 1.4269e+00 9.5100e-01 1.9030e+00 +UPK2 ENST00000264031 2.9877e-08 1.3652e+00 8.2000e-01 1.9030e+00 +AC008060.7 ENST00000401499 4.5284e-03 1.2242e+00 4.9900e-01 1.9030e+00 +FAM209B ENST00000371325 1.7979e-04 1.2788e+00 6.2900e-01 1.9030e+00 +LRTM1 ENST00000273286 3.3678e-16 1.4561e+00 1.0120e+00 1.9030e+00 +NEUROG3 ENST00000242462 5.9611e-06 1.3218e+00 7.2100e-01 1.9030e+00 +KRTAP13-3 ENST00000390690 8.5439e-02 1.1507e+00 2.8300e-01 1.9040e+00 +CALML3 ENST00000315238 9.0968e-04 1.2632e+00 5.7400e-01 1.9040e+00 +PDF ENST00000288022 5.8706e-06 1.3264e+00 7.2300e-01 1.9040e+00 +AC114494.1 ENST00000596131 8.5067e-02 1.1618e+00 2.8400e-01 1.9040e+00 +CCK ENST00000396169 3.3034e-05 1.3050e+00 6.8000e-01 1.9040e+00 +LCE2D ENST00000368784 8.5242e-02 1.1566e+00 2.8400e-01 1.9040e+00 +LCE3D ENST00000368787 2.0613e-02 1.1979e+00 4.1000e-01 1.9040e+00 +CHCHD2 ENST00000395422 1.7328e-07 1.3585e+00 7.9400e-01 1.9040e+00 +DEFB112 ENST00000322246 2.0684e-02 1.1939e+00 4.0900e-01 1.9040e+00 +SPRR2F ENST00000468739 8.5180e-02 1.1584e+00 2.8400e-01 1.9040e+00 +SPANXN5 ENST00000375511 8.5244e-02 1.1565e+00 2.8400e-01 1.9040e+00 +RP11-408E5.4 ENST00000382988 8.5277e-02 1.1555e+00 2.8400e-01 1.9040e+00 +CASC10 ENST00000377113 8.4846e-02 1.1686e+00 2.8500e-01 1.9050e+00 +RLN2 ENST00000381627 9.0025e-04 1.2690e+00 5.7600e-01 1.9050e+00 +GOLGA8O ENST00000509311 1.7023e-07 1.3626e+00 7.9600e-01 1.9050e+00 +AC138647.1 ENST00000427937 2.0424e-02 1.2089e+00 4.1200e-01 1.9050e+00 +RNASE4 ENST00000555835 1.7566e-04 1.2889e+00 6.3300e-01 1.9050e+00 +C5orf63 ENST00000535381 4.4611e-03 1.2355e+00 5.0200e-01 1.9050e+00 +OR8J1 ENST00000303039 1.0089e-06 1.3463e+00 7.6200e-01 1.9050e+00 +MAP1LC3C ENST00000357246 5.8124e-06 1.3295e+00 7.2500e-01 1.9050e+00 +RP11-536G4.1 ENST00000553095 8.4786e-02 1.1704e+00 2.8500e-01 1.9050e+00 +RP11-6L6.2 ENST00000504313 1.7559e-04 1.2890e+00 6.3300e-01 1.9050e+00 +OR11H4 ENST00000315409 4.7248e-09 1.3861e+00 8.5100e-01 1.9050e+00 +OR1L3 ENST00000304820 1.7569e-04 1.2888e+00 6.3300e-01 1.9050e+00 +MT1A ENST00000290705 4.4674e-03 1.2345e+00 5.0200e-01 1.9050e+00 +SCGB2A2 ENST00000227918 1.7485e-04 1.2909e+00 6.3300e-01 1.9050e+00 +ZNF493 ENST00000392288 5.8290e-06 1.3286e+00 7.2400e-01 1.9050e+00 +PRDX1 ENST00000262746 7.6959e-10 1.3974e+00 8.7600e-01 1.9050e+00 +GSC2 ENST00000086933 4.4347e-03 1.2401e+00 5.0300e-01 1.9050e+00 +CLEC3A ENST00000299642 1.9968e-11 1.4176e+00 9.1900e-01 1.9050e+00 +HBZ ENST00000252951 2.0559e-02 1.2011e+00 4.1000e-01 1.9050e+00 +AL391421.1 ENST00000372387 4.4636e-03 1.2351e+00 5.0200e-01 1.9050e+00 +GPR31 ENST00000366834 2.0514e-02 1.2036e+00 4.1100e-01 1.9050e+00 +LINC01119 ENST00000422294 4.3811e-03 1.2496e+00 5.0600e-01 1.9060e+00 +KRT81 ENST00000327741 1.2108e-18 1.4817e+00 1.0550e+00 1.9060e+00 +DNAH17-AS1 ENST00000598378 8.3797e-02 1.2017e+00 2.8900e-01 1.9060e+00 +ADIPOQ ENST00000412955 4.6434e-09 1.3895e+00 8.5300e-01 1.9060e+00 +C10orf105 ENST00000441508 8.4246e-02 1.1872e+00 2.8700e-01 1.9060e+00 +CCL7 ENST00000378569 8.9294e-04 1.2736e+00 5.7700e-01 1.9060e+00 +OR1I1 ENST00000209540 5.7475e-06 1.3329e+00 7.2600e-01 1.9060e+00 +OR2V1 ENST00000329365 1.6993e-07 1.3631e+00 7.9600e-01 1.9060e+00 +TFF1 ENST00000291527 8.8929e-04 1.2760e+00 5.7800e-01 1.9060e+00 +PRED62 ENST00000593412 8.4250e-02 1.1871e+00 2.8700e-01 1.9060e+00 +C12orf76 ENST00000309050 9.8749e-07 1.3520e+00 7.6500e-01 1.9060e+00 +GJB7 ENST00000525899 9.8644e-07 1.3523e+00 7.6500e-01 1.9060e+00 +LY6G6E ENST00000383418 4.3870e-03 1.2485e+00 5.0600e-01 1.9060e+00 +RIIAD1 ENST00000479191 3.1906e-05 1.3175e+00 6.8500e-01 1.9060e+00 +OR3A3 ENST00000291231 1.7143e-04 1.2996e+00 6.3700e-01 1.9070e+00 +OR4C11 ENST00000302231 5.6002e-06 1.3408e+00 7.3000e-01 1.9070e+00 +C19orf73 ENST00000408991 8.3294e-02 1.2184e+00 2.9000e-01 1.9070e+00 +C1QL1 ENST00000253407 5.6243e-06 1.3395e+00 7.2900e-01 1.9070e+00 +OR10AG1 ENST00000312345 3.1694e-05 1.3199e+00 6.8600e-01 1.9070e+00 +RP11-552I14.1 ENST00000547418 4.3619e-03 1.2530e+00 5.0700e-01 1.9070e+00 +SLIRP ENST00000557342 9.7265e-07 1.3560e+00 7.6600e-01 1.9070e+00 +OR1L4 ENST00000259466 3.1586e-05 1.3211e+00 6.8600e-01 1.9070e+00 +CSHL1 ENST00000309894 3.0815e-12 1.4318e+00 9.4100e-01 1.9070e+00 +FAM9A ENST00000543214 3.0977e-12 1.4310e+00 9.4100e-01 1.9070e+00 +LSMD1 ENST00000333775 9.7053e-07 1.3566e+00 7.6700e-01 1.9070e+00 +RP11-127H5.1 ENST00000521923 8.8702e-04 1.2774e+00 5.7800e-01 1.9070e+00 +NPW ENST00000329610 8.8233e-04 1.2804e+00 5.7900e-01 1.9070e+00 +FABP1 ENST00000295834 9.8037e-07 1.3539e+00 7.6600e-01 1.9070e+00 +C1orf210 ENST00000523677 1.7017e-04 1.3028e+00 6.3800e-01 1.9070e+00 +LCE1A ENST00000335123 4.3743e-03 1.2508e+00 5.0600e-01 1.9070e+00 +CT83 ENST00000371894 8.3699e-02 1.2049e+00 2.8900e-01 1.9070e+00 +MT1M ENST00000379818 4.3473e-03 1.2556e+00 5.0800e-01 1.9070e+00 +HMGB4 ENST00000522796 4.3480e-03 1.2555e+00 5.0800e-01 1.9070e+00 +COX19 ENST00000344111 4.3158e-03 1.2614e+00 5.0900e-01 1.9080e+00 +MUCL1 ENST00000308796 3.0923e-05 1.3289e+00 6.8900e-01 1.9080e+00 +AC008394.1 ENST00000445770 8.3114e-02 1.2244e+00 2.9100e-01 1.9080e+00 +RP11-195B21.3 ENST00000417488 8.2654e-02 1.2403e+00 2.9200e-01 1.9080e+00 +ZNF552 ENST00000391701 8.6839e-04 1.2896e+00 5.8200e-01 1.9080e+00 +C14orf144 ENST00000419115 1.9885e-02 1.2419e+00 4.1800e-01 1.9080e+00 +TEX37 ENST00000303254 3.1157e-05 1.3261e+00 6.8800e-01 1.9080e+00 +IFIT1B ENST00000371809 3.1227e-05 1.3253e+00 6.8800e-01 1.9080e+00 +SPTSSB ENST00000359175 8.6955e-04 1.2888e+00 5.8200e-01 1.9080e+00 +RNASE6 ENST00000304677 8.2292e-02 1.2532e+00 2.9400e-01 1.9090e+00 +OR52R1 ENST00000356069 2.6505e-08 1.3909e+00 8.3300e-01 1.9090e+00 +SH3BGRL2 ENST00000369838 1.5983e-07 1.3777e+00 8.0300e-01 1.9090e+00 +OR2S2 ENST00000341959 1.6621e-04 1.3134e+00 6.4200e-01 1.9090e+00 +ZBED3 ENST00000255198 8.2483e-02 1.2464e+00 2.9300e-01 1.9090e+00 +KB-1980E6.3 ENST00000523572 8.1407e-02 1.2859e+00 2.9700e-01 1.9100e+00 +HOPX ENST00000554144 5.3973e-06 1.3523e+00 7.3500e-01 1.9100e+00 +NPIPB15 ENST00000429990 5.3603e-06 1.3545e+00 7.3500e-01 1.9100e+00 +AC011294.3 ENST00000451905 4.2268e-03 1.2781e+00 5.1400e-01 1.9100e+00 +GSTA5 ENST00000370989 1.7989e-11 1.4343e+00 9.2800e-01 1.9100e+00 +KRTAP2-4 ENST00000394015 8.4684e-04 1.3043e+00 5.8700e-01 1.9100e+00 +C1orf189 ENST00000368525 2.5894e-08 1.3960e+00 8.3500e-01 1.9100e+00 +CHCHD10 ENST00000484558 5.3661e-06 1.3541e+00 7.3500e-01 1.9100e+00 +OR1L6 ENST00000304720 3.0047e-05 1.3395e+00 6.9400e-01 1.9100e+00 +LYPD3 ENST00000244333 1.8345e-11 1.4312e+00 9.2600e-01 1.9100e+00 +FAM229A ENST00000432622 8.0917e-02 1.3049e+00 2.9900e-01 1.9110e+00 +C20orf187 ENST00000378252 4.1750e-03 1.2882e+00 5.1600e-01 1.9110e+00 +DEFB106B ENST00000335479 8.1151e-02 1.2958e+00 2.9800e-01 1.9110e+00 +OR2AP1 ENST00000321688 2.9797e-05 1.3426e+00 6.9500e-01 1.9110e+00 +NUPR1 ENST00000395641 4.1502e-03 1.2931e+00 5.1800e-01 1.9110e+00 +C5orf56 ENST00000337752 4.1687e-03 1.2895e+00 5.1700e-01 1.9110e+00 +CCDC54 ENST00000261058 1.1084e-10 1.4276e+00 9.0900e-01 1.9110e+00 +PRAMEF22 ENST00000376187 4.1746e-03 1.2883e+00 5.1600e-01 1.9110e+00 +HBQ1 ENST00000199708 8.2894e-04 1.3170e+00 5.9100e-01 1.9120e+00 +TAF9B ENST00000341864 1.0850e-10 1.4313e+00 9.1100e-01 1.9120e+00 +KRTAP4-7 ENST00000391417 1.5907e-04 1.3335e+00 6.4900e-01 1.9120e+00 +POTEI ENST00000451531 4.1618e-09 1.4113e+00 8.6400e-01 1.9120e+00 +RP11-187E13.2 ENST00000556949 1.9191e-02 1.2883e+00 4.2700e-01 1.9120e+00 +OR8K1 ENST00000279783 5.1722e-06 1.3658e+00 7.4000e-01 1.9120e+00 +AC016885.1 ENST00000598428 8.0463e-02 1.3231e+00 3.0000e-01 1.9120e+00 +AP005482.1 ENST00000400514 8.0286e-02 1.3303e+00 3.0100e-01 1.9120e+00 +PF4V1 ENST00000226524 8.1618e-04 1.3263e+00 5.9400e-01 1.9130e+00 +SLC9B1P1 ENST00000331172 4.0587e-03 1.3119e+00 5.2200e-01 1.9130e+00 +ABHD1 ENST00000316470 3.3799e-25 1.5346e+00 1.1440e+00 1.9130e+00 +KRTAP5-4 ENST00000399682 1.8983e-02 1.3032e+00 4.3000e-01 1.9130e+00 +LSM10 ENST00000315732 4.0741e-03 1.3087e+00 5.2200e-01 1.9130e+00 +ZNF717 ENST00000422325 1.8983e-02 1.3032e+00 4.3000e-01 1.9130e+00 +TAS2R4 ENST00000247881 5.0890e-06 1.3710e+00 7.4200e-01 1.9130e+00 +RP11-160N1.10 ENST00000377548 7.9994e-02 1.3425e+00 3.0200e-01 1.9130e+00 +BLOC1S3 ENST00000433642 4.0770e-03 1.3081e+00 5.2100e-01 1.9130e+00 +AC137932.1 ENST00000602042 7.9566e-02 1.3607e+00 3.0300e-01 1.9130e+00 +RMI2 ENST00000312499 1.8953e-02 1.3053e+00 4.3000e-01 1.9130e+00 +OR8U1 ENST00000302270 8.7306e-07 1.3856e+00 7.8000e-01 1.9130e+00 +TMEM86B ENST00000327042 5.0655e-06 1.3725e+00 7.4300e-01 1.9130e+00 +RBL1 ENST00000598590 7.9639e-02 1.3576e+00 3.0300e-01 1.9130e+00 +MAGEC1 ENST00000285879 7.9896e-02 1.3466e+00 3.0200e-01 1.9130e+00 +LCE1D ENST00000326233 4.0569e-03 1.3122e+00 5.2200e-01 1.9130e+00 +OR52N4 ENST00000317254 5.1320e-06 1.3683e+00 7.4100e-01 1.9130e+00 +IFNL3 ENST00000413851 2.4233e-08 1.4107e+00 8.4300e-01 1.9140e+00 +ISCA2 ENST00000556816 2.4343e-08 1.4097e+00 8.4200e-01 1.9140e+00 +BIK ENST00000216115 5.0334e-06 1.3745e+00 7.4400e-01 1.9140e+00 +CXCL5 ENST00000296027 5.0431e-06 1.3739e+00 7.4400e-01 1.9140e+00 +HNRNPA1L2 ENST00000342657 1.8776e-02 1.3184e+00 4.3300e-01 1.9140e+00 +RP11-553A10.1 ENST00000383686 4.0523e-03 1.3132e+00 5.2300e-01 1.9140e+00 +MALSU1 ENST00000466681 1.6777e-11 1.4457e+00 9.3400e-01 1.9140e+00 +FBXL8 ENST00000258200 3.9237e-09 1.4233e+00 8.7000e-01 1.9140e+00 +OR52J3 ENST00000380370 4.9269e-06 1.3814e+00 7.4700e-01 1.9150e+00 +KLHL25 ENST00000337975 1.5932e-15 1.4860e+00 1.0210e+00 1.9150e+00 +GOLGA6L19 ENST00000557886 7.9334e-04 1.3437e+00 5.9900e-01 1.9150e+00 +TIMM10B ENST00000254616 8.5093e-07 1.3928e+00 7.8300e-01 1.9150e+00 +NUDT7 ENST00000268533 8.4378e-07 1.3952e+00 7.8400e-01 1.9150e+00 +RP11-93B14.6 ENST00000370520 7.8497e-02 1.4089e+00 3.0700e-01 1.9150e+00 +CSTA ENST00000264474 1.5316e-04 1.3512e+00 6.5500e-01 1.9150e+00 +CSTL1 ENST00000347397 2.3758e-08 1.4152e+00 8.4500e-01 1.9150e+00 +HIST1H2BI ENST00000377733 3.9846e-03 1.3277e+00 5.2600e-01 1.9150e+00 +RP11-279O9.4 ENST00000512874 1.8680e-02 1.3257e+00 4.3400e-01 1.9150e+00 +RP11-116D17.1 ENST00000547948 7.8342e-02 1.4162e+00 3.0800e-01 1.9150e+00 +SCGB1A1 ENST00000278282 7.9919e-04 1.3392e+00 5.9800e-01 1.9150e+00 +KRTAP2-1 ENST00000391419 3.9974e-03 1.3249e+00 5.2600e-01 1.9150e+00 +C9orf16 ENST00000372994 1.8442e-02 1.3442e+00 4.3700e-01 1.9160e+00 +OR51A4 ENST00000380373 3.9172e-03 1.3427e+00 5.3000e-01 1.9160e+00 +VENTX ENST00000325980 2.7462e-05 1.3737e+00 7.0700e-01 1.9160e+00 +ZIK1 ENST00000597850 2.7592e-05 1.3718e+00 7.0600e-01 1.9160e+00 +JSRP1 ENST00000300961 6.1014e-10 1.4407e+00 8.9800e-01 1.9160e+00 +HIST1H2AL ENST00000357320 7.9028e-04 1.3461e+00 6.0000e-01 1.9160e+00 +FAM107A ENST00000394481 8.2783e-07 1.4006e+00 7.8600e-01 1.9160e+00 +OR2T1 ENST00000366474 6.1880e-10 1.4380e+00 8.9700e-01 1.9160e+00 +LYRM1 ENST00000396052 3.7249e-09 1.4341e+00 8.7600e-01 1.9170e+00 +LTB ENST00000429299 9.6063e-11 1.4529e+00 9.2200e-01 1.9170e+00 +DEC1 ENST00000374016 2.6727e-05 1.3843e+00 7.1100e-01 1.9170e+00 +BID ENST00000317361 1.5646e-11 1.4573e+00 9.4100e-01 1.9170e+00 +INSL6 ENST00000381641 3.7340e-09 1.4336e+00 8.7500e-01 1.9170e+00 +MSRA ENST00000317173 1.5332e-15 1.4910e+00 1.0240e+00 1.9170e+00 +RBM12B-AS1 ENST00000391680 1.8345e-02 1.3519e+00 4.3900e-01 1.9170e+00 +FGFBP2 ENST00000259989 3.8934e-03 1.3481e+00 5.3100e-01 1.9170e+00 +DSCR4 ENST00000328264 7.7840e-04 1.3556e+00 6.0300e-01 1.9170e+00 +SELV ENST00000335426 9.6824e-11 1.4514e+00 9.2200e-01 1.9170e+00 +IL32 ENST00000525643 3.7471e-09 1.4329e+00 8.7500e-01 1.9170e+00 +SPANXD ENST00000370515 7.7485e-02 1.4583e+00 3.1100e-01 1.9170e+00 +IL9 ENST00000274520 8.1087e-07 1.4065e+00 7.8900e-01 1.9170e+00 +GNRH2 ENST00000245983 1.3359e-07 1.4223e+00 8.2400e-01 1.9180e+00 +TMSB10 ENST00000233143 1.8038e-02 1.3772e+00 4.4300e-01 1.9180e+00 +NPFFR1 ENST00000277942 9.5481e-15 1.4881e+00 1.0110e+00 1.9180e+00 +DEFB110 ENST00000371148 1.8029e-02 1.3779e+00 4.4300e-01 1.9180e+00 +C5orf27 ENST00000357880 7.6951e-02 1.4860e+00 3.1300e-01 1.9180e+00 +HIST1H2BC ENST00000314332 3.8196e-03 1.3654e+00 5.3600e-01 1.9180e+00 +FOXR2 ENST00000339140 7.6682e-02 1.5003e+00 3.1400e-01 1.9180e+00 +YBEY ENST00000329319 1.3393e-07 1.4216e+00 8.2400e-01 1.9180e+00 +AC073063.1 ENST00000398089 7.6715e-02 1.4986e+00 3.1400e-01 1.9180e+00 +OR7A10 ENST00000248058 1.8154e-02 1.3674e+00 4.4100e-01 1.9180e+00 +GOLGA8K ENST00000512626 2.3308e-12 1.4751e+00 9.6500e-01 1.9190e+00 +TCL1A ENST00000402399 5.7357e-10 1.4527e+00 9.0500e-01 1.9190e+00 +TDGF1 ENST00000296145 9.1591e-11 1.4615e+00 9.2700e-01 1.9190e+00 +CTSZ ENST00000217131 2.2587e-16 1.5042e+00 1.0420e+00 1.9190e+00 +OR4D11 ENST00000313253 4.5606e-06 1.4070e+00 7.5700e-01 1.9190e+00 +FLG2 ENST00000388718 1.7969e-02 1.3831e+00 4.4400e-01 1.9190e+00 +HIST1H2BB ENST00000357905 3.7893e-03 1.3727e+00 5.3700e-01 1.9190e+00 +GGACT ENST00000376250 7.5371e-04 1.3762e+00 6.0900e-01 1.9190e+00 +BOD1L2 ENST00000585477 7.5648e-02 1.5587e+00 3.1900e-01 1.9190e+00 +EGFL7 ENST00000371699 5.5498e-18 1.5132e+00 1.0660e+00 1.9190e+00 +AC010646.3 ENST00000594059 7.5765e-02 1.5518e+00 3.1800e-01 1.9190e+00 +OR5M3 ENST00000312240 3.5768e-09 1.4426e+00 8.8000e-01 1.9190e+00 +C10orf62 ENST00000370640 4.4990e-06 1.4116e+00 7.5900e-01 1.9200e+00 +ICAM3 ENST00000160262 2.7302e-25 1.5526e+00 1.1560e+00 1.9200e+00 +NPIPB8 ENST00000529716 3.7575e-03 1.3805e+00 5.3900e-01 1.9200e+00 +RPS4Y2 ENST00000288666 7.4913e-04 1.3802e+00 6.1000e-01 1.9200e+00 +OR13H1 ENST00000338616 2.5456e-05 1.4037e+00 7.1800e-01 1.9200e+00 +C6orf164 ENST00000369570 1.7709e-02 1.4057e+00 4.4800e-01 1.9200e+00 +NPS ENST00000398023 1.4091e-04 1.3917e+00 6.6900e-01 1.9200e+00 +SPATA31A6 ENST00000332857 2.5549e-05 1.4023e+00 7.1800e-01 1.9200e+00 +ZNF816 ENST00000357666 1.4159e-04 1.3893e+00 6.6800e-01 1.9200e+00 +CCL17 ENST00000219244 1.3932e-04 1.3974e+00 6.7100e-01 1.9210e+00 +FAM104B ENST00000425133 1.7574e-02 1.4180e+00 4.5000e-01 1.9210e+00 +C1orf147 ENST00000367119 1.7509e-02 1.4239e+00 4.5100e-01 1.9210e+00 +FAM115C ENST00000444908 2.0765e-08 1.4462e+00 8.6000e-01 1.9210e+00 +C2orf27B ENST00000303798 7.4656e-02 1.6197e+00 3.2300e-01 1.9210e+00 +RP11-812E19.9 ENST00000558425 7.5529e-07 1.4272e+00 7.9800e-01 1.9210e+00 +CRP ENST00000255030 3.6969e-03 1.3958e+00 5.4300e-01 1.9210e+00 +CTB-78H18.1 ENST00000524175 1.7537e-02 1.4213e+00 4.5000e-01 1.9210e+00 +AC011997.1 ENST00000409845 1.3749e-04 1.4041e+00 6.7300e-01 1.9210e+00 +HIST2H3PS2 ENST00000392948 3.7116e-03 1.3920e+00 5.4200e-01 1.9210e+00 +TMEM236 ENST00000377495 1.7249e-02 1.4485e+00 4.5400e-01 1.9220e+00 +RARRES3 ENST00000255688 1.2234e-07 1.4452e+00 8.3400e-01 1.9220e+00 +SPINT3 ENST00000217428 1.7290e-02 1.4445e+00 4.5400e-01 1.9220e+00 +RP11-817J15.3 ENST00000537079 7.4255e-02 1.6459e+00 3.2400e-01 1.9220e+00 +AL022328.1 ENST00000595015 1.7243e-02 1.4491e+00 4.5500e-01 1.9220e+00 +AL627171.1 ENST00000358799 7.4186e-02 1.6505e+00 3.2500e-01 1.9220e+00 +FUT2 ENST00000425340 5.3218e-14 1.5008e+00 1.0060e+00 1.9230e+00 +IGFL1 ENST00000437936 1.9891e-08 1.4564e+00 8.6400e-01 1.9230e+00 +PLGLB1 ENST00000355705 7.3156e-02 1.7228e+00 3.2900e-01 1.9230e+00 +RP11-521M14.2 ENST00000521869 7.3616e-02 1.6897e+00 3.2700e-01 1.9230e+00 +C15orf53 ENST00000318792 1.7120e-02 1.4612e+00 4.5600e-01 1.9230e+00 +PRB1 ENST00000500254 8.3839e-11 1.4777e+00 9.3500e-01 1.9230e+00 +CCDC28B ENST00000373602 3.2253e-09 1.4648e+00 8.9100e-01 1.9230e+00 +CST7 ENST00000480798 1.2199e-07 1.4459e+00 8.3500e-01 1.9230e+00 +CSAG1 ENST00000370287 3.6070e-03 1.4195e+00 5.4800e-01 1.9230e+00 +CIDEB ENST00000336557 8.2186e-15 1.5086e+00 1.0230e+00 1.9230e+00 +SPANXC ENST00000358993 7.2819e-02 1.7482e+00 3.3000e-01 1.9240e+00 +ZACN ENST00000334586 4.2739e-22 1.5501e+00 1.1290e+00 1.9240e+00 +HIST2H3D ENST00000331491 7.0344e-04 1.4222e+00 6.2200e-01 1.9240e+00 +AP002348.1 ENST00000375081 7.2758e-02 1.7528e+00 3.3100e-01 1.9240e+00 +DUOXA2 ENST00000323030 1.2666e-15 1.5159e+00 1.0380e+00 1.9240e+00 +TEX22 ENST00000451127 6.9502e-04 1.4305e+00 6.2400e-01 1.9240e+00 +THYN1 ENST00000341541 1.9691e-16 1.5214e+00 1.0520e+00 1.9240e+00 +OR8J3 ENST00000301529 7.2480e-02 1.7744e+00 3.3200e-01 1.9240e+00 +OR9A4 ENST00000548136 1.1843e-07 1.4538e+00 8.3800e-01 1.9240e+00 +MT4 ENST00000219162 1.3052e-04 1.4309e+00 6.8200e-01 1.9240e+00 +GOLGA8T ENST00000569052 1.2558e-11 1.4951e+00 9.6100e-01 1.9250e+00 +CT62 ENST00000449977 1.6698e-02 1.5047e+00 4.6300e-01 1.9250e+00 +PRR25 ENST00000301698 5.0229e-10 1.4790e+00 9.1800e-01 1.9250e+00 +AC018867.1 ENST00000396985 7.2047e-02 1.8092e+00 3.3400e-01 1.9250e+00 +RP1-241P17.4 ENST00000449327 7.1659e-02 1.8417e+00 3.3500e-01 1.9250e+00 +LCE2C ENST00000368783 7.1993e-02 1.8136e+00 3.3400e-01 1.9250e+00 +OR6F1 ENST00000302084 6.9042e-04 1.4351e+00 6.2600e-01 1.9250e+00 +UTS2R ENST00000313135 2.3172e-05 1.4426e+00 7.3300e-01 1.9250e+00 +TCEAL6 ENST00000372774 1.6648e-02 1.5100e+00 4.6400e-01 1.9250e+00 +RP11-15E18.4 ENST00000592917 7.1012e-02 1.8989e+00 3.3800e-01 1.9260e+00 +FLJ20306 ENST00000601673 7.1040e-02 1.8963e+00 3.3800e-01 1.9260e+00 +C20orf166 ENST00000370527 3.4664e-03 1.4593e+00 5.5700e-01 1.9260e+00 +KIAA0087 ENST00000242109 3.4494e-03 1.4644e+00 5.5800e-01 1.9260e+00 +C9orf116 ENST00000429260 2.2657e-05 1.4522e+00 7.3600e-01 1.9260e+00 +NMRK2 ENST00000168977 1.9248e-12 1.5063e+00 9.8300e-01 1.9260e+00 +U82695.9 ENST00000428676 1.6529e-02 1.5231e+00 4.6600e-01 1.9260e+00 +EIF3C ENST00000331666 2.2907e-05 1.4475e+00 7.3500e-01 1.9260e+00 +LCE3B ENST00000335633 3.4323e-03 1.4696e+00 5.5900e-01 1.9260e+00 +OR5K4 ENST00000354924 3.9605e-06 1.4559e+00 7.7700e-01 1.9260e+00 +OR8B2 ENST00000375013 1.6474e-02 1.5292e+00 4.6700e-01 1.9260e+00 +SULT1C3 ENST00000329106 4.4266e-18 1.5395e+00 1.0820e+00 1.9260e+00 +KLRF2 ENST00000535540 7.7125e-11 1.4934e+00 9.4400e-01 1.9260e+00 +POLR2J2 ENST00000591000 1.6555e-02 1.5202e+00 4.6500e-01 1.9260e+00 +KCNE1 ENST00000337385 3.3960e-03 1.4807e+00 5.6200e-01 1.9270e+00 +LENEP ENST00000392487 3.3892e-03 1.4828e+00 5.6200e-01 1.9270e+00 +SPATA33 ENST00000301031 1.2570e-04 1.4509e+00 6.8800e-01 1.9270e+00 +CST4 ENST00000217423 6.6761e-07 1.4645e+00 8.1400e-01 1.9270e+00 +FGF22 ENST00000215530 6.6707e-07 1.4647e+00 8.1400e-01 1.9270e+00 +MYEOV ENST00000308946 3.3849e-03 1.4842e+00 5.6300e-01 1.9270e+00 +NPIPB7 ENST00000452313 1.6363e-02 1.5417e+00 4.6800e-01 1.9270e+00 +ZNF155 ENST00000407951 6.6195e-07 1.4671e+00 8.1500e-01 1.9270e+00 +OR56A3 ENST00000329564 2.9344e-09 1.4856e+00 9.0100e-01 1.9270e+00 +OR5L2 ENST00000378397 2.2583e-05 1.4536e+00 7.3700e-01 1.9270e+00 +CXXC11 ENST00000343216 1.6289e-02 1.5503e+00 4.7000e-01 1.9270e+00 +KRTAP24-1 ENST00000340345 6.5742e-07 1.4693e+00 8.1600e-01 1.9270e+00 +PGA5 ENST00000312403 4.6125e-10 1.4965e+00 9.2700e-01 1.9280e+00 +RP11-139J15.7 ENST00000606425 1.2257e-04 1.4645e+00 6.9300e-01 1.9280e+00 +PPAPDC1B ENST00000424479 1.8573e-12 1.5123e+00 9.8600e-01 1.9280e+00 +RP11-321M21.3 ENST00000578340 6.9975e-02 1.9993e+00 3.4300e-01 1.9280e+00 +PLA2G10 ENST00000438167 6.9507e-02 2.0484e+00 3.4500e-01 1.9280e+00 +CRYZ ENST00000417775 5.6616e-23 1.5682e+00 1.1470e+00 1.9280e+00 +AC011475.1 ENST00000430975 7.0058e-02 1.9907e+00 3.4300e-01 1.9280e+00 +AKR1B15 ENST00000457545 3.6787e-22 1.5648e+00 1.1380e+00 1.9280e+00 +NEU2 ENST00000233840 4.5314e-14 1.5246e+00 1.0200e+00 1.9280e+00 +AKR7A3 ENST00000361640 1.0209e-19 1.5521e+00 1.1070e+00 1.9280e+00 +TAS2R39 ENST00000446620 1.0789e-07 1.4791e+00 8.4900e-01 1.9280e+00 +OR2T10 ENST00000330500 6.5559e-04 1.4719e+00 6.3600e-01 1.9280e+00 +CLEC1A ENST00000315330 2.6288e-17 1.5452e+00 1.0760e+00 1.9290e+00 +CLPSL1 ENST00000373861 2.1662e-05 1.4717e+00 7.4300e-01 1.9290e+00 +AE000662.92 ENST00000557595 1.1973e-04 1.4774e+00 6.9700e-01 1.9290e+00 +ZNF678 ENST00000343776 1.5898e-02 1.5975e+00 4.7600e-01 1.9290e+00 +CGB8 ENST00000448456 1.5956e-02 1.5904e+00 4.7500e-01 1.9290e+00 +HIST1H4I ENST00000354348 1.5809e-02 1.6088e+00 4.7800e-01 1.9290e+00 +CNPY1 ENST00000321736 2.1539e-05 1.4742e+00 7.4400e-01 1.9290e+00 +C8G ENST00000224181 2.6521e-17 1.5441e+00 1.0760e+00 1.9290e+00 +CDPF1 ENST00000314567 2.1482e-05 1.4754e+00 7.4400e-01 1.9290e+00 +C5orf47 ENST00000340147 1.0442e-07 1.4882e+00 8.5300e-01 1.9290e+00 +SMN1 ENST00000380707 1.5829e-02 1.6063e+00 4.7700e-01 1.9290e+00 +SPRR2D ENST00000368757 1.5926e-02 1.5941e+00 4.7600e-01 1.9290e+00 +PRAC1 ENST00000290294 1.5930e-02 1.5936e+00 4.7600e-01 1.9290e+00 +OR10G4 ENST00000320891 2.1457e-05 1.4759e+00 7.4500e-01 1.9290e+00 +OR10J1 ENST00000423932 6.3754e-07 1.4789e+00 8.2000e-01 1.9290e+00 +PTPN20A ENST00000374339 1.5945e-02 1.5917e+00 4.7500e-01 1.9290e+00 +SCGB1C1 ENST00000342878 2.1497e-05 1.4751e+00 7.4400e-01 1.9290e+00 +AL161645.2 ENST00000599428 6.8126e-02 2.2107e+00 3.5200e-01 1.9300e+00 +WFS1 ENST00000226760 1.6231e-38 1.6193e+00 1.2730e+00 1.9300e+00 +DEFB4B ENST00000318157 6.7977e-02 2.2298e+00 3.5300e-01 1.9300e+00 +SMIM21 ENST00000579022 2.1196e-05 1.4813e+00 7.4700e-01 1.9300e+00 +SPRR1B ENST00000307098 6.3211e-04 1.4989e+00 6.4300e-01 1.9300e+00 +OTOS ENST00000391989 2.0966e-05 1.4862e+00 7.4800e-01 1.9300e+00 +CCR5 ENST00000343801 4.3094e-10 1.5107e+00 9.3400e-01 1.9300e+00 +UBBP4 ENST00000578713 3.6230e-06 1.4885e+00 7.8900e-01 1.9300e+00 +LRRN4CL ENST00000317449 2.0393e-05 1.4987e+00 7.5300e-01 1.9310e+00 +MRPL23 ENST00000397298 1.6288e-08 1.5056e+00 8.8700e-01 1.9310e+00 +RP11-322E11.6 ENST00000589258 1.5411e-02 1.6621e+00 4.8500e-01 1.9310e+00 +OR1F1 ENST00000304646 3.5616e-06 1.4949e+00 7.9200e-01 1.9310e+00 +ANKRD20A3 ENST00000254835 3.1925e-03 1.5486e+00 5.7600e-01 1.9310e+00 +NBPF15 ENST00000442702 6.0603e-07 1.4950e+00 8.2600e-01 1.9310e+00 +ZNF705G ENST00000400156 1.6471e-08 1.5028e+00 8.8600e-01 1.9310e+00 +MC3R ENST00000243911 9.9877e-08 1.5007e+00 8.5900e-01 1.9310e+00 +OR2Z1 ENST00000324060 6.0814e-07 1.4939e+00 8.2600e-01 1.9310e+00 +OR4C16 ENST00000314634 5.9911e-07 1.4987e+00 8.2800e-01 1.9310e+00 +OR4K13 ENST00000315693 9.9300e-08 1.5023e+00 8.5900e-01 1.9310e+00 +OR4Q3 ENST00000331723 1.6435e-08 1.5033e+00 8.8600e-01 1.9310e+00 +IAPP ENST00000240652 3.1814e-03 1.5526e+00 5.7700e-01 1.9310e+00 +OR7D4 ENST00000308682 1.5502e-02 1.6496e+00 4.8300e-01 1.9310e+00 +UBE2NL ENST00000370494 1.5382e-02 1.6662e+00 4.8500e-01 1.9310e+00 +INSL4 ENST00000239316 1.1355e-04 1.5073e+00 7.0600e-01 1.9320e+00 +RASSF6 ENST00000342081 2.7376e-26 1.5923e+00 1.1880e+00 1.9320e+00 +OR13C4 ENST00000277216 1.5755e-08 1.5141e+00 8.9100e-01 1.9320e+00 +PRAMEF4 ENST00000235349 1.0209e-11 1.5324e+00 9.8100e-01 1.9320e+00 +IL3 ENST00000296870 2.5874e-09 1.5143e+00 9.1400e-01 1.9320e+00 +FAM24A ENST00000368894 1.5222e-02 1.6891e+00 4.8800e-01 1.9320e+00 +NPIPB6 ENST00000532254 6.1348e-04 1.5217e+00 6.4900e-01 1.9320e+00 +TMEM170A ENST00000561878 5.7160e-07 1.5140e+00 8.3400e-01 1.9330e+00 +GLRX ENST00000379979 5.6744e-07 1.5164e+00 8.3500e-01 1.9330e+00 +RP11-324D17.1 ENST00000561084 3.0941e-03 1.5851e+00 5.8300e-01 1.9330e+00 +AMY1B ENST00000330330 6.0271e-04 1.5355e+00 6.5300e-01 1.9330e+00 +AL139333.1 ENST00000398400 6.6279e-02 2.4775e+00 3.6100e-01 1.9330e+00 +AL646016.1 ENST00000596886 6.6274e-02 2.4784e+00 3.6100e-01 1.9330e+00 +IFI27L2 ENST00000238609 1.1149e-04 1.5179e+00 7.0900e-01 1.9330e+00 +GJD4 ENST00000321660 1.4965e-02 1.7276e+00 4.9300e-01 1.9330e+00 +MED11 ENST00000293777 9.3635e-08 1.5192e+00 8.6700e-01 1.9330e+00 +OR51B5 ENST00000300773 9.5367e-08 1.5139e+00 8.6400e-01 1.9330e+00 +OR52K2 ENST00000325719 5.6952e-07 1.5152e+00 8.3500e-01 1.9330e+00 +KRTAP27-1 ENST00000382835 6.6018e-02 2.5209e+00 3.6200e-01 1.9330e+00 +KRTAP4-9 ENST00000391415 1.1095e-04 1.5207e+00 7.1000e-01 1.9330e+00 +KRTAP5-9 ENST00000528743 1.4981e-02 1.7251e+00 4.9200e-01 1.9330e+00 +CLDN25 ENST00000453129 1.5149e-08 1.5242e+00 8.9500e-01 1.9340e+00 +RP11-276H1.3 ENST00000312019 1.4890e-02 1.7393e+00 4.9400e-01 1.9340e+00 +OVCH2 ENST00000454689 2.5933e-35 1.6227e+00 1.2600e+00 1.9340e+00 +MBD3L5 ENST00000329753 6.5468e-02 2.6183e+00 3.6500e-01 1.9340e+00 +HOXC12 ENST00000243103 2.4299e-09 1.5290e+00 9.2100e-01 1.9340e+00 +TAAR5 ENST00000258034 6.2057e-11 1.5357e+00 9.6500e-01 1.9340e+00 +ASMT ENST00000381241 1.2722e-20 1.5790e+00 1.1320e+00 1.9340e+00 +HBA2 ENST00000251595 3.0630e-03 1.5973e+00 5.8600e-01 1.9340e+00 +HBD ENST00000380299 1.9236e-05 1.5256e+00 7.6200e-01 1.9340e+00 +FGL1 ENST00000398056 1.6765e-25 1.5954e+00 1.1840e+00 1.9340e+00 +PRAMEF20 ENST00000316412 3.0211e-03 1.6141e+00 5.8900e-01 1.9340e+00 +OR52B2 ENST00000530810 1.4968e-08 1.5274e+00 8.9700e-01 1.9340e+00 +OR52E4 ENST00000316987 5.5930e-07 1.5212e+00 8.3700e-01 1.9340e+00 +GOLGA6D ENST00000434739 9.1588e-08 1.5256e+00 8.6900e-01 1.9340e+00 +AC062017.1 ENST00000413029 3.0253e-03 1.6124e+00 5.8800e-01 1.9340e+00 +OR5K1 ENST00000332650 5.6457e-07 1.5181e+00 8.3600e-01 1.9340e+00 +HIST1H2AB ENST00000259791 5.7284e-04 1.5764e+00 6.6300e-01 1.9350e+00 +MUC7 ENST00000413702 1.4582e-02 1.7896e+00 5.0000e-01 1.9350e+00 +OR9K2 ENST00000305377 5.3659e-07 1.5351e+00 8.4300e-01 1.9350e+00 +UQCR11 ENST00000591899 1.0553e-04 1.5505e+00 7.1900e-01 1.9350e+00 +GZMB ENST00000216341 3.6674e-14 1.5570e+00 1.0380e+00 1.9350e+00 +RAB42 ENST00000373826 2.9709e-03 1.6350e+00 5.9300e-01 1.9350e+00 +APOC4 ENST00000419266 8.8930e-08 1.5343e+00 8.7300e-01 1.9350e+00 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8.4500e-01 1.9360e+00 +WFDC10A ENST00000372643 1.4415e-02 1.8184e+00 5.0300e-01 1.9360e+00 +FOLR4 ENST00000440961 5.5093e-15 1.5663e+00 1.0560e+00 1.9360e+00 +C15ORF37 ENST00000542003 3.1345e-06 1.5443e+00 8.1000e-01 1.9360e+00 +IDI2 ENST00000277517 2.3124e-09 1.5408e+00 9.2700e-01 1.9360e+00 +SYT8 ENST00000381968 9.8941e-25 1.6022e+00 1.1820e+00 1.9360e+00 +DEFB125 ENST00000382410 1.4469e-02 1.8090e+00 5.0200e-01 1.9360e+00 +NUTM2A ENST00000381707 5.3583e-07 1.5356e+00 8.4300e-01 1.9360e+00 +HIST1H2AG ENST00000359193 5.5075e-04 1.6094e+00 6.7100e-01 1.9370e+00 +OR13C3 ENST00000374781 8.5387e-08 1.5464e+00 8.7800e-01 1.9370e+00 +PPDPF ENST00000370179 1.0213e-04 1.5705e+00 7.2500e-01 1.9370e+00 +RP11-219B4.5 ENST00000546501 1.4201e-02 1.8573e+00 5.0700e-01 1.9370e+00 +KCNE2 ENST00000290310 1.0145e-04 1.5746e+00 7.2600e-01 1.9370e+00 +GPR141 ENST00000447769 8.5310e-08 1.5467e+00 8.7800e-01 1.9370e+00 +TAS2R41 ENST00000408916 1.3825e-12 1.5635e+00 1.0130e+00 1.9370e+00 +AL135998.1 ENST00000399979 6.3159e-02 3.1343e+00 3.7700e-01 1.9370e+00 +ZNF468 ENST00000595646 1.0049e-04 1.5805e+00 7.2800e-01 1.9370e+00 +TMEM105 ENST00000332900 1.4225e-02 1.8528e+00 5.0700e-01 1.9370e+00 +OR4A47 ENST00000446524 8.3071e-08 1.5547e+00 8.8100e-01 1.9380e+00 +KRTAP3-3 ENST00000391586 5.4788e-04 1.6139e+00 6.7200e-01 1.9380e+00 +AC005544.1 ENST00000375684 1.3987e-02 1.8983e+00 5.1200e-01 1.9380e+00 +KDELR3 ENST00000409006 5.3760e-11 1.5650e+00 9.7900e-01 1.9380e+00 +OR6C65 ENST00000379665 1.7684e-05 1.5661e+00 7.7500e-01 1.9380e+00 +OR6C70 ENST00000327335 4.9830e-07 1.5605e+00 8.5200e-01 1.9380e+00 +FAM9C ENST00000333995 4.8778e-07 1.5680e+00 8.5500e-01 1.9390e+00 +CST2 ENST00000304725 8.0628e-08 1.5638e+00 8.8500e-01 1.9390e+00 +C2orf88 ENST00000340623 2.7643e-03 1.7307e+00 6.1000e-01 1.9390e+00 +EME2 ENST00000568449 3.7560e-23 1.6087e+00 1.1730e+00 1.9390e+00 +NBPF14 ENST00000310701 3.0119e-36 1.6423e+00 1.2780e+00 1.9390e+00 +OR5D14 ENST00000335605 2.8827e-06 1.5784e+00 8.2200e-01 1.9390e+00 +FAM27B ENST00000377484 6.1241e-02 3.7661e+00 3.8800e-01 1.9390e+00 +AMZ1 ENST00000312371 3.7114e-23 1.6100e+00 1.1740e+00 1.9390e+00 +NPIPA8 ENST00000525596 6.0896e-02 3.9100e+00 3.9000e-01 1.9390e+00 +AL137026.1 ENST00000593376 5.9917e-02 4.3887e+00 3.9600e-01 1.9400e+00 +HIST1H4E ENST00000360441 1.3453e-02 2.0116e+00 5.2300e-01 1.9400e+00 +HIST3H3 ENST00000366696 1.6542e-05 1.5996e+00 7.8600e-01 1.9400e+00 +OR5AR1 ENST00000302969 7.6881e-08 1.5785e+00 8.9100e-01 1.9400e+00 +OR6C68 ENST00000548615 1.3380e-02 2.0284e+00 5.2400e-01 1.9400e+00 +DEFB131 ENST00000334879 1.3450e-02 2.0122e+00 5.2300e-01 1.9400e+00 +SPRR2E ENST00000368751 6.0135e-02 4.2719e+00 3.9500e-01 1.9400e+00 +ARMS2 ENST00000528446 5.1801e-04 1.6633e+00 6.8300e-01 1.9400e+00 +RP11-297N6.4 ENST00000533405 1.3358e-02 2.0336e+00 5.2500e-01 1.9400e+00 +HCAR3 ENST00000528880 7.8636e-08 1.5715e+00 8.8800e-01 1.9400e+00 +NPIPA7 ENST00000530217 6.0667e-02 4.0119e+00 3.9200e-01 1.9400e+00 +AC007401.2 ENST00000406220 2.7199e-03 1.7537e+00 6.1400e-01 1.9400e+00 +AL033381.1 ENST00000314040 1.3359e-02 2.0333e+00 5.2500e-01 1.9400e+00 +RFPL3 ENST00000249007 1.6582e-05 1.5983e+00 7.8500e-01 1.9400e+00 +AL353354.1 ENST00000321830 1.3153e-02 2.0833e+00 5.2900e-01 1.9410e+00 +HIST1H4G ENST00000244537 1.3198e-02 2.0720e+00 5.2800e-01 1.9410e+00 +PRAMEF19 ENST00000540591 5.9654e-02 4.5394e+00 3.9800e-01 1.9410e+00 +RP11-481A20.11 ENST00000527396 5.1106e-04 1.6757e+00 6.8600e-01 1.9410e+00 +PTRHD1 ENST00000328379 4.6245e-07 1.5870e+00 8.6200e-01 1.9410e+00 +CORT ENST00000377049 1.3143e-02 2.0858e+00 5.2900e-01 1.9410e+00 +CCDC167 ENST00000373408 4.6515e-07 1.5849e+00 8.6200e-01 1.9410e+00 +NDUFB3 ENST00000237889 1.6105e-05 1.6134e+00 7.9000e-01 1.9410e+00 +OR10K2 ENST00000314902 2.7284e-06 1.6016e+00 8.3000e-01 1.9410e+00 +NUPR1L ENST00000329309 5.0652e-04 1.6839e+00 6.8800e-01 1.9410e+00 +ZNF785 ENST00000395216 2.7478e-06 1.5985e+00 8.2900e-01 1.9410e+00 +GAGE1 ENST00000381700 1.3113e-02 2.0932e+00 5.3000e-01 1.9410e+00 +PTH2 ENST00000270631 2.6248e-03 1.8061e+00 6.2200e-01 1.9420e+00 +LINC01118 ENST00000409912 1.9119e-09 1.5878e+00 9.4800e-01 1.9420e+00 +NUDT1 ENST00000397049 7.4464e-12 1.5930e+00 1.0110e+00 1.9420e+00 +HIST1H2AH ENST00000377459 4.9143e-04 1.7124e+00 6.9400e-01 1.9420e+00 +SAA2 ENST00000526900 2.7019e-06 1.6057e+00 8.3200e-01 1.9420e+00 +AC005841.1 ENST00000382678 2.9965e-10 1.5912e+00 9.7200e-01 1.9420e+00 +XXbac-BPG32J3.20 ENST00000461287 8.9666e-05 1.6549e+00 7.4800e-01 1.9420e+00 +CTD-2054N24.2 ENST00000560059 2.6117e-03 1.8138e+00 6.2300e-01 1.9420e+00 +HIST1H2BN ENST00000396980 4.9469e-04 1.7061e+00 6.9300e-01 1.9420e+00 +OR5H14 ENST00000437310 4.4964e-07 1.5971e+00 8.6600e-01 1.9420e+00 +PSG4 ENST00000405312 5.9115e-29 1.6412e+00 1.2370e+00 1.9430e+00 +BEX5 ENST00000543160 2.5394e-03 1.8575e+00 6.3000e-01 1.9430e+00 +C2CD4B ENST00000380392 8.8732e-05 1.6621e+00 7.5000e-01 1.9430e+00 +SSMEM1 ENST00000297819 2.7770e-14 1.6019e+00 1.0620e+00 1.9430e+00 +VCX2 ENST00000317103 5.8136e-02 5.6758e+00 4.0700e-01 1.9430e+00 +C8orf74 ENST00000304519 7.0341e-12 1.6045e+00 1.0170e+00 1.9430e+00 +SPATA31A7 ENST00000355045 2.5685e-03 1.8395e+00 6.2700e-01 1.9430e+00 +KRTAP10-6 ENST00000400368 1.8374e-09 1.5980e+00 9.5200e-01 1.9430e+00 +OR4K1 ENST00000285600 6.9454e-08 1.6109e+00 9.0400e-01 1.9430e+00 +ALG1L ENST00000340333 1.0994e-08 1.6123e+00 9.3300e-01 1.9440e+00 +RP11-67H2.1 ENST00000521500 1.2526e-02 2.2563e+00 5.4300e-01 1.9440e+00 +PXT1 ENST00000454782 2.5199e-06 1.6362e+00 8.4200e-01 1.9440e+00 +SLC10A2 ENST00000245312 9.5802e-17 1.6188e+00 1.1080e+00 1.9440e+00 +ANKRD20A4 ENST00000357336 1.6819e-13 1.6104e+00 1.0520e+00 1.9440e+00 +C19orf80 ENST00000252453 6.8776e-12 1.6090e+00 1.0190e+00 1.9440e+00 +MESP1 ENST00000300057 8.6067e-05 1.6832e+00 7.5600e-01 1.9440e+00 +NUTM2E ENST00000429984 1.4976e-05 1.6520e+00 8.0200e-01 1.9440e+00 +RP11-247C2.2 ENST00000514871 4.6915e-04 1.7579e+00 7.0400e-01 1.9440e+00 +LMF2 ENST00000474879 2.3979e-50 1.6805e+00 1.3580e+00 1.9440e+00 +AC010441.1 ENST00000600109 1.4806e-05 1.6582e+00 8.0400e-01 1.9440e+00 +S100A7A ENST00000368729 2.5230e-03 1.8679e+00 6.3200e-01 1.9440e+00 +OCM ENST00000242104 1.0885e-08 1.6152e+00 9.3400e-01 1.9440e+00 +OR51A7 ENST00000359350 2.5439e-06 1.6320e+00 8.4100e-01 1.9440e+00 +TXNRD3NB ENST00000383572 4.2326e-07 1.6195e+00 8.7400e-01 1.9440e+00 +CYP2D6 ENST00000360608 1.0793e-25 1.6361e+00 1.2100e+00 1.9440e+00 +HIST1H3B ENST00000244661 1.4796e-05 1.6585e+00 8.0400e-01 1.9440e+00 +TIFAB ENST00000537858 1.4279e-05 1.6782e+00 8.0900e-01 1.9450e+00 +DPRX ENST00000376650 2.4069e-06 1.6568e+00 8.4900e-01 1.9450e+00 +KIAA1456 ENST00000524591 1.6974e-09 1.6187e+00 9.6100e-01 1.9450e+00 +OR7C2 ENST00000248072 5.6235e-02 8.3506e+00 4.1900e-01 1.9450e+00 +C14orf178 ENST00000355883 4.6544e-04 1.7659e+00 7.0500e-01 1.9450e+00 +AC008372.1 ENST00000596936 5.5720e-02 9.5976e+00 4.2300e-01 1.9450e+00 +TMEM207 ENST00000354905 4.2258e-11 1.6167e+00 1.0040e+00 1.9450e+00 +C9orf139 ENST00000314330 2.4581e-03 1.9108e+00 6.3800e-01 1.9450e+00 +AC016757.3 ENST00000409070 2.4322e-03 1.9287e+00 6.4100e-01 1.9450e+00 +AL355490.1 ENST00000439965 1.4329e-05 1.6763e+00 8.0900e-01 1.9450e+00 +HIST1H2BO ENST00000303806 4.5605e-04 1.7867e+00 7.1000e-01 1.9450e+00 +AMELY ENST00000215479 8.3683e-05 1.7032e+00 7.6100e-01 1.9450e+00 +FTL ENST00000331825 1.6617e-09 1.6243e+00 9.6400e-01 1.9460e+00 +POLR2L ENST00000322028 4.5417e-04 1.7910e+00 7.1000e-01 1.9460e+00 +KRTAP4-2 ENST00000377726 1.2090e-02 2.3997e+00 5.5400e-01 1.9460e+00 +OR8H1 ENST00000313022 8.1158e-05 1.7254e+00 7.6600e-01 1.9460e+00 +CD1A ENST00000289429 4.1954e-24 1.6427e+00 1.2010e+00 1.9460e+00 +hsa-mir-150 ENST00000602157 5.5262e-02 1.1073e+01 4.2600e-01 1.9460e+00 +ACTBL2 ENST00000423391 5.8166e-16 1.6268e+00 1.1010e+00 1.9460e+00 +GNG13 ENST00000248150 8.0284e-05 1.7334e+00 7.6800e-01 1.9460e+00 +CBWD5 ENST00000377395 4.5369e-04 1.7921e+00 7.1100e-01 1.9460e+00 +IQCF3 ENST00000456080 4.3339e-04 1.8409e+00 7.2000e-01 1.9470e+00 +HIST1H2AD ENST00000341023 1.3501e-05 1.7101e+00 8.1900e-01 1.9470e+00 +NPIPB3 ENST00000458643 2.3295e-03 2.0052e+00 6.5100e-01 1.9470e+00 +KRTAP6-1 ENST00000329122 2.3165e-03 2.0155e+00 6.5300e-01 1.9470e+00 +TBC1D3F ENST00000327454 1.3666e-05 1.7031e+00 8.1700e-01 1.9470e+00 +TMEM14B ENST00000379542 9.7154e-09 1.6490e+00 9.4800e-01 1.9470e+00 +HES4 ENST00000428771 1.3746e-05 1.6997e+00 8.1600e-01 1.9470e+00 +KRTAP13-2 ENST00000399889 1.3605e-05 1.7057e+00 8.1700e-01 1.9470e+00 +ZNF812 ENST00000457674 2.2548e-06 1.6870e+00 8.5800e-01 1.9470e+00 +AC006435.1 ENST00000609667 6.1673e-08 1.6504e+00 9.1900e-01 1.9470e+00 +C10orf25 ENST00000298298 3.7114e-07 1.6700e+00 8.9200e-01 1.9480e+00 +FAM211B ENST00000318753 9.0241e-13 1.6439e+00 1.0530e+00 1.9480e+00 +TP53AIP1 ENST00000531399 1.3043e-05 1.7303e+00 8.2400e-01 1.9480e+00 +DNASE1 ENST00000246949 6.9801e-21 1.6476e+00 1.1730e+00 1.9480e+00 +MPZL3 ENST00000278949 2.2417e-14 1.6382e+00 1.0810e+00 1.9480e+00 +C13orf45 ENST00000318245 9.3942e-09 1.6592e+00 9.5200e-01 1.9480e+00 +CXCL2 ENST00000508487 3.6079e-07 1.6813e+00 8.9600e-01 1.9480e+00 +HRNR ENST00000368801 4.2580e-04 1.8604e+00 7.2400e-01 1.9480e+00 +RP11-527L4.2 ENST00000565120 1.1627e-02 2.5796e+00 5.6500e-01 1.9480e+00 +GAGE2B ENST00000381725 2.2911e-03 2.0363e+00 6.5500e-01 1.9480e+00 +TRAPPC2L ENST00000301021 3.6837e-11 1.6477e+00 1.0180e+00 1.9480e+00 +C21orf128 ENST00000329015 2.2227e-03 2.0951e+00 6.6300e-01 1.9490e+00 +IFITM5 ENST00000382614 2.1754e-06 1.7041e+00 8.6400e-01 1.9490e+00 +SPINK6 ENST00000325630 3.5317e-07 1.6900e+00 8.9900e-01 1.9490e+00 +C20orf144 ENST00000375222 2.2238e-03 2.0941e+00 6.6300e-01 1.9490e+00 +FAM111A ENST00000528737 2.2250e-03 2.0930e+00 6.6300e-01 1.9490e+00 +FAM86C1 ENST00000359244 5.5551e-12 1.6537e+00 1.0400e+00 1.9490e+00 +NME3 ENST00000219302 5.7291e-08 1.6758e+00 9.2800e-01 1.9490e+00 +DIRC3 ENST00000423123 3.4129e-07 1.7039e+00 9.0400e-01 1.9500e+00 +PGPEP1L ENST00000378919 8.7056e-09 1.6829e+00 9.6100e-01 1.9500e+00 +ZNF701 ENST00000540331 5.4866e-08 1.6911e+00 9.3400e-01 1.9500e+00 +OR4A5 ENST00000319760 1.2516e-05 1.7550e+00 8.3100e-01 1.9500e+00 +OR10H3 ENST00000305892 2.1689e-03 2.1451e+00 6.6900e-01 1.9500e+00 +BRICD5 ENST00000328540 1.1472e-17 1.6561e+00 1.1390e+00 1.9500e+00 +MS4A6A ENST00000412309 8.3775e-13 1.6588e+00 1.0600e+00 1.9500e+00 +RP11-514P8.7 ENST00000514917 1.1149e-02 2.8040e+00 5.7800e-01 1.9500e+00 +TPSAB1 ENST00000338844 1.2733e-13 1.6616e+00 1.0770e+00 1.9500e+00 +OR2T27 ENST00000344889 1.2132e-05 1.7742e+00 8.3600e-01 1.9500e+00 +MT2A ENST00000245185 1.2279e-05 1.7667e+00 8.3400e-01 1.9500e+00 +OR5M10 ENST00000526812 1.0843e-02 2.9745e+00 5.8600e-01 1.9510e+00 +GPBAR1 ENST00000522678 1.3633e-09 1.6787e+00 9.8600e-01 1.9510e+00 +PRAMEF17 ENST00000376098 5.3177e-08 1.7023e+00 9.3800e-01 1.9510e+00 +PRAMEF26 ENST00000423177 3.3135e-07 1.7162e+00 9.0800e-01 1.9510e+00 +C3orf72 ENST00000383165 7.0177e-05 1.8386e+00 7.9300e-01 1.9510e+00 +MRPL34 ENST00000252602 6.9136e-05 1.8511e+00 7.9600e-01 1.9510e+00 +SPAG11A ENST00000326558 6.9645e-05 1.8450e+00 7.9400e-01 1.9510e+00 +RPA3 ENST00000223129 8.5529e-09 1.6885e+00 9.6300e-01 1.9510e+00 +SERHL2 ENST00000327678 2.8325e-15 1.6726e+00 1.1120e+00 1.9520e+00 +AC009892.10 ENST00000456337 1.0406e-02 3.2664e+00 5.9900e-01 1.9520e+00 +DEFB115 ENST00000400552 2.0641e-03 2.2533e+00 6.8100e-01 1.9520e+00 +MLANA ENST00000381477 1.2584e-09 1.7017e+00 9.9500e-01 1.9520e+00 +CT47B1 ENST00000371311 7.6299e-09 1.7256e+00 9.7700e-01 1.9530e+00 +GAGE12J ENST00000442437 1.9883e-03 2.3420e+00 6.9100e-01 1.9530e+00 +CPZ ENST00000360986 8.8063e-36 1.6987e+00 1.3120e+00 1.9530e+00 +SMIM22 ENST00000589327 6.5039e-05 1.9035e+00 8.0700e-01 1.9530e+00 +AP003068.23 ENST00000526623 2.0020e-03 2.3252e+00 6.8900e-01 1.9530e+00 +AQP7 ENST00000297988 4.0504e-16 1.6841e+00 1.1310e+00 1.9530e+00 +HIST1H4D ENST00000340756 1.9851e-03 2.3460e+00 6.9100e-01 1.9530e+00 +C19orf24 ENST00000409293 2.8876e-07 1.7756e+00 9.2700e-01 1.9540e+00 +BGLAP ENST00000368272 4.6155e-08 1.7550e+00 9.5600e-01 1.9540e+00 +RP1L1 ENST00000382483 1.8205e-10 1.7165e+00 1.0260e+00 1.9540e+00 +C19orf83 ENST00000593161 1.9397e-03 2.4045e+00 6.9700e-01 1.9540e+00 +PATE1 ENST00000305738 7.3818e-09 1.7366e+00 9.8100e-01 1.9540e+00 +DEFB116 ENST00000400549 1.9336e-03 2.4127e+00 6.9800e-01 1.9540e+00 +FUT3 ENST00000303225 6.2991e-05 1.9322e+00 8.1300e-01 1.9540e+00 +CRCT1 ENST00000368790 1.9397e-03 2.4045e+00 6.9700e-01 1.9540e+00 +HIST1H4C ENST00000377803 3.5964e-04 2.0679e+00 7.6000e-01 1.9540e+00 +HIST1H4L ENST00000355981 3.4971e-04 2.1066e+00 7.6600e-01 1.9540e+00 +PSG8 ENST00000306511 1.6761e-23 1.6950e+00 1.2250e+00 1.9550e+00 +OR11H1 ENST00000252835 1.0253e-05 1.8847e+00 8.6400e-01 1.9550e+00 +OXCT2 ENST00000327582 2.7337e-07 1.8004e+00 9.3500e-01 1.9550e+00 +SULT6B1 ENST00000260637 3.0560e-20 1.6974e+00 1.1920e+00 1.9550e+00 +OR5F1 ENST00000278409 5.9115e-05 1.9914e+00 8.2500e-01 1.9550e+00 +ZNF836 ENST00000322146 1.0252e-05 1.8847e+00 8.6400e-01 1.9550e+00 +ANKRD20A2 ENST00000377601 3.3379e-04 2.1740e+00 7.7600e-01 1.9560e+00 +AHSP ENST00000302312 3.2870e-04 2.1971e+00 7.7900e-01 1.9560e+00 +HMHB1 ENST00000289448 9.4526e-03 4.2247e+00 6.2900e-01 1.9560e+00 +OR56B1 ENST00000317121 1.0582e-09 1.7538e+00 1.0150e+00 1.9560e+00 +S100A2 ENST00000368708 5.8403e-05 2.0031e+00 8.2700e-01 1.9560e+00 +FABP9 ENST00000379071 6.7502e-09 1.7671e+00 9.9200e-01 1.9560e+00 +OR4X2 ENST00000302329 6.7397e-09 1.7676e+00 9.9200e-01 1.9560e+00 +GIMAP4 ENST00000255945 1.7434e-03 2.7143e+00 7.2400e-01 1.9570e+00 +DSCR8 ENST00000357704 5.4635e-05 2.0698e+00 8.4000e-01 1.9570e+00 +DUSP21 ENST00000339042 3.2350e-04 2.2216e+00 7.8200e-01 1.9570e+00 +DEFB132 ENST00000382376 1.7672e-03 2.6707e+00 7.2100e-01 1.9570e+00 +DEFB134 ENST00000526438 1.7412e-03 2.7185e+00 7.2400e-01 1.9570e+00 +C9orf92 ENST00000380683 4.1133e-08 1.8003e+00 9.7100e-01 1.9570e+00 +AL133481.1 ENST00000538322 1.7438e-03 2.7135e+00 7.2400e-01 1.9570e+00 +CCDC144NL ENST00000327925 9.0476e-14 1.7290e+00 1.1090e+00 1.9570e+00 +RP11-272B17.2 ENST00000548613 5.5715e-05 2.0498e+00 8.3600e-01 1.9570e+00 +S100A5 ENST00000368718 5.5111e-05 2.0609e+00 8.3800e-01 1.9570e+00 +OR4C15 ENST00000314644 6.5425e-09 1.7780e+00 9.9600e-01 1.9570e+00 +MYL5 ENST00000400159 8.4023e-14 1.7443e+00 1.1160e+00 1.9580e+00 +CH17-132F21.1 ENST00000603238 1.7229e-03 2.7533e+00 7.2700e-01 1.9580e+00 +APRT ENST00000378364 5.4539e-13 1.7501e+00 1.1010e+00 1.9580e+00 +RP11-351M8.1 ENST00000560560 8.9472e-06 1.9841e+00 8.8700e-01 1.9580e+00 +TNFRSF13B ENST00000261652 2.0908e-15 1.7261e+00 1.1380e+00 1.9580e+00 +OR4M2 ENST00000332663 3.9447e-08 1.8173e+00 9.7700e-01 1.9580e+00 +HIST1H3E ENST00000360408 1.4382e-06 1.9273e+00 9.2700e-01 1.9590e+00 +HIST3H2BB ENST00000369160 5.1581e-05 2.1309e+00 8.5100e-01 1.9590e+00 +OR5H15 ENST00000356526 8.6800e-06 2.0076e+00 8.9200e-01 1.9590e+00 +OR6C4 ENST00000394256 5.6330e-09 1.8322e+00 1.0140e+00 1.9590e+00 +ZNF765 ENST00000396408 8.6566e-06 2.0097e+00 8.9300e-01 1.9590e+00 +OR14J1 ENST00000377160 1.6678e-03 2.8665e+00 7.3500e-01 1.9590e+00 +DEFB106A ENST00000335186 8.5821e-03 5.9568e+00 6.5900e-01 1.9590e+00 +GNG10 ENST00000374293 5.1789e-05 2.1265e+00 8.5000e-01 1.9590e+00 +AL645922.1 ENST00000594256 1.6012e-03 3.0214e+00 7.4600e-01 1.9600e+00 +HIST1H4K ENST00000357549 1.5737e-03 3.0925e+00 7.5000e-01 1.9600e+00 +SERPINB12 ENST00000269491 2.7720e-25 1.7314e+00 1.2600e+00 1.9600e+00 +FLG ENST00000368799 2.8793e-04 2.4175e+00 8.0800e-01 1.9600e+00 +LEUTX ENST00000396841 1.5990e-03 3.0271e+00 7.4600e-01 1.9600e+00 +OR52M1 ENST00000360213 5.5596e-09 1.8371e+00 1.0160e+00 1.9600e+00 +CST1 ENST00000304749 3.3855e-08 1.8822e+00 9.9700e-01 1.9600e+00 +DEFB108B ENST00000328698 1.6040e-03 3.0145e+00 7.4500e-01 1.9600e+00 +KNCN ENST00000396314 4.7870e-05 2.2154e+00 8.6500e-01 1.9610e+00 +ANKRD65 ENST00000537107 5.0619e-09 1.8729e+00 1.0280e+00 1.9610e+00 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1.7656e+00 1.3300e+00 1.9640e+00 +C2orf83 ENST00000264387 6.7173e-06 2.2297e+00 9.3600e-01 1.9640e+00 +PLA2G1B ENST00000308366 1.0057e-10 1.8938e+00 1.0910e+00 1.9650e+00 +RP11-318A15.7 ENST00000587459 1.0263e-06 2.1554e+00 9.7900e-01 1.9650e+00 +TMEM125 ENST00000432792 1.0028e-06 2.1730e+00 9.8200e-01 1.9650e+00 +IMP3 ENST00000314852 1.5469e-07 2.1039e+00 1.0150e+00 1.9660e+00 +TPSG1 ENST00000234798 7.5883e-15 1.8503e+00 1.1770e+00 1.9660e+00 +AC005493.1 ENST00000399077 1.2042e-03 4.8133e+00 8.1900e-01 1.9660e+00 +GHRL ENST00000335542 1.3921e-11 1.9066e+00 1.1200e+00 1.9660e+00 +DEFB4A ENST00000302247 1.1637e-03 5.1765e+00 8.2800e-01 1.9670e+00 +NBPF8 ENST00000369365 1.4181e-07 2.1592e+00 1.0280e+00 1.9670e+00 +NBPF9 ENST00000375552 9.5156e-39 1.7841e+00 1.3780e+00 1.9670e+00 +RP11-467N20.5 ENST00000558241 2.2113e-08 2.0896e+00 1.0530e+00 1.9670e+00 +SMCO4 ENST00000298966 1.9629e-04 3.3814e+00 8.9100e-01 1.9670e+00 +MC1R ENST00000555147 8.1075e-11 1.9675e+00 1.1160e+00 1.9670e+00 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4.4132e-06 2.7177e+00 1.0070e+00 1.9700e+00 +NBPF20 ENST00000369202 1.9221e-22 1.8724e+00 1.2990e+00 1.9710e+00 +DEFA6 ENST00000297436 4.2537e-06 2.7705e+00 1.0130e+00 1.9710e+00 +HIST1H2BD ENST00000289316 4.2079e-06 2.7864e+00 1.0150e+00 1.9710e+00 +HIST1H2BE ENST00000356530 4.1485e-06 2.8076e+00 1.0170e+00 1.9710e+00 +HIST1H2BK ENST00000396891 4.2884e-06 2.7587e+00 1.0120e+00 1.9710e+00 +C1QTNF8 ENST00000328449 1.2959e-12 2.0392e+00 1.1870e+00 1.9720e+00 +HIST1H2BH ENST00000356350 3.8304e-06 2.9325e+00 1.0310e+00 1.9720e+00 +HIST1H3A ENST00000357647 6.2930e-07 2.5976e+00 1.0540e+00 1.9720e+00 +CTD-2228K2.5 ENST00000342584 5.9245e-07 2.6647e+00 1.0630e+00 1.9720e+00 +MIB1 ENST00000261537 3.3574e-88 1.8273e+00 1.5430e+00 1.9730e+00 +SMIM3 ENST00000526627 1.3765e-04 5.2945e+00 9.6700e-01 1.9730e+00 +HIST1H2AM ENST00000359611 5.4464e-07 2.7643e+00 1.0760e+00 1.9730e+00 +CT45A5 ENST00000463085 1.3301e-08 2.4046e+00 1.1210e+00 1.9730e+00 +KCNV2 ENST00000382082 1.1944e-26 1.8753e+00 1.3430e+00 1.9730e+00 +HIST1H2BG ENST00000244601 4.8893e-07 2.9031e+00 1.0920e+00 1.9740e+00 +PRB2 ENST00000389362 1.2951e-08 2.4237e+00 1.1240e+00 1.9740e+00 +OXER1 ENST00000378661 7.3192e-08 2.6965e+00 1.1210e+00 1.9750e+00 +HIST1H1A ENST00000244573 7.1262e-08 2.7238e+00 1.1250e+00 1.9750e+00 +SMAD6 ENST00000288840 3.6282e-20 1.9705e+00 1.3090e+00 1.9750e+00 +SLC10A1 ENST00000216540 4.7887e-16 2.0431e+00 1.2650e+00 1.9750e+00 +KRTAP5-10 ENST00000398531 1.9223e-05 4.2158e+00 1.0360e+00 1.9750e+00 +OR4C13 ENST00000555099 2.5329e-10 2.3434e+00 1.1820e+00 1.9750e+00 +NUDT19 ENST00000397061 2.9701e-15 2.0839e+00 1.2610e+00 1.9750e+00 +CST9L ENST00000376979 5.9920e-12 2.2067e+00 1.2090e+00 1.9750e+00 +GOLGA8S ENST00000562295 1.6694e-28 1.9237e+00 1.3810e+00 1.9760e+00 +NBPF16 ENST00000417839 1.5992e-05 5.1330e+00 1.0700e+00 1.9760e+00 +OR4C3 ENST00000319856 2.3900e-10 2.3758e+00 1.1890e+00 1.9760e+00 +AGR3 ENST00000310398 2.2088e-19 2.0001e+00 1.3080e+00 1.9760e+00 +GOLGA8H ENST00000566740 5.4636e-36 1.8975e+00 1.4230e+00 1.9770e+00 +PUSL1 ENST00000379031 2.6543e-20 2.0302e+00 1.3320e+00 1.9770e+00 +OR2AG1 ENST00000307401 3.1156e-11 2.3779e+00 1.2210e+00 1.9770e+00 +PRB4 ENST00000279575 1.2854e-09 2.6151e+00 1.1960e+00 1.9770e+00 +C4orf6 ENST00000195455 7.4562e-09 2.9011e+00 1.1950e+00 1.9780e+00 +PRAMEF6 ENST00000376189 2.6109e-11 2.4732e+00 1.2400e+00 1.9780e+00 +HBB ENST00000335295 1.2274e-09 2.6505e+00 1.2020e+00 1.9780e+00 +OR4C46 ENST00000328188 3.5175e-08 3.7150e+00 1.2190e+00 1.9800e+00 +DEFB135 ENST00000382208 1.5600e-06 5.8226e+00 1.1740e+00 1.9800e+00 +GOLGA8R ENST00000327271 2.5398e-12 2.6273e+00 1.2960e+00 1.9810e+00 +PSG2 ENST00000406487 1.3820e-30 2.0346e+00 1.4430e+00 1.9810e+00 +HIST1H2BF ENST00000359985 3.2385e-08 3.8799e+00 1.2300e+00 1.9810e+00 +GJB2 ENST00000382844 6.5620e-16 2.6153e+00 1.3870e+00 1.9840e+00 +TRIM48 ENST00000417545 1.0995e-27 2.2282e+00 1.4790e+00 1.9850e+00 +PSG1 ENST00000244296 1.6242e-29 2.2608e+00 1.5060e+00 1.9860e+00 +NBPF10 ENST00000342960 4.1008e-85 2.0068e+00 1.6420e+00 1.9880e+00 +LZTR1 ENST00000215739 1.0211e-92 2.2804e+00 1.7540e+00 1.9940e+00 +CD36 ENST00000435819 1.0857e-60 2.8168e+00 1.7690e+00 1.9950e+00 +SSX1 ENST00000376919 3.6857e-45 6.5019e+00 1.8260e+00 1.9960e+00 +COX7B2 ENST00000396533 NA NA NA NA +DUX4L4 ENST00000538692 NA NA NA NA +EBLN1 ENST00000422359 NA NA NA NA +EBLN2 ENST00000533473 NA NA NA NA +H1FNT ENST00000335017 NA NA NA NA +H2AFB1 ENST00000354461 NA NA NA NA +H3F3C ENST00000340398 NA NA NA NA +HUS1B ENST00000380907 NA NA NA NA +IRGM ENST00000522154 NA NA NA NA +MT1HL1 ENST00000464121 NA NA NA NA +CKS1B ENST00000600888 NA NA NA NA +RFPL4B ENST00000441065 NA NA NA NA +FAM183B ENST00000409072 NA NA NA NA +VN1R1 ENST00000321039 NA NA NA NA +VN1R2 ENST00000341702 NA NA NA NA +VN1R4 ENST00000311170 NA NA NA NA +HEPN1 ENST00000408930 NA NA NA NA +PRKACG ENST00000377276 NA NA NA NA +RP11-382J12.1 ENST00000499227 NA NA NA NA +RP11-3B7.1 ENST00000440528 NA NA NA NA +RP11-429E11.3 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NA NA NA +OR7D2 ENST00000344248 NA NA NA NA +OR7E24 ENST00000456448 NA NA NA NA +OR7G1 ENST00000541538 NA NA NA NA +OR7G2 ENST00000305456 NA NA NA NA +OR7G3 ENST00000305444 NA NA NA NA +OR8D1 ENST00000357821 NA NA NA NA +ZNF600 ENST00000338230 NA NA NA NA +ZNF645 ENST00000323684 NA NA NA NA diff --git a/exomiser-core/src/main/resources/templates/results.html b/exomiser-core/src/main/resources/templates/results.html index 21abbb0bc..9368d2ff8 100644 --- a/exomiser-core/src/main/resources/templates/results.html +++ b/exomiser-core/src/main/resources/templates/results.html @@ -165,13 +165,15 @@

-

Exomiser Score: 1.005

+

Exomiser Score: 1.00 + (p=0.1e-4) +

-

Phenotype Score: 1.005

+

Phenotype Score: 1.00

-

Variant Score: 1.005

+

Variant Score: 1.00

@@ -218,8 +220,9 @@

-

Exomiser Score: 1.005 +

Exomiser Score: + 1.005 + (p=0.1e-4)

@@ -266,17 +269,18 @@

Variant Score:

+ th:each="acmgAssignment: ${geneScore.getAcmgAssignments()}" + th:with="variantEvaluation = ${acmgAssignment.variantEvaluation()}">
MISSENSE SNV - - chr10:g.123256215T>G [0/1] - - chr10:g.123256215T>G [0/1] + 10 Mb + + rs141235720 @@ -296,27 +300,49 @@

Variant Score: 12345 -

-
- ClinVar: - +
+
+ Exomiser ACMG: + + BENIGN + LIKELY_BENIGN + LIKELY_PATHOGENIC + PATHOGENIC + UNCERTAIN_SIGNIFICANCE + NOT_AVAILABLE + + [PVS1, BP2] + + +
+
+ ClinVar: + BENIGN - BENIGN_OR_LIKELY_BENIGN - LIKELY_BENIGN - LIKELY_PATHOGENIC - PATHOGENIC_OR_LIKELY_PATHOGENIC - PATHOGENIC - UNCERTAIN_SIGNIFICANCE - + BENIGN_OR_LIKELY_BENIGN + LIKELY_BENIGN + LIKELY_PATHOGENIC + PATHOGENIC_OR_LIKELY_PATHOGENIC + PATHOGENIC + UNCERTAIN_SIGNIFICANCE + (criteria_provided,_single_submitter) @@ -389,8 +415,8 @@

Variant Score: MISSENSE SNV - - chr10:g.123256215T>G [0/1] + chr10:g.123256215T>G [0/1] + 10 Mb @@ -415,6 +441,28 @@

Variant Score:

+ + + + + + + + + + + + + + + + + + + + + +
ClinVar: Unanalysed Variants
MISSENSE - - chr10:g.123256215T>G [0/1] + chr10:g.123256215T>G [0/1] + 10 Mb hpoIds = List.of("HP:0000001"); final GenomeAnalysisService genomeAnalysisService = TestFactory.buildDefaultHg19GenomeAnalysisService(); @@ -71,7 +69,7 @@ public abstract class AnalysisRunnerTestBase { Analysis makeAnalysis(AnalysisStep... analysisSteps) { return Analysis.builder() - .steps(Arrays.asList(analysisSteps)) + .steps(List.of(analysisSteps)) .build(); } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStepTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStepTest.java index 97a91c716..e5935574a 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStepTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisStepTest.java @@ -101,4 +101,9 @@ public void testIsVariantFilterPrioritiser() { assertThat(OMIM_PRIORITY.isVariantFilter(), is(false)); } + @Test + public void testIsGenePrioritiser() { + assertThat(OMIM_PRIORITY.isGenePrioritiser(), is(true)); + } + } \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisTest.java index 569384c67..787d0eb1f 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisTest.java @@ -186,6 +186,23 @@ public void testGetMainPrioritiserTypeNoPrioritisersSet() { assertThat(instance.getMainPrioritiserType(), equalTo(PriorityType.NONE)); } + @Test + public void testGetMainPrioritiser() { + Prioritiser prioritiser = new NoneTypePrioritiser(); + Analysis instance = newBuilder() + .addStep(new OmimPriority(TestPriorityServiceFactory.stubPriorityService())) + .addStep(prioritiser) + .build(); + assertThat(instance.getMainPrioritiser(), equalTo(prioritiser)); + } + + @Test + public void testGetMainPrioritiserNoPrioritisersSet() { + Analysis instance = newBuilder() + .build(); + assertThat(instance.getMainPrioritiser(), equalTo(null)); + } + @Test public void testGetAnalysisStepsReturnsListOfStepsAdded() { List steps = getAnalysisSteps(); diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/CombinedScorePvalueCalculatorTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/CombinedScorePvalueCalculatorTest.java new file mode 100644 index 000000000..17a943641 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/CombinedScorePvalueCalculatorTest.java @@ -0,0 +1,58 @@ +package org.monarchinitiative.exomiser.core.analysis.util; + +import org.junit.jupiter.api.Test; +import org.monarchinitiative.exomiser.core.genome.TestFactory; +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.phenotype.PhenotypeTerm; +import org.monarchinitiative.exomiser.core.prioritisers.HiPhiveOptions; +import org.monarchinitiative.exomiser.core.prioritisers.HiPhivePriority; +import org.monarchinitiative.exomiser.core.prioritisers.Prioritiser; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; +import org.monarchinitiative.exomiser.core.prioritisers.service.TestPriorityServiceFactory; +import org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix; + +import java.util.List; +import java.util.stream.Collectors; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.*; + +public class CombinedScorePvalueCalculatorTest { + + @Test + public void testZeroValueInput() { + var instance = new CombinedScorePvalueCalculator(0, PriorityType.NONE, new double[]{}, 0); + assertThat(instance.calculatePvalueFromCombinedScore(0.5), equalTo(1.0)); + } + + @Test + public void testWithRandomScoresConstructor() { + var instance = CombinedScorePvalueCalculator.withRandomScores(10_000, 35_000, 250); + + assertThat(instance.calculatePvalueFromCombinedScore(1.0), closeTo(0.0, 0.001)); + assertThat(instance.calculatePvalueFromCombinedScore(0.5), closeTo(0.5, 0.01)); + assertThat(instance.calculatePvalueFromCombinedScore(0.0), equalTo(1.0)); + + assertThat(instance.calculatePvalueFromCombinedScore(0.012), closeTo(instance.calculatePvalueFromCombinedScore(0.012), 0.001)); + assertThat(instance.calculatePvalueFromCombinedScore(0.112), closeTo(instance.calculatePvalueFromCombinedScore(0.112), 0.001)); + assertThat(instance.calculatePvalueFromCombinedScore(0.25), closeTo(instance.calculatePvalueFromCombinedScore(0.25), 0.001)); + assertThat(instance.calculatePvalueFromCombinedScore(0.566), closeTo(instance.calculatePvalueFromCombinedScore(0.566), 0.001)); + assertThat(instance.calculatePvalueFromCombinedScore(0.756), closeTo(instance.calculatePvalueFromCombinedScore(0.756), 0.001)); + assertThat(instance.calculatePvalueFromCombinedScore(0.99), closeTo(instance.calculatePvalueFromCombinedScore(0.99), 0.001)); + } + + @Test + public void testStaticConstructor() { + Prioritiser prioritiser = new HiPhivePriority(HiPhiveOptions.defaults(), DataMatrix.empty(), TestPriorityServiceFactory.testPriorityService()); + List phenotypicFeatures = TestPriorityServiceFactory.pfeifferSyndromePhenotypes().stream().map(PhenotypeTerm::getId).collect(Collectors.toList()); + List genes = TestFactory.buildGenes(); + var instance = CombinedScorePvalueCalculator.of(20_000, prioritiser, phenotypicFeatures, genes, genes.size()); + assertThat(instance.calculatePvalueFromCombinedScore(0.89), greaterThan(0.0)); + } + + @Test + void testZeroValueCombinedScoreHasPvalueOfOne() { + var instance = CombinedScorePvalueCalculator.withRandomScores(10_000, 25_000, 200); + assertThat(instance.calculatePvalueFromCombinedScore(0), equalTo(1.0)); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraintTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraintTest.java new file mode 100644 index 000000000..fdb7df1b2 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraintTest.java @@ -0,0 +1,41 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util; + +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +class GeneConstraintTest { + + @ParameterizedTest + @CsvSource({ + "0.7635, false", + "0.76349, true", + }) + void testGeneIsLofIntolerant(double louf, boolean expected) { + GeneConstraint instance = new GeneConstraint("GENE1", "ENST000000000", 0, louf, 0, 0); + assertThat(instance.loeuf(), equalTo(louf)); + assertThat(instance.isLossOfFunctionIntolerant(), equalTo(expected)); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraintsTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraintsTest.java new file mode 100644 index 000000000..9f342806e --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/GeneConstraintsTest.java @@ -0,0 +1,34 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util; + +import org.junit.jupiter.api.Test; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +class GeneConstraintsTest { + + @Test + void geneContraint() { + assertThat(GeneConstraints.geneContraint("USP9X"), equalTo(new GeneConstraint("USP9X", "ENST00000324545", 1.0, 0.010698, 0.003, 0.051))); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020ClassifierTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020ClassifierTest.java new file mode 100644 index 000000000..e7b396a62 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020ClassifierTest.java @@ -0,0 +1,174 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +class Acgs2020ClassifierTest { + + private final Acgs2020Classifier instance = new Acgs2020Classifier(); + + private AcmgEvidence parseAcmgEvidence(String criteria) { + AcmgEvidence.Builder acmgEvidenceBuilder = AcmgEvidence.builder(); + for (String criterion : criteria.split(" ")) { + String[] criteriaModifier = criterion.split("_"); + AcmgCriterion acmgCriterion = AcmgCriterion.valueOf(criteriaModifier[0]); + if (criteriaModifier.length == 2) { + AcmgCriterion.Evidence evidence = AcmgCriterion.Evidence.parseValue(criteriaModifier[1]); + acmgEvidenceBuilder.add(acmgCriterion, evidence); + } else { +// AcmgCriterion acmgCriterion = AcmgCriterion.valueOf(criterion); + acmgEvidenceBuilder.add(acmgCriterion); + } + } + return acmgEvidenceBuilder.build(); + } + + @ParameterizedTest + @CsvSource({ + "PVS1 PP5_VeryStrong", +// (a) 1 Very strong (PVS1) AND +// ≥1 Strong (PS1–PS4) OR + "PVS1 PS1", + "PVS1 PS2", + "PVS1 PS3", + "PVS1 PS4", + "PVS1 PS1 PS2", + "PVS1 PS1 PS2 PS3", +// ≥1 moderate (PM1–PM6) OR + "PVS1 PM1", + "PVS1 PM1 PM2", + "PVS1 PM1 PM2 PM3", + "PVS1 PM1 PM2 PM3 PM4", + "PVS1 PM1 PM2 PP1", +// ≥2 supporting (PP1–PP5) + "PVS1 PP1 PP2", + "PVS1 PP1 PP2 PP3", +// (b) ≥3 Strong (PS1-PS4) + "PS1 PS2 PS3", +// (c) 2 Strong (PS1-PS4) AND +// ≥1 moderate (PM1–PM6) OR + "PS1 PS2 PM1", +// ≥2 supporting (PP1–PP5) + "PS1 PS2 PP1 PP2", +// (d) 1 Strong (PS1-PS4) AND +// ≥3 moderate (PM1–PM6) OR + "PS1 PM1 PM2 PM3", +// ≥2 moderate (PM1–PM6) AND ≥2 supporting (PP1–PP5) OR + "PS1 PM1 PM2 PP1 PP2", +// ≥1 moderate (PM1–PM6) AND ≥4 supporting (PP1–PP5) + "PS1 PM1 PP1 PP2 PP3 PP4", + }) + void classifiesPathogenic(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.PATHOGENIC)); + } + + @ParameterizedTest + @CsvSource({ +// (c) >=2 Strong + "PS1 PS2", +// (b) 1 Strong (PS1–PS4) AND +// 1–2 moderate (PM1–PM6) OR + "PS1 PM1 PM2", +// ≥2 supporting (PP1–PP5) + "PS1 PP1 PP2", + "PS1 PP1 PP2 PP3", +// (c) ≥3 Moderate (PM1–PM6) OR + "PM1 PM2 PM3", +// 2 Moderate (PM1–PM6) AND ≥2 supporting (PP1–PP5) OR + "PM1 PM2 PP1 PP2", + "PM1 PM2 PP1 PP2 PP3", + "PM1 PM2 PP1 PP2 PP3 PP4", +// 1 Moderate (PM1–PM6) AND ≥4 supporting (PP1–PP5) + "PM1 PP1 PP2 PP3 PP4", + "PM1 PP1 PP2 PP3 PP4 PP5", + "PM1 PP1 PP2 PP3", // VUS_Hot - we can only assign 3 out of + }) + void classifiesLikelyPathogenic(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.LIKELY_PATHOGENIC)); + } + + @ParameterizedTest + @CsvSource({ +// (i) 1 Stand-alone (BA1) + "BA1", + "BA1 BS1 BP1", +// OR (ii) ≥2 Strong (BS1–BS4) + "BS1 BS2", + "BS1 BS2 BS3" + }) + void classifiesBenign(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.BENIGN)); + } + + @ParameterizedTest + @CsvSource({ +// (i) 1 Strong (BS1–BS4) and 1 supporting (BP1–BP7) + "BS1 BP1", +// OR (ii) ≥2 Supporting (BP1–BP7) + "BP1 BP2", + "BP1 BP2 BP3", + }) + void classifiesLikelyBenign(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.LIKELY_BENIGN)); + } + + @ParameterizedTest + @CsvSource({ +// (i) Other criteria shown above are not met + "PVS1 PP1", + "PS1 PP1", // VUS_Hot + "PM1 PM2 PP1", // VUS_Hot +// "PM1 PP1 PP2 PP3", // VUS_Hot - classified as LP + "PS1", // VUS_Warm + "PM1 PM2", // VUS_Warm + "PM1 PP1 PP2", // VUS_Warm + "PP1 PP2 PP3 PP4", // VUS_Warm + "PM1 PP2", // VUS_Tepid + "PP1 PP2 PP3", // VUS_Warm + "PM1", // VUS_Cool + "PP1 PP2", // VUS_Warm + "PP1", // VUS_Cold +// OR (ii) the criteria for benign and pathogenic are contradictory + "PS1 BP1", + "BS1 BP1 PVS1 PS1", + "BA1 PVS1 PM1", + "BP1 BP2 BP3 PM1 PP1 PP2 PP3 PP4", + }) + void classifiesUncertain(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.UNCERTAIN_SIGNIFICANCE)); + } + + @Test + void noEvidenceClassifiesUnknown() { + assertThat(instance.classify(AcmgEvidence.empty()), equalTo(AcmgClassification.UNCERTAIN_SIGNIFICANCE)); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015ClassifierTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015ClassifierTest.java new file mode 100644 index 000000000..64629e1d3 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015ClassifierTest.java @@ -0,0 +1,147 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +class Acmg2015ClassifierTest { + + private final Acmg2015Classifier instance = new Acmg2015Classifier(); + + private AcmgEvidence parseAcmgEvidence(String criteria) { + AcmgEvidence.Builder acmgEvidenceBuilder = AcmgEvidence.builder(); + for (String criterion : criteria.split(" ")) { + AcmgCriterion acmgCriterion = AcmgCriterion.valueOf(criterion); + acmgEvidenceBuilder.add(acmgCriterion); + } + return acmgEvidenceBuilder.build(); + } + + @ParameterizedTest + @CsvSource({ +// (i) 1 Very strong (PVS1) +// AND (a) ≥1 Strong (PS1–PS4) + "PVS1 PS1", + "PVS1 PS2", + "PVS1 PS3", + "PVS1 PS4", + "PVS1 PS1 PS2", + "PVS1 PS1 PS2 PS3", + "PVS1 PS1 PM1 PP1", +// OR (b) ≥2 Moderate (PM1–PM6) + "PVS1 PM1 PM2", + "PVS1 PM1 PM2 PM3", + "PVS1 PM1 PM2 PM3 PM4", + "PVS1 PM1 PM2 PP1", +// OR (c) 1 Moderate (PM1–PM6) and 1 supporting (PP1–PP5) + "PVS1 PM1 PP1", + "PVS1 PM1 PP1 PP2", +// OR (d) ≥2 Supporting (PP1–PP5) + "PVS1 PP1 PP2", + "PVS1 PP1 PP2 PP3", + }) + void classifiesPathogenic(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.PATHOGENIC)); + } + + @ParameterizedTest + @CsvSource({ +// (i) 1 Very strong (PVS1) AND 1 moderate (PM1–PM6) + "PVS1 PM1", +// OR (ii) 1 Strong (PS1–PS4) AND 1–2 moderate (PM1–PM6) + "PS1 PM1 PM2", +// OR (iii) 1 Strong (PS1–PS4) AND ≥2 supporting (PP1–PP5) + "PS1 PP1 PP2", + "PS1 PP1 PP2 PP3", +// OR (iv) ≥3 Moderate (PM1–PM6) + "PM1 PM2 PM3", +// OR (v) 2 Moderate (PM1–PM6) AND ≥2 supporting (PP1–PP5) + "PM1 PM2 PP1 PP2", + "PM1 PM2 PP1 PP2 PP3", + "PM1 PM2 PP1 PP2 PP3 PP4", +// OR (vi) 1 Moderate (PM1–PM6) AND ≥4 supporting (PP1–PP5) + "PM1 PP1 PP2 PP3 PP4", + "PM1 PP1 PP2 PP3 PP4 PP5", + }) + void classifiesLikelyPathogenic(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.LIKELY_PATHOGENIC)); + } + + @ParameterizedTest + @CsvSource({ +// (i) 1 Stand-alone (BA1) + "BA1", + "BA1 BS1 BP1", +// OR (ii) ≥2 Strong (BS1–BS4) + "BS1 BS2", + "BS1 BS2 BS3" + }) + void classifiesBenign(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.BENIGN)); + } + + @ParameterizedTest + @CsvSource({ +// (i) 1 Strong (BS1–BS4) and 1 supporting (BP1–BP7) + "BS1 BP1", +// OR (ii) ≥2 Supporting (BP1–BP7) + "BP1 BP2", + "BP1 BP2 BP3", + }) + void classifiesLikelyBenign(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.LIKELY_BENIGN)); + } + + @ParameterizedTest + @CsvSource({ +// (i) Other criteria shown above are not met + "PVS1 PP1", + "PS1 PP1", // VUS_Hot + "PM1 PM2 PP1", // VUS_Hot +// "PM1 PP1 PP2 PP3", // VUS_Hot - classified as LP + "PS1", // VUS_Warm + "PM1 PM2", // VUS_Warm + "PM1 PP1 PP2", // VUS_Warm + "PP1 PP2 PP3 PP4", // VUS_Warm + "PM1 PP2", // VUS_Tepid + "PP1 PP2 PP3", // VUS_Warm + "PM1", // VUS_Cool + "PP1 PP2", // VUS_Warm + "PP1", // VUS_Cold +// OR (ii) the criteria for benign and pathogenic are contradictory + "BS1 BP1 PVS1 PS1", + "BA1 PVS1 PM1", + "BP1 BP2 BP3 PM1 PP1 PP2 PP3 PP4", + }) + void classifiesUncertain(String criteria) { + AcmgEvidence acmgEvidence = parseAcmgEvidence(criteria); + assertThat(instance.classify(acmgEvidence), equalTo(AcmgClassification.UNCERTAIN_SIGNIFICANCE)); + } + +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssignerTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssignerTest.java new file mode 100644 index 000000000..0bce7474e --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssignerTest.java @@ -0,0 +1,634 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import de.charite.compbio.jannovar.annotation.VariantEffect; +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.junit.jupiter.api.Nested; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; +import org.monarchinitiative.exomiser.core.genome.TestFactory; +import org.monarchinitiative.exomiser.core.model.*; +import org.monarchinitiative.exomiser.core.model.Pedigree.Individual.Status; +import org.monarchinitiative.exomiser.core.model.frequency.Frequency; +import org.monarchinitiative.exomiser.core.model.frequency.FrequencyData; +import org.monarchinitiative.exomiser.core.model.frequency.FrequencySource; +import org.monarchinitiative.exomiser.core.model.pathogenicity.ClinVarData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityScore; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; +import org.monarchinitiative.exomiser.core.prioritisers.model.InheritanceMode; + +import java.util.List; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.*; +import static org.monarchinitiative.exomiser.core.model.Pedigree.Individual; +import static org.monarchinitiative.exomiser.core.model.Pedigree.Individual.Sex.FEMALE; +import static org.monarchinitiative.exomiser.core.model.Pedigree.Individual.Sex.MALE; +import static org.monarchinitiative.exomiser.core.model.Pedigree.justProband; + +class Acmg2015EvidenceAssignerTest { + + @Test + void throwsExceptionWithMismatchedIds() { + assertThrows(IllegalArgumentException.class, () -> new Acmg2015EvidenceAssigner("Zaphod", justProband("Ford", MALE))); + } + + @Test + void testAssignsPVS1() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + // requires variant to be on a transcript predicted to undergo NMD in a LoF-intolerant gene for full PVS1 + TranscriptAnnotation transcriptAnnotation = TranscriptAnnotation.builder() + .variantEffect(VariantEffect.START_LOST) + .rankType(TranscriptAnnotation.RankType.EXON) + .rank(1) + .rankTotal(5) + .build(); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .variantEffect(VariantEffect.START_LOST) + .annotations(List.of(transcriptAnnotation)) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PVS1).build())); + } + + @ParameterizedTest + @CsvSource({ + "MALE, AUTOSOMAL_DOMINANT, AUTOSOMAL_DOMINANT, true", + "FEMALE, AUTOSOMAL_DOMINANT, AUTOSOMAL_DOMINANT, true", + "UNKNOWN, AUTOSOMAL_DOMINANT, AUTOSOMAL_DOMINANT, true", + + "MALE, AUTOSOMAL_RECESSIVE, AUTOSOMAL_RECESSIVE, true", + "FEMALE, AUTOSOMAL_RECESSIVE, AUTOSOMAL_RECESSIVE, true", + "UNKNOWN, AUTOSOMAL_RECESSIVE, AUTOSOMAL_RECESSIVE, true", + + "MALE, AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, false", + "FEMALE, AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, false", + "UNKNOWN, AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, false", + + "MALE, X_RECESSIVE, X_RECESSIVE, true", + "FEMALE, X_RECESSIVE, X_RECESSIVE, true", + "UNKNOWN, X_RECESSIVE, X_RECESSIVE, false", + + "MALE, X_DOMINANT, X_DOMINANT, true", + "FEMALE, X_DOMINANT, X_DOMINANT, true", + "UNKNOWN, X_DOMINANT, X_DOMINANT, true", + }) + void testAssignsPVS1(Pedigree.Individual.Sex probandSex, InheritanceMode diseaseInheritanceMode, ModeOfInheritance modeOfInheritance, boolean expectPvs1) { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", probandSex)); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + TranscriptAnnotation transcriptAnnotation = TranscriptAnnotation.builder() + .variantEffect(VariantEffect.START_LOST) + .rankType(TranscriptAnnotation.RankType.EXON) + .rank(1) + .rankTotal(5) + .build(); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .variantEffect(VariantEffect.START_LOST) + .annotations(List.of(transcriptAnnotation)) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(diseaseInheritanceMode).diseaseType(Disease.DiseaseType.DISEASE).build(); + List knownDiseases = diseaseInheritanceMode.isCompatibleWith(modeOfInheritance) ? List.of(cowdenSyndrome) : List.of(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, modeOfInheritance, List.of(variantEvaluation), knownDiseases, List.of()); + AcmgEvidence expected = expectPvs1 ? AcmgEvidence.builder().add(PVS1).build() : AcmgEvidence.empty(); + assertThat(acmgEvidence, equalTo(expected)); + } + + @Test + void testAssignsPS2() { + Individual proband = Individual.builder().id("proband").motherId("mother").fatherId("father").sex(MALE).status(Status.AFFECTED).build(); + Individual mother = Individual.builder().id("mother").sex(FEMALE).status(Status.UNAFFECTED).build(); + Individual father = Individual.builder().id("father").sex(MALE).status(Status.UNAFFECTED).build(); + Pedigree pedigree = Pedigree.of(proband, mother, father); + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", pedigree); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.het()), + SampleData.of("mother", SampleGenotype.homRef()), + SampleData.of("father", SampleGenotype.homRef()) + )) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PS2).build())); + } + + @Test + void testAssignsPS2_hasFamilyHistory() { + Individual proband = Individual.builder().id("proband").motherId("mother").fatherId("father").sex(MALE).status(Status.AFFECTED).build(); + Individual mother = Individual.builder().id("mother").sex(FEMALE).status(Status.UNAFFECTED).build(); + Individual father = Individual.builder().id("father").sex(MALE).status(Status.UNAFFECTED).build(); + Pedigree pedigree = Pedigree.of(proband, mother, father); + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", pedigree); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.het()), + SampleData.of("mother", SampleGenotype.het()), // Unaffected mother has same genotype - can't be PS2 + SampleData.of("father", SampleGenotype.homRef()) + )) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.empty())); + } + + @Test + void testAssignsPM2() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", Pedigree.empty()); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 12345, "A", "G") + // n.b. missing frequency data - will trigger PM2 + .frequencyData(FrequencyData.of()) + .build(); + // Requires variant to be in gene associated with a disorder in order that any ACMG criteria can be applied + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_RECESSIVE).diseaseType(Disease.DiseaseType.DISEASE).build(); + + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PM2).build())); + } + + @Test + void testVariantMustBeInGeneWithKnownDiseaseAssociationForAcmgCriteriaToBeAssigned() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", Pedigree.empty()); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(1, 12345, "A", "G") + // n.b. missing frequency data - should trigger PM2 + .frequencyData(FrequencyData.of()) + .build(); + // Requires variant to be in gene associated with a disorder in order that any ACMG criteria can be applied + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(), List.of()); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.empty())); + } + + @Test + void testAssignsPM3() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", null); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89000000, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.parseGenotype("0|1")) + )) + .build(); + + VariantEvaluation pathogenic = TestFactory.variantBuilder(10, 89624227, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. start loss variant - will trigger PVS1 + .variantEffect(VariantEffect.START_LOST) + .pathogenicityData(PathogenicityData.of(ClinVarData.builder().primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).reviewStatus("reviewed by expert panel").build())) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.parseGenotype("1|0")) + )) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_RECESSIVE).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_RECESSIVE, List.of(variantEvaluation, pathogenic), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + AcmgEvidence expected = AcmgEvidence.builder().add(AcmgCriterion.PM3).build(); + assertThat(acmgEvidence, equalTo(expected)); + } + + @Test + void testAssignsBP2_InCisWithPathAR() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", Pedigree.empty()); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89000000, "A", "G") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.parseGenotype("0|1")) + )) + .build(); + + VariantEvaluation pathogenic = TestFactory.variantBuilder(10, 89624227, "A", "G") + .pathogenicityData(PathogenicityData.of(ClinVarData.builder().primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).reviewStatus("reviewed by expert panel").build())) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.parseGenotype("0|1")) + )) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_RECESSIVE).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_RECESSIVE, List.of(variantEvaluation, pathogenic), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + AcmgEvidence expected = AcmgEvidence.builder().add(AcmgCriterion.BP2).build(); + assertThat(acmgEvidence, equalTo(expected)); + } + + @Test + void testAssignsBP2_InTransWithPathAD() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", Pedigree.empty()); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89000000, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.parseGenotype("0|1")) + )) + .build(); + + VariantEvaluation pathogenic = TestFactory.variantBuilder(10, 89624227, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. start loss variant - will trigger PVS1 + .variantEffect(VariantEffect.START_LOST) + .pathogenicityData(PathogenicityData.of(ClinVarData.builder().primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).reviewStatus("reviewed by expert panel").build())) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.parseGenotype("1|0")) + )) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation, pathogenic), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + AcmgEvidence expected = AcmgEvidence.builder().add(AcmgCriterion.BP2).build(); + assertThat(acmgEvidence, equalTo(expected)); + } + + @Test + void testAssignsPM4() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("MUC6") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .variantEffect(VariantEffect.STOP_LOST) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PM4).build())); + } + + @Test + void testAssignsPM4_NotAssignedPM4WhenPVS1Present() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + + TranscriptAnnotation startLostAnnotation = TranscriptAnnotation.builder() + .geneSymbol("PTEN") + .accession("ENST00000371953.7") + .variantEffect(VariantEffect.START_LOST) + .rankType(TranscriptAnnotation.RankType.EXON) + .rank(1) + .rankTotal(9) + .build(); + + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + // haploinsufficient gene + .geneSymbol("PTEN") + .annotations(List.of(startLostAnnotation)) // prevent PM4 as PVS1 already triggered + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .variantEffect(VariantEffect.STOP_LOST) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PVS1).build())); + } + + @Nested + class ComputationalEvidence { + + @Test + void testAssignsPP3() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of( + PathogenicityScore.of(PathogenicitySource.REVEL, 1.0f), + PathogenicityScore.of(PathogenicitySource.MVP, 1.0f) + )) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PP3, Evidence.STRONG).build())); + } + + @ParameterizedTest + @CsvSource ({ + "MVP, 1.0f, , ", + "REVEL, 1.0f, PP3, STRONG" + }) + void testAssignsPP3_singleScoreIsInsufficientUnlessItsRevel(PathogenicitySource pathogenicitySource, float pathogenicityScore, AcmgCriterion acmgCriterion, Evidence evidence) { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of(PathogenicityScore.of(pathogenicitySource, pathogenicityScore))) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + + AcmgEvidence expected = acmgCriterion == null ? AcmgEvidence.empty() : AcmgEvidence.builder().add(acmgCriterion, evidence).build(); + assertThat(acmgEvidence, equalTo(expected)); + } + + @Test + void testAssignsPP3_majorityMustBePath() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of( + PathogenicityScore.of(PathogenicitySource.POLYPHEN, 1.0f), + PathogenicityScore.of(PathogenicitySource.MVP, 1.0f), + PathogenicityScore.of(PathogenicitySource.M_CAP, 0.0f) + )) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PP3).build())); + } + + @Test + void testPP3andPM4_majorityMustBePathOrBenign() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of( + PathogenicityScore.of(PathogenicitySource.POLYPHEN, 1.0f), + PathogenicityScore.of(PathogenicitySource.MVP, 1.0f), + PathogenicityScore.of(PathogenicitySource.M_CAP, 0.0f), + PathogenicityScore.of(PathogenicitySource.MUTATION_TASTER, 0.0f) + )) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.empty())); + } + + @Test + void testAssignsBP4() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of( + PathogenicityScore.of(PathogenicitySource.POLYPHEN, 0.0f), + PathogenicityScore.of(PathogenicitySource.MVP, 0.0f) + )) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.BP4).build())); + } + + @ParameterizedTest + @CsvSource ({ + "CADD, 0.0f, , ", + "REVEL, 0.0f, BP4, VERY_STRONG" + }) + void testAssignsBP4_singleScoreIsInsufficientIfNotRevel(PathogenicitySource pathogenicitySource, float pathogenicityScore, AcmgCriterion acmgCriterion, Evidence evidence) { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of(PathogenicityScore.of(pathogenicitySource, pathogenicityScore))) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + + AcmgEvidence expected = acmgCriterion == null ? AcmgEvidence.empty() : AcmgEvidence.builder().add(acmgCriterion, evidence).build(); + assertThat(acmgEvidence, equalTo(expected)); + } + + void testAssignsBP4_majorityMustBeBenign() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of( + PathogenicityScore.of(PathogenicitySource.POLYPHEN, 0.0f), + PathogenicityScore.of(PathogenicitySource.MVP, 0.0f), + PathogenicityScore.of(PathogenicitySource.M_CAP, 1.0f) + )) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.BP4).build())); + } + + @ParameterizedTest + @CsvSource ({ + "0.932, PP3, STRONG", + "0.773, PP3, MODERATE", + "0.644f, PP3, SUPPORTING", + + "0.290f, BP4, SUPPORTING", + "0.183f, BP4, MODERATE", + "0.016f, BP4, STRONG", + "0.003f, BP4, VERY_STRONG", + }) + public void testRevelOverridesAllOtherScores(float revelScore, AcmgCriterion acmgCriterion, Evidence evidence) { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .pathogenicityData(PathogenicityData.of( + // REVEL, if present, should be used as the sole means of classifying the PP3/BP4 + PathogenicityScore.of(PathogenicitySource.REVEL, revelScore), + PathogenicityScore.of(PathogenicitySource.MVP, 0.0f), + PathogenicityScore.of(PathogenicitySource.POLYPHEN, 1.0f), + PathogenicityScore.of(PathogenicitySource.SIFT, 0.0f), + PathogenicityScore.of(PathogenicitySource.M_CAP, 1.0f) + )) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(acmgCriterion, evidence).build())); + } + } + + // PP4 + @Test + void testAssignsPP4() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) // prevent PM2 assignment + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // High phenotype match triggers - PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.6, cowdenSyndrome, List.of())); + + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), compatibleDiseaseMatches); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.PP4).build())); + } + + @Nested + class ClinicalEvidence { + + @ParameterizedTest + @CsvSource( + delimiter = ';', + value = { + "criteria provided, single submitter; SUPPORTING", + "criteria provided, multiple submitters, no conflicts; STRONG", + "reviewed by expert panel; STRONG", + "practice guideline; STRONG", + }) + void testAssignsPP5(String reviewStatus, AcmgCriterion.Evidence evidence) { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", Pedigree.empty()); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89000000, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .pathogenicityData(PathogenicityData.of(ClinVarData.builder().primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).reviewStatus(reviewStatus).build())) + .build(); + + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(PP5, evidence).build())); + } + + @ParameterizedTest + @CsvSource( + delimiter = ';', + value = { + "criteria provided, single submitter; SUPPORTING", + "criteria provided, multiple submitters, no conflicts; STRONG", + "reviewed by expert panel; STRONG", + "practice guideline; STRONG", + }) + void testAssignsBP6(String reviewStatus, AcmgCriterion.Evidence evidence) { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", Pedigree.empty()); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/127667/ + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89622915, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AFRICAN_INC_AFRICAN_AMERICAN, 1.42f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .pathogenicityData(PathogenicityData.of(ClinVarData.builder().primaryInterpretation(ClinVarData.ClinSig.BENIGN).reviewStatus(reviewStatus).build())) + .build(); + + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(BP6, evidence).build())); + } + } + + @Test + void testAssignsBA1() { + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + // high allele freq - triggers BA1 assignment + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 5.0f))) + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), List.of()); + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(AcmgCriterion.BA1).build())); + } + + @Test + void testAssignsBS4() { + Individual proband = Individual.builder().id("proband").motherId("mother").fatherId("father").sex(MALE).status(Status.AFFECTED).build(); + Individual mother = Individual.builder().id("mother").sex(FEMALE).status(Status.AFFECTED).build(); + Individual father = Individual.builder().id("father").sex(MALE).status(Status.UNAFFECTED).build(); + Pedigree pedigree = Pedigree.of(proband, mother, father); + Acmg2015EvidenceAssigner instance = new Acmg2015EvidenceAssigner("proband", pedigree); + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + // n.b. PTEN is a haploinsufficient gene + .geneSymbol("PTEN") + // n.b. has frequency data - will not trigger PM2 + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AMERICAN, 0.1f))) + // n.b. missense variant - will not trigger PVS1 + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .sampleGenotypes(SampleGenotypes.of( + SampleData.of("proband", SampleGenotype.het()), + SampleData.of("mother", SampleGenotype.homRef()), // Affected mother has different genotype - can't be PS2 + SampleData.of("father", SampleGenotype.homRef()) + )) + .build(); + Disease cowdenSyndrome = Disease.builder().diseaseId("OMIM:158350").diseaseName("COWDEN SYNDROME 1; CWS1").inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT).diseaseType(Disease.DiseaseType.DISEASE).build(); + // n.b. low phenotype score - will not trigger PP4 + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + AcmgEvidence acmgEvidence = instance.assignVariantAcmgEvidence(variantEvaluation, ModeOfInheritance.AUTOSOMAL_DOMINANT, List.of(variantEvaluation), List.of(cowdenSyndrome), compatibleDiseaseMatches); + + assertThat(acmgEvidence, equalTo(AcmgEvidence.builder().add(BS4).build())); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentCalculatorTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentCalculatorTest.java new file mode 100644 index 000000000..7b1c7b928 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentCalculatorTest.java @@ -0,0 +1,179 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import de.charite.compbio.jannovar.annotation.VariantEffect; +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.junit.jupiter.api.Test; +import org.monarchinitiative.exomiser.core.filters.FilterResult; +import org.monarchinitiative.exomiser.core.filters.FilterType; +import org.monarchinitiative.exomiser.core.genome.TestFactory; +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.model.frequency.Frequency; +import org.monarchinitiative.exomiser.core.model.frequency.FrequencyData; +import org.monarchinitiative.exomiser.core.model.frequency.FrequencySource; +import org.monarchinitiative.exomiser.core.model.pathogenicity.ClinVarData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityData; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityScore; +import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource; +import org.monarchinitiative.exomiser.core.phenotype.ModelPhenotypeMatch; +import org.monarchinitiative.exomiser.core.prioritisers.OmimPriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; +import org.monarchinitiative.exomiser.core.prioritisers.model.InheritanceMode; + +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.monarchinitiative.exomiser.core.model.Pedigree.Individual.Sex.MALE; +import static org.monarchinitiative.exomiser.core.model.Pedigree.justProband; + +/** + * This is not a unit test - it is a full integration test of the ACMG assignment process + */ +class AcmgAssignmentCalculatorTest { + + @Test + void calculatePathAcmgAssignments() { + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + TranscriptAnnotation startLostAnnotation = TranscriptAnnotation.builder() + .geneSymbol("PTEN") + .accession("ENST00000371953.7") + .variantEffect(VariantEffect.START_LOST) + .rankType(TranscriptAnnotation.RankType.EXON) + .rank(1) + .rankTotal(9) + .build(); + + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .variantEffect(VariantEffect.START_LOST) + .annotations(List.of(startLostAnnotation)) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .pathogenicityData(PathogenicityData.of(ClinVarData.builder() + .primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).reviewStatus("reviewed by expert panel").build(), + PathogenicityScore.of(PathogenicitySource.REVEL, 1.0f), PathogenicityScore.of(PathogenicitySource.MVP, 1.0f))) + .filterResults(FilterResult.pass(FilterType.FREQUENCY_FILTER), FilterResult.pass(FilterType.PATHOGENICITY_FILTER)) + .build(); + + Disease cowdenSyndrome = Disease.builder() + .diseaseId("OMIM:158350") + .diseaseName("COWDEN SYNDROME 1; CWS1") + .inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT) + .diseaseType(Disease.DiseaseType.DISEASE) + .build(); + OmimPriorityResult omimPriorityResult = new OmimPriorityResult(12345, "PTEN", 1.0, List.of(cowdenSyndrome), Map.of()); + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(1.0, cowdenSyndrome, List.of())); + + Gene gene = new Gene("PTEN", 12345); + gene.addVariant(variantEvaluation); + gene.addPriorityResult(omimPriorityResult); + + AcmgEvidence acmgEvidence = AcmgEvidence.builder() + .add(AcmgCriterion.PVS1) + .add(AcmgCriterion.PM2) + .add(AcmgCriterion.PP3, AcmgCriterion.Evidence.STRONG) + .add(AcmgCriterion.PP4) + .add(AcmgCriterion.PP5, AcmgCriterion.Evidence.STRONG) + .build(); + AcmgAssignment acmgAssignment = AcmgAssignment.of(variantEvaluation, gene.getGeneIdentifier(), ModeOfInheritance.AUTOSOMAL_DOMINANT, cowdenSyndrome, acmgEvidence, AcmgClassification.PATHOGENIC); + + AcmgEvidenceAssigner acmgEvidenceAssigner = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + AcmgAssignmentCalculator instance = new AcmgAssignmentCalculator(acmgEvidenceAssigner, new Acgs2020Classifier()); + List acmgAssignments = instance.calculateAcmgAssignments(ModeOfInheritance.AUTOSOMAL_DOMINANT, gene, List.of(variantEvaluation), compatibleDiseaseMatches); + assertThat(acmgAssignments, equalTo(List.of(acmgAssignment))); + } + + @Test + void calculateVusAcmgAssignments() { + // https://www.ncbi.nlm.nih.gov/clinvar/variation/484600/ 3* PATHOGENIC variant - reviewed by expert panel + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89624227, "A", "G") + .geneSymbol("PTEN") + .variantEffect(VariantEffect.MISSENSE_VARIANT) + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AFRICAN_INC_AFRICAN_AMERICAN, 0.5f))) + .pathogenicityData(PathogenicityData.of(PathogenicityScore.of(PathogenicitySource.REVEL, 0.5f))) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .filterResults(FilterResult.pass(FilterType.FREQUENCY_FILTER), FilterResult.pass(FilterType.PATHOGENICITY_FILTER)) + .build(); + + Disease cowdenSyndrome = Disease.builder() + .diseaseId("OMIM:158350") + .diseaseName("COWDEN SYNDROME 1; CWS1") + .inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT) + .diseaseType(Disease.DiseaseType.DISEASE) + .build(); + OmimPriorityResult omimPriorityResult = new OmimPriorityResult(12345, "PTEN", 1.0, List.of(cowdenSyndrome), Map.of()); + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + + Gene gene = new Gene("PTEN", 12345); + gene.addVariant(variantEvaluation); + gene.addPriorityResult(omimPriorityResult); + + AcmgEvidence acmgEvidence = AcmgEvidence.empty(); + AcmgAssignment acmgAssignment = AcmgAssignment.of(variantEvaluation, gene.getGeneIdentifier(), ModeOfInheritance.AUTOSOMAL_DOMINANT, cowdenSyndrome, acmgEvidence, AcmgClassification.UNCERTAIN_SIGNIFICANCE); + + AcmgEvidenceAssigner acmgEvidenceAssigner = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + AcmgAssignmentCalculator instance = new AcmgAssignmentCalculator(acmgEvidenceAssigner, new Acgs2020Classifier()); + List acmgAssignments = instance.calculateAcmgAssignments(ModeOfInheritance.AUTOSOMAL_DOMINANT, gene, List.of(variantEvaluation), compatibleDiseaseMatches); + assertThat(acmgAssignments, equalTo(List.of(acmgAssignment))); + } + + @Test + void calculateBenignAcmgAssignments() { + // https://www.ncbi.nlm.nih.gov/clinvar/variation/127667/ - BA1: Allele frequency of 0.0142 (1.42%, 23/1618 alleles) in the African subpopulation of the gnomAD cohort. + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(10, 89622915, "A", "G") + .geneSymbol("PTEN") + .variantEffect(VariantEffect.SYNONYMOUS_VARIANT) + .frequencyData(FrequencyData.of(Frequency.of(FrequencySource.EXAC_AFRICAN_INC_AFRICAN_AMERICAN, 50.0f))) + .pathogenicityData(PathogenicityData.of(PathogenicityScore.of(PathogenicitySource.REVEL, 0.0f), PathogenicityScore.of(PathogenicitySource.MVP, 0.0f))) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .filterResults(FilterResult.fail(FilterType.FREQUENCY_FILTER), FilterResult.pass(FilterType.PATHOGENICITY_FILTER)) + .build(); + + Disease cowdenSyndrome = Disease.builder() + .diseaseId("OMIM:158350") + .diseaseName("COWDEN SYNDROME 1; CWS1") + .inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT) + .diseaseType(Disease.DiseaseType.DISEASE) + .build(); + OmimPriorityResult omimPriorityResult = new OmimPriorityResult(12345, "PTEN", 1.0, List.of(cowdenSyndrome), Map.of()); + List> compatibleDiseaseMatches = List.of(ModelPhenotypeMatch.of(0.5, cowdenSyndrome, List.of())); + + Gene gene = new Gene("PTEN", 12345); + gene.addVariant(variantEvaluation); + gene.addPriorityResult(omimPriorityResult); + + AcmgEvidence acmgEvidence = AcmgEvidence.builder() + .add(AcmgCriterion.BA1) + .add(AcmgCriterion.BP4, AcmgCriterion.Evidence.VERY_STRONG) + .build(); + AcmgAssignment acmgAssignment = AcmgAssignment.of(variantEvaluation, gene.getGeneIdentifier(), ModeOfInheritance.AUTOSOMAL_DOMINANT, cowdenSyndrome, acmgEvidence, AcmgClassification.BENIGN); + + AcmgEvidenceAssigner acmgEvidenceAssigner = new Acmg2015EvidenceAssigner("proband", justProband("proband", MALE)); + AcmgAssignmentCalculator instance = new AcmgAssignmentCalculator(acmgEvidenceAssigner, new Acgs2020Classifier()); + List acmgAssignments = instance.calculateAcmgAssignments(ModeOfInheritance.AUTOSOMAL_DOMINANT, gene, List.of(variantEvaluation), compatibleDiseaseMatches); + assertThat(acmgAssignments, equalTo(List.of(acmgAssignment))); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentTest.java new file mode 100644 index 000000000..fdda91bc0 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgAssignmentTest.java @@ -0,0 +1,49 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import de.charite.compbio.jannovar.annotation.VariantEffect; +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.junit.jupiter.api.Test; +import org.monarchinitiative.exomiser.core.genome.TestFactory; +import org.monarchinitiative.exomiser.core.model.GeneIdentifier; +import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; + +import java.util.List; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +class AcmgAssignmentTest { + + @Test + void testAutosomalDominant() { + TranscriptAnnotation transcriptAnnotation = TranscriptAnnotation.builder().accession("ENST12345678").geneSymbol("GENE1").hgvsProtein("p.1234A>-").hgvsCdna("c.2346A>T").variantEffect(VariantEffect.STOP_GAINED).build(); + VariantEvaluation variantEvaluation = TestFactory.variantBuilder(1, 12335, "A", "T").annotations(List.of(transcriptAnnotation)).build(); + GeneIdentifier geneIdentifier = GeneIdentifier.builder().geneId("HGNC:1").geneSymbol("GENE1").build(); + Disease disease = Disease.builder().diseaseId("OMIM:12345").diseaseName("Disease").build(); + AcmgEvidence acmgEvidence = AcmgEvidence.builder().add(AcmgCriterion.PVS1).add(AcmgCriterion.PS1).add(AcmgCriterion.PP4, AcmgCriterion.Evidence.STRONG).build(); + AcmgAssignment instance = AcmgAssignment.of(variantEvaluation, geneIdentifier, ModeOfInheritance.AUTOSOMAL_DOMINANT, disease, acmgEvidence, AcmgClassification.PATHOGENIC); + assertThat(instance.toDisplayString(), equalTo("1-12335-A-T, NC_000001.10:g.12335A>T, GENE1(ENST12345678):c.2346A>T:p.1234A>-, PATHOGENIC, [PVS1, PS1, PP4_Strong], Disease (OMIM:12345), AUTOSOMAL_DOMINANT")); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterionTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterionTest.java new file mode 100644 index 000000000..f0939d4f2 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterionTest.java @@ -0,0 +1,56 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import org.junit.jupiter.api.Test; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.Evidence; + +class AcmgCriterionTest { + + @Test + void testEvidenceDisplayString() { + assertThat(Evidence.STAND_ALONE.displayString(), equalTo("StandAlone")); + assertThat(Evidence.VERY_STRONG.displayString(), equalTo("VeryStrong")); + assertThat(Evidence.STRONG.displayString(), equalTo("Strong")); + assertThat(Evidence.MODERATE.displayString(), equalTo("Moderate")); + assertThat(Evidence.SUPPORTING.displayString(), equalTo("Supporting")); + } + + @Test + void testEvidenceParseValue() { + assertThat(Evidence.parseValue("STAND_ALONE"), equalTo(Evidence.STAND_ALONE)); + assertThat(Evidence.parseValue("StandAlone"), equalTo(Evidence.STAND_ALONE)); + assertThat(Evidence.parseValue("VeryStrong"), equalTo(Evidence.VERY_STRONG)); + assertThat(Evidence.parseValue("Strong"), equalTo(Evidence.STRONG)); + assertThat(Evidence.parseValue("Moderate"), equalTo(Evidence.MODERATE)); + assertThat(Evidence.parseValue("Supporting"), equalTo(Evidence.SUPPORTING)); + } + + @Test + void testEvidenceParseValueNotRecognisedThrowsException() { + assertThrows(IllegalArgumentException.class, () -> Evidence.parseValue("Invalid input")); + } + +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceTest.java new file mode 100644 index 000000000..72e8860e7 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidenceTest.java @@ -0,0 +1,221 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.core.analysis.util.acmg; + +import org.junit.jupiter.api.Test; + +import java.util.Map; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgCriterion.*; + +public class AcmgEvidenceTest { + + @Test + void testEmptyBuilder() { + assertThat(AcmgEvidence.builder().build(), equalTo(AcmgEvidence.empty())); + } + + @Test + void testEmptyStaticFactory() { + assertThat(AcmgEvidence.of(Map.of()), equalTo(AcmgEvidence.empty())); + } + + @Test + void testStaticFactoryDefaultEvidence() { + AcmgEvidence instance = AcmgEvidence.of(Map.of(PVS1, PVS1.evidence(), PS1, PS1.evidence())); + assertThat(instance.toString(), equalTo("[PVS1, PS1]")); + } + + @Test + public void testToStringDefaultEvidence() { + AcmgEvidence instance = AcmgEvidence.builder().add(PVS1).add(PS1).build(); + assertThat(instance.toString(), equalTo("[PVS1, PS1]")); + } + + @Test + public void testToStringModifiedEvidence() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1, Evidence.STRONG) + .add(PS1, Evidence.MODERATE) + .add(PP3, Evidence.VERY_STRONG) + .build(); + assertThat(instance.toString(), equalTo("[PVS1_Strong, PS1_Moderate, PP3_VeryStrong]")); + } + + @Test + public void testGetEvidenceOverwriteInputInBuilder() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1, Evidence.STRONG) + .add(PVS1) + .build(); + assertThat(instance.criterionEvidence(PVS1), equalTo(PVS1.evidence())); + } + + @Test + public void testGetEvidenceDefaultValue() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1) + .build(); + assertThat(instance.criterionEvidence(PVS1), equalTo(PVS1.evidence())); + } + + @Test + public void testGetEvidenceModifiedValue() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1, Evidence.MODERATE) + .build(); + assertThat(instance.criterionEvidence(PVS1), equalTo(Evidence.MODERATE)); + } + + @Test + public void testGetEvidenceNoValue() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1, Evidence.MODERATE) + .build(); + assertThat(instance.criterionEvidence(PM3), equalTo(null)); + } + + @Test + public void testContainsEvidence() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1, Evidence.MODERATE) + .build(); + assertThat(instance.hasCriterion(PVS1), equalTo(true)); + assertThat(instance.hasCriterion(PM3), equalTo(false)); + } + + @Test + public void testBuilderContainsEvidence() { + AcmgEvidence.Builder instance = AcmgEvidence.builder() + .add(PVS1, Evidence.MODERATE); + assertThat(instance.contains(PVS1), equalTo(true)); + assertThat(instance.contains(PM3), equalTo(false)); + } + + @Test + public void testSizeWhenEmpty() { + AcmgEvidence instance = AcmgEvidence.builder().build(); + assertThat(instance.size(), equalTo(0)); + } + + @Test + public void testSizeWithElement() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1) + .build(); + assertThat(instance.size(), equalTo(1)); + } + + @Test + public void testIsEmpty() { + AcmgEvidence instance = AcmgEvidence.builder().build(); + assertThat(instance.isEmpty(), equalTo(true)); + } + + @Test + public void testNotEmpty() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1) + .build(); + assertThat(instance.isEmpty(), equalTo(false)); + } + + @Test + void testPvs() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1) + .add(PM1, Evidence.VERY_STRONG) + .build(); + assertThat(instance.pvs(), equalTo(2)); + } + + @Test + void testPs() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PS1) + .build(); + assertThat(instance.ps(), equalTo(1)); + } + + @Test + void testPm() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PM1) + .build(); + assertThat(instance.pm(), equalTo(1)); + } + + @Test + void testPp() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PP1) + .build(); + assertThat(instance.pp(), equalTo(1)); + } + + @Test + void testBa() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(BA1) + .build(); + assertThat(instance.ba(), equalTo(1)); + } + + @Test + void testBs() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(BS1) + .build(); + assertThat(instance.bs(), equalTo(1)); + } + + @Test + void testBp() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(BP1) + .build(); + assertThat(instance.bp(), equalTo(1)); + } + + @Test + void testEmptyCounts() { + AcmgEvidence instance = AcmgEvidence.builder() + .build(); + assertThat(instance.pvs(), equalTo(0)); + assertThat(instance.ps(), equalTo(0)); + assertThat(instance.pm(), equalTo(0)); + assertThat(instance.pp(), equalTo(0)); + assertThat(instance.ba(), equalTo(0)); + assertThat(instance.bs(), equalTo(0)); + assertThat(instance.bp(), equalTo(0)); + } + + @Test + void testEvidence() { + AcmgEvidence instance = AcmgEvidence.builder() + .add(PVS1) + .add(PM1, Evidence.VERY_STRONG) + .build(); + assertThat(instance.evidence(), equalTo(Map.of(PVS1, PVS1.evidence(), PM1, Evidence.VERY_STRONG))); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestGeneFactory.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestGeneFactory.java index 6a078ee48..d94b01331 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestGeneFactory.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestGeneFactory.java @@ -20,11 +20,9 @@ package org.monarchinitiative.exomiser.core.genome; -import com.google.common.collect.ImmutableList; import org.monarchinitiative.exomiser.core.model.Gene; import org.monarchinitiative.exomiser.core.model.GeneIdentifier; -import java.util.Arrays; import java.util.List; /** @@ -74,7 +72,7 @@ class TestGeneFactory { .ucscId("uc031uto.3") .build(); - private static final List GENE_IDENTIFIERS = ImmutableList.of(FGFR2_IDENTIFIER, SHH_IDENTIFIER, GNRHR2_IDENTIFIER, RBM8A_IDENTIFIER); + private static final List GENE_IDENTIFIERS = List.of(FGFR2_IDENTIFIER, SHH_IDENTIFIER, GNRHR2_IDENTIFIER, RBM8A_IDENTIFIER); private TestGeneFactory() {} @@ -93,6 +91,6 @@ static List buildGeneIdentifiers() { * @return a mutable list of newly instantiated Gene instances build from fully formed GeneIdentifiers. */ static List buildGenes() { - return Arrays.asList(new Gene(FGFR2_IDENTIFIER), new Gene(SHH_IDENTIFIER), new Gene(GNRHR2_IDENTIFIER), new Gene(RBM8A_IDENTIFIER)); + return List.of(new Gene(FGFR2_IDENTIFIER), new Gene(SHH_IDENTIFIER), new Gene(GNRHR2_IDENTIFIER), new Gene(RBM8A_IDENTIFIER)); } } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteListTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteListTest.java index 9ecbbd113..87253e646 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteListTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/InMemoryVariantWhiteListTest.java @@ -20,7 +20,6 @@ package org.monarchinitiative.exomiser.core.genome.dao; -import com.google.common.collect.ImmutableSet; import org.junit.jupiter.api.Test; import org.monarchinitiative.exomiser.core.genome.TestFactory; import org.monarchinitiative.exomiser.core.model.AlleleProtoAdaptor; @@ -28,6 +27,7 @@ import org.monarchinitiative.exomiser.core.proto.AlleleProto; import java.util.Collections; +import java.util.Set; import static org.hamcrest.CoreMatchers.equalTo; import static org.hamcrest.CoreMatchers.is; @@ -52,7 +52,7 @@ void willAcceptEmptySet() { @Test void testContains() { Variant whiteListedVariant = TestFactory.variantBuilder(1, 234567, "A", "G").build(); - ImmutableSet whitelistedKeys = ImmutableSet.of(AlleleProtoAdaptor.toAlleleKey(whiteListedVariant)); + Set whitelistedKeys = Set.of(AlleleProtoAdaptor.toAlleleKey(whiteListedVariant)); VariantWhiteList instance = InMemoryVariantWhiteList.of(whitelistedKeys); assertThat(instance.contains(whiteListedVariant), is(true)); diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/jannovar/JannovarDataFactoryTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/jannovar/JannovarDataFactoryTest.java index 0938902f8..6f2241d33 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/jannovar/JannovarDataFactoryTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/jannovar/JannovarDataFactoryTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -25,9 +25,7 @@ import de.charite.compbio.jannovar.reference.TranscriptModel; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; -import org.junitpioneer.jupiter.TempDirectory.TempDir; +import org.junit.jupiter.api.io.TempDir; import org.monarchinitiative.exomiser.core.genome.GeneFactory; import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; import org.monarchinitiative.exomiser.core.genome.JannovarVariantAnnotator; @@ -53,7 +51,7 @@ /** * @author Jules Jacobsen */ -@ExtendWith(TempDirectory.class) +//@ExtendWith(TempDirectory.class) class JannovarDataFactoryTest { private final Path iniFile = Paths.get("src/test/resources/jannovar/default_sources.ini"); diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneScoreTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneScoreTest.java index f6eb8a1f0..feee6f363 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneScoreTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneScoreTest.java @@ -22,10 +22,15 @@ import de.charite.compbio.jannovar.mendel.ModeOfInheritance; import org.junit.jupiter.api.Test; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgAssignment; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgClassification; +import org.monarchinitiative.exomiser.core.analysis.util.acmg.AcmgEvidence; import org.monarchinitiative.exomiser.core.genome.TestFactory; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; -import java.util.Arrays; import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; import static org.hamcrest.CoreMatchers.equalTo; import static org.hamcrest.MatcherAssert.assertThat; @@ -64,6 +69,14 @@ public void getCombinedScore() { assertThat(instance.getCombinedScore(), equalTo(1d)); } + @Test + public void getPvalue() { + GeneScore instance = GeneScore.builder() + .pValue(0.00001d) + .build(); + assertThat(instance.pValue(), equalTo(0.00001d)); + } + @Test public void getPhenotypeScore() { GeneScore instance = GeneScore.builder() @@ -93,6 +106,16 @@ public void getContributingVariants() { assertThat(instance.getContributingVariants(), equalTo(contributingVariants)); } + @Test + void testAcmgAssignment() { + AcmgAssignment acmgAssignment = AcmgAssignment.of(TestFactory.variantBuilder(1, 12335, "T", "C").build(), TestFactory.newGeneFGFR2().getGeneIdentifier(), ModeOfInheritance.AUTOSOMAL_DOMINANT, Disease.builder().build(), AcmgEvidence.builder().build(), AcmgClassification.PATHOGENIC); + + GeneScore instance = GeneScore.builder() + .acmgAssignments(List.of(acmgAssignment)) + .build(); + assertThat(instance.getAcmgAssignments(), equalTo(List.of(acmgAssignment))); + } + @Test public void equals() { assertThat(GeneScore.builder().build(), equalTo(GeneScore.builder().build())); @@ -127,12 +150,14 @@ public void testCompareTo() { GeneScore four = GeneScore.builder().combinedScore(0.25).geneIdentifier(second).build(); GeneScore five = GeneScore.builder().combinedScore(0.25).geneIdentifier(third).build(); GeneScore six = GeneScore.builder().combinedScore(0.125).geneIdentifier(third).build(); + GeneScore seven = GeneScore.builder().combinedScore(0.0).phenotypeScore(0.6).geneIdentifier(second).build(); + GeneScore eight = GeneScore.builder().combinedScore(0.0).phenotypeScore(0.5).geneIdentifier(first).build(); - List geneScores = Arrays.asList(two, three, six, one, five, four); - - geneScores.sort(GeneScore::compareTo); + List geneScores = Stream.of(two, three, six, one, five, four, eight, seven) + .sorted() + .collect(Collectors.toUnmodifiableList()); - assertThat(geneScores, equalTo(List.of(one, two, three, four, five, six))); + assertThat(geneScores, equalTo(List.of(one, two, three, four, five, six, seven, eight))); } @Test @@ -142,8 +167,9 @@ public void testToString() { .combinedScore(1) .phenotypeScore(1) .variantScore(1) + .pValue(0.0001) .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) .build(); - assertThat(instance.toString(), equalTo("GeneScore{geneIdentifier=GeneIdentifier{geneId='HGNC:12345', geneSymbol='TEST1', hgncId='', hgncSymbol='', entrezId='', ensemblId='', ucscId=''}, modeOfInheritance=AUTOSOMAL_DOMINANT, combinedScore=1.0, phenotypeScore=1.0, variantScore=1.0, contributingVariants=[]}")); + assertThat(instance.toString(), equalTo("GeneScore{geneIdentifier=GeneIdentifier{geneId='HGNC:12345', geneSymbol='TEST1', hgncId='', hgncSymbol='', entrezId='', ensemblId='', ucscId=''}, modeOfInheritance=AUTOSOMAL_DOMINANT, combinedScore=1.0, phenotypeScore=1.0, variantScore=1.0, pValue=1.0E-4, contributingVariants=[]}")); } } \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneTest.java index 6a9eb57e2..84e7254d1 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/GeneTest.java @@ -25,6 +25,9 @@ */ package org.monarchinitiative.exomiser.core.model; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.ObjectWriter; import de.charite.compbio.jannovar.mendel.ModeOfInheritance; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -32,6 +35,9 @@ import org.monarchinitiative.exomiser.core.filters.FilterType; import org.monarchinitiative.exomiser.core.genome.TestFactory; import org.monarchinitiative.exomiser.core.prioritisers.*; +import org.monarchinitiative.exomiser.core.prioritisers.model.Disease; +import org.monarchinitiative.exomiser.core.writers.JsonVariantMixin; +import org.monarchinitiative.svart.Variant; import java.util.*; @@ -718,4 +724,42 @@ public void testInheritanceModeComparator() { public void testToString() { assertThat(instance.toString(), equalTo("Gene{geneSymbol='GENE1', entrezGeneId=1234567, compatibleWith=[], filterStatus=PASSED, failedFilterTypes=[], passedFilterTypes=[], combinedScore=0.0, phenotypeScore=0.0, variantScore=0.0, variants=0}")); } + + @Test + void testGetAssociatedDiseases() { + Gene instance = TestFactory.newGeneFGFR2(); + assertThat(instance.getAssociatedDiseases().isEmpty(), is(true)); + Disease pfeifferSyndrome = Disease.builder().diseaseId("OMIM:101600").diseaseName("Pfeiffer syndrome").build(); + OmimPriorityResult priorityResult = new OmimPriorityResult(instance.getEntrezGeneID(), instance.getGeneSymbol(), 1.0, List.of(pfeifferSyndrome), Map.of()); + instance.addPriorityResult(priorityResult); + assertThat(instance.getAssociatedDiseases(), equalTo(List.of(pfeifferSyndrome))); + } + + @Test + public void testGetCompatibleGeneScores() throws Exception { + Gene instance = TestFactory.newGeneFGFR2(); + // Hmm... this is a bit of a WFT - why does this need to be set rather than computed from the variants? + // ... because it gets set once by the InheritanceModeAnalyser after all the variants have been filtered + instance.setCompatibleInheritanceModes(EnumSet.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + assertThat(instance.getCompatibleGeneScores().isEmpty(), is(true)); + + GeneScore adGeneScore = GeneScore.builder() + .geneIdentifier(instance.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .phenotypeScore(0.5d) + .variantScore(0.5d) + .combinedScore(0.5d) + .pValue(0.0000001) + .build(); + + instance.addGeneScore(adGeneScore); + + ObjectWriter objectWriter = new ObjectMapper() + .addMixIn(Variant.class, JsonVariantMixin.class) + .setDefaultPropertyInclusion(JsonInclude.Include.NON_DEFAULT) + .writerWithDefaultPrettyPrinter(); + System.out.println(objectWriter.writeValueAsString(instance)); + + assertThat(instance.getCompatibleGeneScores(), equalTo(List.of(adGeneScore))); + } } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/SampleGenotypeTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/SampleGenotypeTest.java index 1d161ba92..37d3e6318 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/SampleGenotypeTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/SampleGenotypeTest.java @@ -20,8 +20,11 @@ package org.monarchinitiative.exomiser.core.model; -import com.google.common.collect.ImmutableList; import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; + +import java.util.List; import static org.hamcrest.CoreMatchers.*; import static org.hamcrest.MatcherAssert.assertThat; @@ -39,14 +42,14 @@ public void testUnobserved() { @Test public void testHetUnphased() { - assertThat(SampleGenotype.of(AlleleCall.REF, AlleleCall.ALT).getCalls(), equalTo(ImmutableList.of(AlleleCall.REF, AlleleCall.ALT))); - assertThat(SampleGenotype.of(AlleleCall.ALT, AlleleCall.REF).getCalls(), equalTo(ImmutableList.of(AlleleCall.REF, AlleleCall.ALT))); + assertThat(SampleGenotype.of(AlleleCall.REF, AlleleCall.ALT).getCalls(), equalTo(List.of(AlleleCall.REF, AlleleCall.ALT))); + assertThat(SampleGenotype.of(AlleleCall.ALT, AlleleCall.REF).getCalls(), equalTo(List.of(AlleleCall.REF, AlleleCall.ALT))); } @Test public void testHetPhased() { - assertThat(SampleGenotype.phased(AlleleCall.REF, AlleleCall.ALT).getCalls(), equalTo(ImmutableList.of(AlleleCall.REF, AlleleCall.ALT))); - assertThat(SampleGenotype.phased(AlleleCall.ALT, AlleleCall.REF).getCalls(), equalTo(ImmutableList.of(AlleleCall.ALT, AlleleCall.REF))); + assertThat(SampleGenotype.phased(AlleleCall.REF, AlleleCall.ALT).getCalls(), equalTo(List.of(AlleleCall.REF, AlleleCall.ALT))); + assertThat(SampleGenotype.phased(AlleleCall.ALT, AlleleCall.REF).getCalls(), equalTo(List.of(AlleleCall.ALT, AlleleCall.REF))); } @Test @@ -242,4 +245,33 @@ void testIsNoCall() { assertThat(SampleGenotype.parseGenotype("0/1").isNoCall(), equalTo(false)); assertThat(SampleGenotype.parseGenotype("1/1/2").isNoCall(), equalTo(false)); } + + private boolean possibleDeNovo(SampleGenotype ancestorGenotype, SampleGenotype probandGenotype) { + return (ancestorGenotype.isNoCall() || ancestorGenotype.isHomRef()) && (probandGenotype.isHet() || probandGenotype.isHomAlt()); + } + + private boolean familyHistoryOfAllele(SampleGenotype ancestorGenotype, SampleGenotype probandGenotype) { + return (ancestorGenotype.isHet() || ancestorGenotype.isHomAlt()) && (probandGenotype.isHet() || probandGenotype.isHomAlt()); + } + + @ParameterizedTest + @CsvSource({ + "., 0/1, true", + "./., 0/1, true", + "./., 0/0, false", + "./1, 0/0, false", + "./1, 0/1, false", + "./1, 1/1, false", + "1/1, 1/1, false", + // "1/1, 0/0, true", this should return true, but is currently broken. However, Exomiser will remove 0/0 proband variants. + "0/1, 1/1, false", + "0/1, 0/1, false", + "0/1, 0/0, false", + "0/0, 0/1, true", + }) + void testPossibleDeNovo(String parent, String proband, boolean possibleDeNovo) { + SampleGenotype parentGenotype = SampleGenotype.parseGenotype(parent); + SampleGenotype probandGenotype = SampleGenotype.parseGenotype(proband); + assertThat(possibleDeNovo(parentGenotype, probandGenotype), is(possibleDeNovo)); + } } \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotationTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotationTest.java index 263798eea..f75f2f41a 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotationTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/TranscriptAnnotationTest.java @@ -99,4 +99,16 @@ public void testDistanceFromNearestGene() { assertThat(annotation.getDistanceFromNearestGene(), equalTo(value)); } + @Test + public void testExonRank() { + TranscriptAnnotation annotation = TranscriptAnnotation.builder() + .rankType(TranscriptAnnotation.RankType.EXON) + .rank(2) + .rankTotal(5) + .build(); + // i.e. Exon 2 of 5 + assertThat(annotation.getRankType(), equalTo(TranscriptAnnotation.RankType.EXON)); + assertThat(annotation.getRank(), equalTo(2)); + assertThat(annotation.getRankTotal(), equalTo(5)); + } } \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java index 4e7f5eaec..c916cca61 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java @@ -52,7 +52,6 @@ import static org.hamcrest.CoreMatchers.equalTo; import static org.hamcrest.CoreMatchers.is; import static org.hamcrest.MatcherAssert.assertThat; -import static org.hamcrest.Matchers.endsWith; import static org.hamcrest.Matchers.lessThan; import static org.junit.jupiter.api.Assertions.assertThrows; @@ -856,13 +855,13 @@ public void testVariantCompareByRank() { @Test public void testToString() { - String expected = "VariantEvaluation{assembly=hg19 chr=1 strand=+ start=1 end=1 length=1 ref=C alt=T id= qual=2.2 SNV SEQUENCE_VARIANT gene=GENE1 score=0.0 UNFILTERED failedFilters=[] passedFilters=[] compatibleWith=[] sampleGenotypes={sample=0/1}}"; + String expected = "VariantEvaluation{assembly=hg19 chr=1 strand=+ start=1 end=1 length=1 ref=C alt=T id= qual=2.2 SNV SEQUENCE_VARIANT gene=GENE1 score=0.0 freqScore=1.0 pathScore=0.0 UNFILTERED failedFilters=[] passedFilters=[] compatibleWith=[] sampleGenotypes={sample=0/1}}"; assertThat(instance.toString(), equalTo(expected)); } @Test public void testToStringVariantContributesToGeneScore() { - String expected = "VariantEvaluation{assembly=hg19 chr=1 strand=+ start=1 end=1 length=1 ref=C alt=T id= qual=2.2 SNV SEQUENCE_VARIANT gene=GENE1 * score=0.0 UNFILTERED failedFilters=[] passedFilters=[] compatibleWith=[] sampleGenotypes={sample=0/1}}"; + String expected = "VariantEvaluation{assembly=hg19 chr=1 strand=+ start=1 end=1 length=1 ref=C alt=T id= qual=2.2 SNV SEQUENCE_VARIANT gene=GENE1 * score=0.0 freqScore=1.0 pathScore=0.0 UNFILTERED failedFilters=[] passedFilters=[] compatibleWith=[] sampleGenotypes={sample=0/1}}"; instance.setContributesToGeneScoreUnderMode(ModeOfInheritance.ANY); assertThat(instance.toString(), equalTo(expected)); } @@ -876,7 +875,7 @@ void testToGnomadSnv() { void testToGnomadSvIns() { VariantEvaluation sv = newBuilder(1, 100, 100, "A", "", 50) .build(); - assertThat(sv.toGnomad(), equalTo("1-100-100-A- 50bp")); + assertThat(sv.toGnomad(), equalTo("1-100-100-A-")); } @ParameterizedTest @@ -904,7 +903,7 @@ void testToGnomadSvIns() { }) void lengthFormat(int changeLength, String expected) { VariantEvaluation sv = newBuilder(1, 100, 100, "A", "", changeLength).build(); - assertThat(sv.toGnomad(), endsWith(expected)); + assertThat(sv.changeLengthString(), equalTo(expected)); } private String toGnomadWithLength(VariantEvaluation.Builder sv, int length) { @@ -915,7 +914,7 @@ private String toGnomadWithLength(VariantEvaluation.Builder sv, int length) { void testToGnomadSvDel() { VariantEvaluation sv = newBuilder(1, 100, 150, "A", "", -50) .build(); - assertThat(sv.toGnomad(), equalTo("1-100-150-A- 50bp")); + assertThat(sv.toGnomad(), equalTo("1-100-150-A-")); } @Test diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java index c0569e064..2fd994592 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java @@ -263,6 +263,21 @@ public void testGetMaxFreqWithData() { assertThat(instance.getMaxFreq(), equalTo(maxFreq)); } + @Test + public void testGetMaxFrequencyWhenNoData() { + assertThat(EMPTY_DATA.getMaxFrequency(), equalTo(null)); + } + + @Test + public void testGetMaxFrequencyWithData() { + Frequency maxFrequency = Frequency.of(GNOMAD_E_OTH, 89.5f); + Frequency minFrequency = Frequency.of(GNOMAD_G_AFR, 0.0002f); + Frequency midFrequency = Frequency.of(GNOMAD_E_AMR, 25.5f); + FrequencyData instance = FrequencyData.of(RS_ID, minFrequency, maxFrequency, midFrequency); + System.out.println(instance.getMaxFrequency()); + assertThat(instance.getMaxFrequency(), equalTo(maxFrequency)); + } + @Test public void testHasFrequencyOverPercentageValue() { float maxFreq = 0.05f; diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDaoTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDaoTest.java index 3ed344d3e..d74861cbb 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDaoTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDaoTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2019 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -38,7 +38,6 @@ import org.springframework.test.context.jdbc.Sql; import org.springframework.test.context.junit.jupiter.SpringExtension; -import java.util.Arrays; import java.util.List; import java.util.Set; @@ -63,12 +62,12 @@ public class DefaultDiseaseDaoTest { private final Disease disease = Disease.builder() .diseaseId("OMIM:101600") - .diseaseName("Craniofacial-skeletal-dermatologic dysplasia") - .associatedGeneId(2263) - .associatedGeneSymbol("FGFR2") - .diseaseType(Disease.DiseaseType.DISEASE) - .inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT) - .phenotypeIds(Arrays.asList("HP:0000174, HP:0000194, HP:0000218, HP:0000238, HP:0000244, HP:0000272, HP:0000303, HP:0000316, HP:0000322, HP:0000324, HP:0000327, HP:0000348, HP:0000431, HP:0000452, HP:0000453, HP:0000470, HP:0000486, HP:0000494, HP:0000508, HP:0000586, HP:0000678, HP:0001156, HP:0001249, HP:0002308, HP:0002676, HP:0002780, HP:0003041, HP:0003070, HP:0003196, HP:0003272, HP:0003307, HP:0003795, HP:0004209, HP:0004322, HP:0004440, HP:0005048, HP:0005280, HP:0005347, HP:0006101, HP:0006110, HP:0009602, HP:0009773, HP:0010055, HP:0010669, HP:0011304".split(", "))) + .diseaseName("Craniofacial-skeletal-dermatologic dysplasia") + .associatedGeneId(2263) + .associatedGeneSymbol("FGFR2") + .diseaseType(Disease.DiseaseType.DISEASE) + .inheritanceMode(InheritanceMode.AUTOSOMAL_DOMINANT) + .phenotypeIds(List.of("HP:0000174, HP:0000194, HP:0000218, HP:0000238, HP:0000244, HP:0000272, HP:0000303, HP:0000316, HP:0000322, HP:0000324, HP:0000327, HP:0000348, HP:0000431, HP:0000452, HP:0000453, HP:0000470, HP:0000486, HP:0000494, HP:0000508, HP:0000586, HP:0000678, HP:0001156, HP:0001249, HP:0002308, HP:0002676, HP:0002780, HP:0003041, HP:0003070, HP:0003196, HP:0003272, HP:0003307, HP:0003795, HP:0004209, HP:0004322, HP:0004440, HP:0005048, HP:0005280, HP:0005347, HP:0006101, HP:0006110, HP:0009602, HP:0009773, HP:0010055, HP:0010669, HP:0011304".split(", "))) .build(); @Test @@ -124,7 +123,32 @@ public void testGetSusceptibilityDiseaseDataAssociatedWithGeneId() { .associatedGeneSymbol("GENE4") .phenotypeIds(ImmutableList.of("HP:0000002")) .build(); - List expected = Lists.newArrayList(disease) ; + List expected = Lists.newArrayList(disease); assertThat(instance.getDiseaseDataAssociatedWithGeneId(4444), equalTo(expected)); } + + @Test + public void testMultipleDiseaseDataAssociatedWithGeneId() { + Disease disease1 = Disease.builder() + .diseaseId("OMIM:765432") + .diseaseName("Test multi-disease gene disease 1") + .diseaseType(Disease.DiseaseType.DISEASE) + .inheritanceMode(InheritanceMode.UNKNOWN) + .associatedGeneId(5555) + .associatedGeneSymbol("GENE5") + .phenotypeIds(ImmutableList.of("HP:0000003")) + .build(); + + Disease disease2 = Disease.builder() + .diseaseId("OMIM:765433") + .diseaseName("Test multi-disease gene disease 2") + .diseaseType(Disease.DiseaseType.DISEASE) + .inheritanceMode(InheritanceMode.UNKNOWN) + .associatedGeneId(5555) + .associatedGeneSymbol("GENE5") + .phenotypeIds(ImmutableList.of("HP:0000004")) + .build(); + + assertThat(instance.getDiseaseDataAssociatedWithGeneId(5555), equalTo(List.of(disease1, disease2))); + } } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceModeTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceModeTest.java index 72153e855..a1c052fc6 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceModeTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/model/InheritanceModeTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2021 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -126,21 +126,28 @@ public void testIsCompatibleWithModeOfInheritance() { assertThat(InheritanceMode.AUTOSOMAL_DOMINANT.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_DOMINANT), is(true)); assertThat(InheritanceMode.AUTOSOMAL_RECESSIVE.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_RECESSIVE), is(true)); assertThat(InheritanceMode.AUTOSOMAL_RECESSIVE.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_DOMINANT), is(false)); + assertThat(InheritanceMode.AUTOSOMAL_RECESSIVE.isCompatibleWith(ModeOfInheritance.ANY), is(true)); assertThat(InheritanceMode.AUTOSOMAL_DOMINANT_AND_RECESSIVE.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_RECESSIVE), is(true)); assertThat(InheritanceMode.AUTOSOMAL_DOMINANT_AND_RECESSIVE.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_DOMINANT), is(true)); + assertThat(InheritanceMode.AUTOSOMAL_DOMINANT_AND_RECESSIVE.isCompatibleWith(ModeOfInheritance.ANY), is(true)); assertThat(InheritanceMode.X_DOMINANT.isCompatibleWith(ModeOfInheritance.X_DOMINANT), is(true)); assertThat(InheritanceMode.X_RECESSIVE.isCompatibleWith(ModeOfInheritance.X_RECESSIVE), is(true)); assertThat(InheritanceMode.X_RECESSIVE.isCompatibleWith(ModeOfInheritance.X_DOMINANT), is(false)); + assertThat(InheritanceMode.X_DOMINANT.isCompatibleWith(ModeOfInheritance.ANY), is(true)); + assertThat(InheritanceMode.X_RECESSIVE.isCompatibleWith(ModeOfInheritance.ANY), is(true)); assertThat(InheritanceMode.X_LINKED.isCompatibleWith(ModeOfInheritance.X_DOMINANT), is(true)); assertThat(InheritanceMode.X_LINKED.isCompatibleWith(ModeOfInheritance.X_RECESSIVE), is(true)); + assertThat(InheritanceMode.X_LINKED.isCompatibleWith(ModeOfInheritance.ANY), is(true)); assertThat(InheritanceMode.MITOCHONDRIAL.isCompatibleWith(ModeOfInheritance.MITOCHONDRIAL), is(true)); + assertThat(InheritanceMode.MITOCHONDRIAL.isCompatibleWith(ModeOfInheritance.ANY), is(true)); assertThat(InheritanceMode.POLYGENIC.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_DOMINANT), is(false)); assertThat(InheritanceMode.POLYGENIC.isCompatibleWith(ModeOfInheritance.AUTOSOMAL_RECESSIVE), is(false)); + assertThat(InheritanceMode.POLYGENIC.isCompatibleWith(ModeOfInheritance.ANY), is(true)); } @Test diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriterTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriterTest.java index 515ec9f81..f160b284b 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriterTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/AnalysisResultsWriterTest.java @@ -28,6 +28,8 @@ import org.monarchinitiative.exomiser.core.analysis.AnalysisResults; import org.monarchinitiative.exomiser.core.analysis.sample.Sample; import org.monarchinitiative.exomiser.core.analysis.util.InheritanceModeOptions; +import org.monarchinitiative.exomiser.core.analysis.util.TestPedigrees; +import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; import org.monarchinitiative.exomiser.core.genome.TestFactory; import org.monarchinitiative.exomiser.core.model.Gene; @@ -39,6 +41,7 @@ import java.util.EnumSet; import java.util.List; import java.util.Set; +import java.util.stream.Collectors; import static org.hamcrest.CoreMatchers.is; import static org.hamcrest.MatcherAssert.assertThat; @@ -71,7 +74,7 @@ private AnalysisResults newAnalysisResults(Sample sample, Analysis analysis) { } @Test - void testWriteToFileOutputsAllModesOfinheritanceForEachFormat() throws Exception { + void testWriteToFileOutputsAllModesOfInheritanceForEachFormat() { String outputPrefix = tempFile.toString(); OutputSettings settings = OutputSettings.builder() @@ -80,7 +83,7 @@ void testWriteToFileOutputsAllModesOfinheritanceForEachFormat() throws Exception .build(); Sample sample = Sample.builder() - .vcfPath(Paths.get("src/test/resources/smallTest.vcf")) + .vcfPath(Paths.get("src/test/resources/Pfeiffer.vcf")) .build(); Analysis analysis = Analysis.builder() @@ -104,7 +107,7 @@ void testWriteToFileOutputsAllModesOfinheritanceForEachFormat() throws Exception } @Test - void testWriteToFileOutputsAllModesOfinheritanceForEachFormatWhenInheritanceModeIsUndefined() throws Exception { + void testWriteToFileOutputsAllModesOfInheritanceForEachFormatWhenInheritanceModeIsUndefined() { String outputPrefix = tempFile.toString(); OutputSettings settings = OutputSettings.builder() @@ -113,7 +116,7 @@ void testWriteToFileOutputsAllModesOfinheritanceForEachFormatWhenInheritanceMode .build(); Sample sample = Sample.builder() - .vcfPath(Paths.get("src/test/resources/smallTest.vcf")) + .vcfPath(Paths.get("src/test/resources/Pfeiffer.vcf")) .build(); Analysis analysis = Analysis.builder() @@ -122,14 +125,15 @@ void testWriteToFileOutputsAllModesOfinheritanceForEachFormatWhenInheritanceMode AnalysisResultsWriter.writeToFile(newAnalysisResults(sample, analysis), settings); for (OutputFormat outputFormat : Arrays.asList(OutputFormat.HTML, OutputFormat.TSV_GENE, OutputFormat.TSV_VARIANT, OutputFormat.VCF)) { - Path outputPath = Paths.get(String.format("%s.%s", outputPrefix, outputFormat.getFileExtension())); + String fileExtension = outputFormat.getFileExtension(); + Path outputPath = Paths.get(String.format("%s.%s", outputPrefix, fileExtension.equals("vcf") ? "vcf.gz" : fileExtension)); assertThat(outputPath.toFile().exists(), is(true)); assertThat(outputPath.toFile().delete(), is(true)); } } @Test - void testWriteToFileOutputsSingleHtmlFileIfPresentInSettings() throws Exception { + void testWriteToFileOutputsSingleHtmlFileIfPresentInSettings() { String outputPrefix = tempFile.toString(); OutputSettings settings = OutputSettings.builder() @@ -147,7 +151,7 @@ void testWriteToFileOutputsSingleHtmlFileIfPresentInSettings() throws Exception } @Test - void testWriteToFileOutputsSingleJsonFileIfPresentInSettings() throws Exception { + void testWriteToFileOutputsSingleJsonFileIfPresentInSettings() { String outputPrefix = tempFile.toString(); OutputSettings settings = OutputSettings.builder() @@ -165,7 +169,7 @@ void testWriteToFileOutputsSingleJsonFileIfPresentInSettings() throws Exception } @Test - void testWriteToFileOutputsSingleJsonOrHtmlFileIfPresentInSettings() throws Exception { + void testWriteToFileOutputsSingleJsonOrHtmlFileIfPresentInSettings() { String outputPrefix = tempFile.toString(); Set singleFileFormats = EnumSet.of(OutputFormat.JSON, OutputFormat.HTML); @@ -186,7 +190,7 @@ void testWriteToFileOutputsSingleJsonOrHtmlFileIfPresentInSettings() throws Exce } @Test - void testWriteToFileDoesNotOutputSingleHtmlFileIfAbsentFromSettings() throws Exception { + void testWriteToFileOutputsSingleHtmlFileIfNoneSpecified() { String outputPrefix = tempFile.toString(); OutputSettings settings = OutputSettings.builder() @@ -199,24 +203,33 @@ void testWriteToFileDoesNotOutputSingleHtmlFileIfAbsentFromSettings() throws Exc AnalysisResultsWriter.writeToFile(newAnalysisResults(sample, analysis), settings); Path outputPath = Paths.get(String.format("%s.%s", outputPrefix, OutputFormat.HTML.getFileExtension())); - assertThat(outputPath.toFile().exists(), is(false)); + assertThat(outputPath.toFile().exists(), is(true)); } @Test void testWriteToFileWithOutputOptions() { String outputPrefix = tempFile.toString(); + List outputFormats = Arrays.stream(OutputFormat.values()).map(OutputFormat::toString).collect(Collectors.toList()); + OutputProto.OutputOptions outputOptions = OutputProto.OutputOptions.newBuilder() .setOutputPrefix(outputPrefix) - .addAllOutputFormats(List.of(OutputFormat.HTML.toString(), OutputFormat.JSON.toString())) + .addAllOutputFormats(outputFormats) + .build(); + + Sample sample = Sample.builder() + .probandSampleName(TestPedigrees.affectedChild().getId()) + .pedigree(TestPedigrees.trioChildAffected()) + .genomeAssembly(GenomeAssembly.HG19) + .vcfPath(Paths.get("src/test/resources/multiSampleWithProbandHomRef.vcf")) .build(); - Sample sample = Sample.builder().build(); Analysis analysis = Analysis.builder().build(); AnalysisResultsWriter.writeToFile(newAnalysisResults(sample, analysis), outputOptions); - for (OutputFormat outputFormat : EnumSet.of(OutputFormat.HTML, OutputFormat.JSON)) { - Path outputPath = Paths.get(String.format("%s.%s", outputPrefix, outputFormat.getFileExtension())); + for (OutputFormat outputFormat : OutputFormat.values()) { + String fileExtension = outputFormat.getFileExtension(); + Path outputPath = Paths.get(String.format("%s.%s", outputPrefix, fileExtension.equals("vcf") ? "vcf.gz" : fileExtension)); assertThat(outputPath.toFile().exists(), is(true)); assertThat(outputPath.toFile().delete(), is(true)); } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/GeneScoreRankerTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/GeneScoreRankerTest.java new file mode 100644 index 000000000..72af68bf3 --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/GeneScoreRankerTest.java @@ -0,0 +1,242 @@ +package org.monarchinitiative.exomiser.core.writers; + +import de.charite.compbio.jannovar.mendel.ModeOfInheritance; +import org.junit.jupiter.api.Test; +import org.monarchinitiative.exomiser.core.analysis.AnalysisResults; +import org.monarchinitiative.exomiser.core.filters.FilterResult; +import org.monarchinitiative.exomiser.core.filters.FilterType; +import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; +import org.monarchinitiative.exomiser.core.genome.TestFactory; +import org.monarchinitiative.exomiser.core.genome.TestVariantFactory; +import org.monarchinitiative.exomiser.core.model.Gene; +import org.monarchinitiative.exomiser.core.model.GeneIdentifier; +import org.monarchinitiative.exomiser.core.model.GeneScore; +import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.prioritisers.HiPhivePriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.MockPriorityResult; +import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; +import org.monarchinitiative.svart.CoordinateSystem; +import org.monarchinitiative.svart.Position; +import org.monarchinitiative.svart.Strand; + +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +import static java.util.stream.Collectors.*; +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.hamcrest.Matchers.in; +import static org.junit.jupiter.api.Assertions.*; + +public class GeneScoreRankerTest { + + @Test + public void mapGenesByGeneIdentifier() { + var fgfr2 = TestFactory.newGeneFGFR2(); + var gnrhr2 = TestFactory.newGeneGNRHR2(); + AnalysisResults analysisResults = AnalysisResults.builder().genes(List.of(fgfr2, gnrhr2)).build(); + + GeneScoreRanker instance = new GeneScoreRanker(analysisResults, OutputSettings.defaults()); + + Map expected = Map.of(fgfr2.getGeneIdentifier(), fgfr2, gnrhr2.getGeneIdentifier(), gnrhr2); + assertThat(instance.mapGenesByGeneIdentifier(), equalTo(expected)); + } + + @Test + public void rankedGenes() { + var fgfr2 = TestFactory.newGeneFGFR2(); + var topGeneScore = GeneScore.builder() + .combinedScore(1.0) + .geneIdentifier(fgfr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + fgfr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + fgfr2.addGeneScore(topGeneScore); + + var gnrhr2 = TestFactory.newGeneGNRHR2(); + var secondGeneScore = GeneScore.builder() + .combinedScore(0.9) + .geneIdentifier(gnrhr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + gnrhr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + gnrhr2.addGeneScore(secondGeneScore); + + AnalysisResults analysisResults = AnalysisResults.builder().genes(List.of(fgfr2, gnrhr2)).build(); + + GeneScoreRanker instance = new GeneScoreRanker(analysisResults, OutputSettings.defaults()); + List expected = List.of( + new GeneScoreRanker.RankedGene(1, fgfr2, topGeneScore), + new GeneScoreRanker.RankedGene(2, gnrhr2, secondGeneScore) + ); + assertThat(instance.rankedGenes().collect(toList()), equalTo(expected)); + } + + @Test + public void rankedGenesWithFailedVariant() { + var fgfr2 = TestFactory.newGeneFGFR2(); + var topGeneScore = GeneScore.builder() + .combinedScore(1.0) + .geneIdentifier(fgfr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + fgfr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + fgfr2.addGeneScore(topGeneScore); + + VariantEvaluation failedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(10), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(1234567), "G", "T") + .filterResults(FilterResult.fail(FilterType.FREQUENCY_FILTER)) + .build(); + fgfr2.addVariant(failedVariant); + + var failedGeneScore = GeneScore.builder() + .combinedScore(0.0) + .geneIdentifier(fgfr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.ANY) + .build(); + + + var gnrhr2 = TestFactory.newGeneGNRHR2(); + var secondGeneScore = GeneScore.builder() + .combinedScore(0.9) + .geneIdentifier(gnrhr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + gnrhr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + gnrhr2.addGeneScore(secondGeneScore); + + AnalysisResults analysisResults = AnalysisResults.builder().genes(List.of(fgfr2, gnrhr2)).build(); + + GeneScoreRanker instance = new GeneScoreRanker(analysisResults, OutputSettings.defaults()); + List expected = List.of( + new GeneScoreRanker.RankedGene(1, fgfr2, topGeneScore), + new GeneScoreRanker.RankedGene(2, gnrhr2, secondGeneScore), + new GeneScoreRanker.RankedGene(3, fgfr2, failedGeneScore) + ); + assertThat(instance.rankedGenes().collect(toList()), equalTo(expected)); + } + + @Test + public void rankedVariants() { + var fgfr2 = TestFactory.newGeneFGFR2(); + var topGeneScore = GeneScore.builder() + .combinedScore(1.0) + .geneIdentifier(fgfr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + fgfr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + fgfr2.addPriorityResult(new MockPriorityResult(PriorityType.HIPHIVE_PRIORITY, fgfr2.getEntrezGeneID(), fgfr2.getGeneSymbol(), 1.0)); + fgfr2.addGeneScore(topGeneScore); + + VariantEvaluation fgfr2TopRankedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(10), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(1234567), "G", "T") + .filterResults(FilterResult.pass(FilterType.FREQUENCY_FILTER)) + .compatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .build(); + fgfr2.addVariant(fgfr2TopRankedVariant); + + + VariantEvaluation fgfr2FailedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(10), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(1234567), "G", "T") + .filterResults(FilterResult.fail(FilterType.FREQUENCY_FILTER)) + .compatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .build(); + fgfr2.addVariant(fgfr2FailedVariant); + + var failedGeneScore = GeneScore.builder() + .combinedScore(0.0) + .geneIdentifier(fgfr2.getGeneIdentifier()) + .phenotypeScore(fgfr2.getPriorityScore()) + .modeOfInheritance(ModeOfInheritance.ANY) + .build(); + + + var gnrhr2 = TestFactory.newGeneGNRHR2(); + var secondGeneScore = GeneScore.builder() + .combinedScore(0.9) + .geneIdentifier(gnrhr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + gnrhr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + gnrhr2.addGeneScore(secondGeneScore); + + VariantEvaluation gnrhr2TopRankedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(7), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(654321), "G", "T") + .filterResults(FilterResult.pass(FilterType.FREQUENCY_FILTER)) + .compatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .build(); + gnrhr2.addVariant(gnrhr2TopRankedVariant); + + + AnalysisResults analysisResults = AnalysisResults.builder().genes(List.of(fgfr2, gnrhr2)).build(); + + GeneScoreRanker instance = new GeneScoreRanker(analysisResults, OutputSettings.defaults()); + var expected = List.of( + new GeneScoreRanker.RankedVariant(1, fgfr2TopRankedVariant, topGeneScore), + new GeneScoreRanker.RankedVariant(2, gnrhr2TopRankedVariant, secondGeneScore), + new GeneScoreRanker.RankedVariant(3, fgfr2FailedVariant, failedGeneScore) + ); + assertThat(instance.rankedVariants().collect(toList()), equalTo(expected)); + } + + @Test + public void rankedContributingVariants() { + var fgfr2 = TestFactory.newGeneFGFR2(); + var topGeneScore = GeneScore.builder() + .combinedScore(1.0) + .geneIdentifier(fgfr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + fgfr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + fgfr2.addPriorityResult(new MockPriorityResult(PriorityType.HIPHIVE_PRIORITY, fgfr2.getEntrezGeneID(), fgfr2.getGeneSymbol(), 1.0)); + fgfr2.addGeneScore(topGeneScore); + + VariantEvaluation fgfr2TopRankedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(10), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(1234567), "G", "T") + .filterResults(FilterResult.pass(FilterType.FREQUENCY_FILTER)) + .compatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .build(); + fgfr2.addVariant(fgfr2TopRankedVariant); + + + VariantEvaluation fgfr2FailedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(10), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(1234567), "G", "T") + .filterResults(FilterResult.fail(FilterType.FREQUENCY_FILTER)) + .compatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .build(); + fgfr2.addVariant(fgfr2FailedVariant); + + + var gnrhr2 = TestFactory.newGeneGNRHR2(); + var secondGeneScore = GeneScore.builder() + .combinedScore(0.9) + .geneIdentifier(gnrhr2.getGeneIdentifier()) + .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) + .build(); + gnrhr2.setCompatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)); + gnrhr2.addGeneScore(secondGeneScore); + + VariantEvaluation gnrhr2TopRankedVariant = VariantEvaluation.builder() + .with(GenomeAssembly.HG19.getContigById(7), "", Strand.POSITIVE, CoordinateSystem.oneBased(), Position.of(654321), "G", "T") + .filterResults(FilterResult.pass(FilterType.FREQUENCY_FILTER)) + .compatibleInheritanceModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .contributingModes(Set.of(ModeOfInheritance.AUTOSOMAL_DOMINANT)) + .build(); + gnrhr2.addVariant(gnrhr2TopRankedVariant); + + + AnalysisResults analysisResults = AnalysisResults.builder().genes(List.of(fgfr2, gnrhr2)).build(); + + GeneScoreRanker instance = new GeneScoreRanker(analysisResults, OutputSettings.builder().outputContributingVariantsOnly(true).build()); + var expected = List.of( + new GeneScoreRanker.RankedVariant(1, fgfr2TopRankedVariant, topGeneScore), + new GeneScoreRanker.RankedVariant(2, gnrhr2TopRankedVariant, secondGeneScore) + ); + assertThat(instance.rankedVariants().collect(toList()), equalTo(expected)); + } +} \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/JsonResultsWriterTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/JsonResultsWriterTest.java index ed7618c70..b3ad2a7e2 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/JsonResultsWriterTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/JsonResultsWriterTest.java @@ -78,6 +78,7 @@ public void setUp() { .variantScore(1.0f) .phenotypeScore(1.0f) .combinedScore(1.0f) + .pValue(0.001) .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_DOMINANT) .contributingVariants(List.of(contributingDominantAndRecessiveVariant)).build() ); @@ -91,6 +92,7 @@ public void setUp() { .variantScore(0.945f) .phenotypeScore(1.0f) .combinedScore(0.945f) + .pValue(0.0005) .modeOfInheritance(ModeOfInheritance.AUTOSOMAL_RECESSIVE) .contributingVariants(List.of(contributingDominantAndRecessiveVariant, contributingRecessiveCompHetVariant)).build() ); diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtilsTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtilsTest.java index 8b32a4ebd..1e285b4c9 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtilsTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ResultsWriterUtilsTest.java @@ -29,6 +29,8 @@ import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; @@ -57,31 +59,27 @@ * @author Jules Jacobsen */ @ExtendWith(MockitoExtension.class) -@MockitoSettings(strictness = Strictness.LENIENT) public class ResultsWriterUtilsTest { private static final String DEFAULT_OUTPUT_DIR = "results"; private final Path vcfPath = Paths.get("wibble"); @Mock - Gene passedGeneOne; + private Gene passedGeneOne; @Mock - Gene passedGeneTwo; + private Gene passedGeneTwo; @Mock - Gene failedGene; + private Gene failedGene; - @BeforeEach - public void before() { + public void registerMocks() { Mockito.when(passedGeneOne.passedFilters()).thenReturn(Boolean.TRUE); Mockito.when(passedGeneTwo.passedFilters()).thenReturn(Boolean.TRUE); Mockito.when(failedGene.passedFilters()).thenReturn(Boolean.FALSE); } private List getGenes() { - List genes = new ArrayList<>(); - genes.add(passedGeneOne); - genes.add(passedGeneTwo); - genes.add(failedGene); + List genes = List.of(passedGeneOne, passedGeneTwo, failedGene); + registerMocks(); return genes; } @@ -94,7 +92,7 @@ void testNullVcfAndEmptyOutputPrefixUsesVcfFileName() { @Test void testEmptyOutputPrefixUsesVcfFileName() { String result = ResultsWriterUtils.makeOutputFilename(Paths.get("/data/vcf/sample1_genome.vcf.gz"), "", OutputFormat.TSV_VARIANT, ModeOfInheritance.AUTOSOMAL_DOMINANT); - assertThat(result, equalTo("results/sample1_genome_exomiser_AD.variants.tsv")); + assertThat(result, equalTo("results/sample1_genome-exomiser_AD.variants.tsv")); } @Test @@ -102,7 +100,7 @@ public void testThatSpecifiedTsvFileExtensionIsPresent() { OutputFormat testedFormat = OutputFormat.TSV_GENE; OutputSettings settings = OutputSettings.builder().build(); String result = ResultsWriterUtils.makeOutputFilename(vcfPath, settings.getOutputPrefix(), testedFormat, ModeOfInheritance.AUTOSOMAL_DOMINANT); - assertThat(result, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_AD.genes.tsv")); + assertThat(result, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_AD.genes.tsv")); } @Test @@ -110,15 +108,14 @@ public void testThatSpecifiedVcfFileExtensionIsPresent() { OutputFormat testedFormat = OutputFormat.VCF; OutputSettings settings = OutputSettings.builder().build(); String result = ResultsWriterUtils.makeOutputFilename(vcfPath, settings.getOutputPrefix(), testedFormat, ModeOfInheritance.AUTOSOMAL_RECESSIVE); - assertThat(result, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_AR.vcf")); + assertThat(result, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_AR.vcf")); } @Test public void testThatSpecifiedOutputFormatDoesNotOverwriteGivenOutputPrefixFileExtension() { OutputFormat testedFormat = OutputFormat.VCF; String outputPrefix = "/user/jules/exomes/analysis/slartibartfast.xml"; - OutputSettings settings = OutputSettings.builder().outputPrefix(outputPrefix).build(); - String result = ResultsWriterUtils.makeOutputFilename(vcfPath, settings.getOutputPrefix(), testedFormat, ModeOfInheritance.X_DOMINANT); + String result = ResultsWriterUtils.makeOutputFilename(vcfPath, outputPrefix, testedFormat, ModeOfInheritance.X_DOMINANT); assertThat(result, equalTo("/user/jules/exomes/analysis/slartibartfast.xml_XD.vcf")); } @@ -127,40 +124,38 @@ public void testDefaultOutputFormatIsNotDestroyedByIncorrectFileExtensionDetecti OutputFormat testedFormat = OutputFormat.HTML; OutputSettings settings = OutputSettings.builder().build(); String result = ResultsWriterUtils.makeOutputFilename(vcfPath, settings.getOutputPrefix(), testedFormat, ModeOfInheritance.ANY); - assertThat(result, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser.html")); + assertThat(result, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser.html")); } @Test public void testOutFileNameIsCombinationOfOutPrefixAndOutFormat() { OutputFormat outFormat = OutputFormat.TSV_GENE; String outFilePrefix = "user/subdir/geno/vcf/F0000009/F0000009"; - OutputSettings settings = OutputSettings.builder().outputPrefix(outFilePrefix).build(); - String actual = ResultsWriterUtils.makeOutputFilename(vcfPath, settings.getOutputPrefix(), outFormat, ModeOfInheritance.AUTOSOMAL_DOMINANT); + String actual = ResultsWriterUtils.makeOutputFilename(vcfPath, outFilePrefix, outFormat, ModeOfInheritance.AUTOSOMAL_DOMINANT); assertThat(actual, equalTo("user/subdir/geno/vcf/F0000009/F0000009_AD.genes.tsv")); } @Test public void testOutputFileNameModeOfInheritanceExtensions() { OutputFormat testedFormat = OutputFormat.HTML; - OutputSettings settings = OutputSettings.builder().build(); String any = ResultsWriterUtils.makeOutputFilename(vcfPath, "", testedFormat, ModeOfInheritance.ANY); - assertThat(any, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser.html")); + assertThat(any, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser.html")); String autoDom = ResultsWriterUtils.makeOutputFilename(vcfPath, "", testedFormat, ModeOfInheritance.AUTOSOMAL_DOMINANT); - assertThat(autoDom, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_AD.html")); + assertThat(autoDom, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_AD.html")); String autoRec = ResultsWriterUtils.makeOutputFilename(vcfPath, "", testedFormat, ModeOfInheritance.AUTOSOMAL_RECESSIVE); - assertThat(autoRec, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_AR.html")); + assertThat(autoRec, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_AR.html")); String xDom = ResultsWriterUtils.makeOutputFilename(vcfPath, "", testedFormat, ModeOfInheritance.X_DOMINANT); - assertThat(xDom, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_XD.html")); + assertThat(xDom, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_XD.html")); String xRec = ResultsWriterUtils.makeOutputFilename(vcfPath, "", testedFormat, ModeOfInheritance.X_RECESSIVE); - assertThat(xRec, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_XR.html")); + assertThat(xRec, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_XR.html")); String mito = ResultsWriterUtils.makeOutputFilename(vcfPath, "", testedFormat, ModeOfInheritance.MITOCHONDRIAL); - assertThat(mito, equalTo(DEFAULT_OUTPUT_DIR + "/wibble_exomiser_MT.html")); + assertThat(mito, equalTo(DEFAULT_OUTPUT_DIR + "/wibble-exomiser_MT.html")); } @Test @@ -210,24 +205,29 @@ public void canMakeFilterReportsFromAnalysis() { @Test public void testMaxPassedGenesWhereMaxGenesIsZero() { - List allPassedGenes = new ArrayList<>(); - allPassedGenes.add(passedGeneOne); - allPassedGenes.add(passedGeneTwo); - assertThat(ResultsWriterUtils.getMaxPassedGenes(getGenes(), 0), equalTo(allPassedGenes)); - } - + assertThat(ResultsWriterUtils.getMaxPassedGenes(getGenes(), 0), equalTo(List.of(passedGeneOne, passedGeneTwo))); + } + @Test public void testMaxPassedGenesWhereMaxGenesIsOne() { - List onePassed = new ArrayList<>(); - onePassed.add(passedGeneOne); - assertThat(ResultsWriterUtils.getMaxPassedGenes(getGenes(), 1), equalTo(onePassed)); - } + assertThat(ResultsWriterUtils.getMaxPassedGenes(getGenes(), 1), equalTo(List.of(passedGeneOne))); + } @Test public void testMaxPassedGenesWhereMaxGenesIsGreaterThanInputSize() { - List allPassedGenes = new ArrayList<>(); - allPassedGenes.add(passedGeneOne); - allPassedGenes.add(passedGeneTwo); - assertThat(ResultsWriterUtils.getMaxPassedGenes(getGenes(), 100), equalTo(allPassedGenes)); + assertThat(ResultsWriterUtils.getMaxPassedGenes(getGenes(), 100), equalTo(List.of(passedGeneOne, passedGeneTwo))); + } + + @ParameterizedTest + @CsvSource({ + "'', " + DEFAULT_OUTPUT_DIR, + "wibble, ''", + "/, /", + "/tmp, /tmp", + "/tmp/wibble/hoopy/frood, /tmp/wibble/hoopy", + "wibble/hoopy/frood, wibble/hoopy", + }) + void testResolveOutputDirEmptyPrefixReturnsDefaultOutput(String outputPrefix, String expectedDir) { + Path outputDir = ResultsWriterUtils.resolveOutputDir(outputPrefix); + assertThat(outputDir, equalTo(Path.of(expectedDir))); } - } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ScoreRankerTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ScoreRankerTest.java new file mode 100644 index 000000000..578e29e0b --- /dev/null +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/writers/ScoreRankerTest.java @@ -0,0 +1,171 @@ +package org.monarchinitiative.exomiser.core.writers; + +import org.junit.jupiter.api.Test; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; + +class ScoreRankerTest { + + @Test + void testOne() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + } + + @Test + void testTwo() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + } + + @Test + void testThree() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(3)); + } + + @Test + void testTwoEqualValues() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(1), equalTo(1)); + } + + @Test + void testTwoEqualValuesThenThirdRanked() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(3)); + } + + @Test + void testOneThenTwoEqualValues() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + } + + @Test + void testOneThenTwoEqualValuesThenThird() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(4)); + } + + @Test + void testOneThenTwoEqualValuesThenFourthAndFifth() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(4)); + assertThat(instance.rank(0.97), equalTo(5)); + } + + @Test + void testOneThenTwoEqualValuesThenFourthFifthAndSixthRank() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(4)); + assertThat(instance.rank(0.97), equalTo(5)); + assertThat(instance.rank(0.96), equalTo(6)); + } + + @Test + void testOneThenTwoEqualValuesThenFourthFifthAndTiedSixthRank() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(4)); + assertThat(instance.rank(0.97), equalTo(5)); + assertThat(instance.rank(0.96), equalTo(6)); + assertThat(instance.rank(0.96), equalTo(6)); + } + + @Test + void testOneThenTwoEqualValuesThenFourthFifthTiedSixthThenSeventh() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(4)); + assertThat(instance.rank(0.97), equalTo(5)); + assertThat(instance.rank(0.96), equalTo(6)); + assertThat(instance.rank(0.96), equalTo(6)); + assertThat(instance.rank(0.95), equalTo(8)); + } + + @Test + void testTwoEqualValuesThenTwoThirdRanked() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(3)); + assertThat(instance.rank(0.99), equalTo(3)); + } + + @Test + void testTwoEqualValuesThenTwoThirdAndAFourthRanked() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(3)); + assertThat(instance.rank(0.99), equalTo(3)); + assertThat(instance.rank(0.98), equalTo(5)); + } + + @Test + void testTwoEqualValuesThenThreeThirdAndAFourthRanked() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(3)); + assertThat(instance.rank(0.99), equalTo(3)); + assertThat(instance.rank(0.99), equalTo(3)); + assertThat(instance.rank(0.98), equalTo(6)); + } + + @Test + void testRanksWithRounding() { + ScoreRanker instance = new ScoreRanker(4); + assertThat(instance.rank(1), equalTo(1)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.99), equalTo(2)); + assertThat(instance.rank(0.98), equalTo(4)); + assertThat(instance.rank(0.97), equalTo(5)); + assertThat(instance.rank(0.9655), equalTo(6)); + assertThat(instance.rank(0.9655), equalTo(6)); + assertThat(instance.rank(0.9655), equalTo(6)); + assertThat(instance.rank(0.9654), equalTo(9)); + } + + @Test + void testRounding() { + ScoreRanker instance = new ScoreRanker(4); +// 30 ECPAS AD 0.3316190399224868 0.5060619479045272 0.7978162169456482 +// 31 MOXD1 AD 0.3222626320487493 0.5000417413721152 0.800000011920929 +// 32 ZNF692 AD 0.32222919382960385 0.5000631910879747 0.7999590635299683 +// 33 PMVK AD 0.3222141018324461 0.5001061507355189 0.7999029159545898 +// 34 A2ML1 AD 0.3221988951499709 0.5000136651897265 0.800000011920929 +// 35 PKM AD 0.3201987097777603 0.5026839997153729 0.7959787249565125 + + assertThat(instance.rank(0.3316190399224868), equalTo(1)); + assertThat(instance.rank(0.3222626320487493), equalTo(2)); + assertThat(instance.rank(0.32222919382960385), equalTo(3)); + assertThat(instance.rank(0.3222141018324461), equalTo(3)); + assertThat(instance.rank(0.3221988951499709), equalTo(3)); + assertThat(instance.rank(0.3201987097777603), equalTo(6)); + } + +} \ No newline at end of file diff --git a/exomiser-core/src/test/resources/sql/diseaseDaoTestData.sql b/exomiser-core/src/test/resources/sql/diseaseDaoTestData.sql index ff16fe7c8..b9394e34f 100644 --- a/exomiser-core/src/test/resources/sql/diseaseDaoTestData.sql +++ b/exomiser-core/src/test/resources/sql/diseaseDaoTestData.sql @@ -1,16 +1,41 @@ -insert into disease values -('OMIM:101600', 'OMIM:176943', 'Craniofacial-skeletal-dermatologic dysplasia', 2263, 'D', 'D'), -('OMIM:101600', 'OMIM:136350', 'Pfeiffer syndrome', 2260, 'D', 'D'), -('ORPHA:11111', null, 'Test CNV disease', 2222, 'C', null), -('OMIM:123456', null, 'Test unconfirmed disease association', 3333, '?', null), -('OMIM:234567', null, 'Test susceptibility disease association', 4444, 'S', null); +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2022 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ +insert into disease +values ('OMIM:101600', 'OMIM:176943', 'Craniofacial-skeletal-dermatologic dysplasia', 2263, 'D', 'D'), + ('OMIM:101600', 'OMIM:136350', 'Pfeiffer syndrome', 2260, 'D', 'D'), + ('ORPHA:11111', null, 'Test CNV disease', 2222, 'C', null), + ('OMIM:123456', null, 'Test unconfirmed disease association', 3333, '?', null), + ('OMIM:234567', null, 'Test susceptibility disease association', 4444, 'S', null), + ('OMIM:765432', null, 'Test multi-disease gene disease 1', 5555, 'D', null), + ('OMIM:765433', null, 'Test multi-disease gene disease 2', 5555, 'D', null); -insert into disease_hp values -('OMIM:101600', 'HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,HP:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304'), -('ORPHA:11111', 'HP:0000001'), -('OMIM:123456', 'HP:0000002'), -('OMIM:234567', 'HP:0000002'); + +insert into disease_hp +values ('OMIM:101600', + 'HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,HP:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304'), + ('ORPHA:11111', 'HP:0000001'), + ('OMIM:123456', 'HP:0000002'), + ('OMIM:234567', 'HP:0000002'), + ('OMIM:765432', 'HP:0000003'), + ('OMIM:765433', 'HP:0000004'); insert into entrez2sym @@ -18,4 +43,5 @@ VALUES (2263, 'FGFR2'), (2260, 'FGFR1'), (2222, 'GENE2'), (3333, 'GENE3'), - (4444, 'GENE4'); \ No newline at end of file + (4444, 'GENE4'), + (5555, 'GENE5'); \ No newline at end of file diff --git a/exomiser-data-genome/pom.xml b/exomiser-data-genome/pom.xml index 010fda18c..759a62574 100644 --- a/exomiser-data-genome/pom.xml +++ b/exomiser-data-genome/pom.xml @@ -31,7 +31,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 diff --git a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/ResourceDownloaderTest.java b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/ResourceDownloaderTest.java index 2d5f1449d..c1c7f8dcf 100644 --- a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/ResourceDownloaderTest.java +++ b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/ResourceDownloaderTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,8 +21,7 @@ package org.monarchinitiative.exomiser.data.genome; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; +import org.junit.jupiter.api.io.TempDir; import org.monarchinitiative.exomiser.data.genome.model.AlleleResource; import org.monarchinitiative.exomiser.data.genome.model.resource.TabixAlleleResource; @@ -33,7 +32,6 @@ import static org.hamcrest.CoreMatchers.is; import static org.hamcrest.MatcherAssert.assertThat; import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junitpioneer.jupiter.TempDirectory.TempDir; /** * @author Jules Jacobsen @@ -41,7 +39,6 @@ class ResourceDownloaderTest { @Test - @ExtendWith(TempDirectory.class) void downloadWithTabixIndex(@TempDir Path tempDir) throws Exception { URL url = Paths.get("src/test/resources/test_empty.vcf.gz").toUri().toURL(); Path alleleGzipFile = tempDir.resolve("test_empty.vcf.gz"); @@ -52,7 +49,6 @@ void downloadWithTabixIndex(@TempDir Path tempDir) throws Exception { } @Test - @ExtendWith(TempDirectory.class) void downloadNonExistentFileThrowsException(@TempDir Path tempDir) throws Exception { URL url = Paths.get("src/test/resources/no_file_here.vcf.gz").toUri().toURL(); Path alleleGzipFile = tempDir.resolve("no_file_here.vcf.gz"); @@ -61,7 +57,6 @@ void downloadNonExistentFileThrowsException(@TempDir Path tempDir) throws Except } @Test - @ExtendWith(TempDirectory.class) void downloadWithoutTabixIndex(@TempDir Path tempDir) throws Exception { URL url = Paths.get("src/test/resources/test_first_ten_dbsnp.vcf.gz").toUri().toURL(); Path alleleGzipFile = tempDir.resolve("test_first_ten_dbsnp.vcf.gz"); diff --git a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/indexers/MvStoreAlleleIndexerTest.java b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/indexers/MvStoreAlleleIndexerTest.java index 8c0c68fe7..b67fdbe2b 100644 --- a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/indexers/MvStoreAlleleIndexerTest.java +++ b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/indexers/MvStoreAlleleIndexerTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2021 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -25,9 +25,7 @@ import org.h2.mvstore.MVMap; import org.h2.mvstore.MVStore; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; -import org.junitpioneer.jupiter.TempDirectory.TempDir; +import org.junit.jupiter.api.io.TempDir; import org.monarchinitiative.exomiser.core.genome.dao.serialisers.MvStoreUtil; import org.monarchinitiative.exomiser.core.model.pathogenicity.ClinVarData; import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey; @@ -393,7 +391,6 @@ public void writeAndUpdateAlleles() throws Exception { @Test - @ExtendWith(TempDirectory.class) public void processAndWriteToDisk(@TempDir Path tempDir) throws Exception { AlleleResource dbSnpResource = new DbSnpAlleleResource("test_first_ten_dbsnp", new URL("http://"), Paths.get("src/test/resources/test_first_ten_dbsnp.vcf.gz")); diff --git a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/EnsemblEnhancerParserTest.java b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/EnsemblEnhancerParserTest.java index e4fe26310..578578311 100644 --- a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/EnsemblEnhancerParserTest.java +++ b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/EnsemblEnhancerParserTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2019 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,9 +21,7 @@ package org.monarchinitiative.exomiser.data.genome.model.parsers.genome; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; -import org.junitpioneer.jupiter.TempDirectory.TempDir; +import org.junit.jupiter.api.io.TempDir; import java.nio.file.Files; import java.nio.file.Path; @@ -39,7 +37,6 @@ public class EnsemblEnhancerParserTest { @Test - @ExtendWith(TempDirectory.class) public void parse(@TempDir Path tempDir) throws Exception { Path inputFile = Paths.get("src/test/resources/genome/ensembl_enhancers.tsv"); Path outputFile = tempDir.resolve("test_ensembl_enhancers.pg"); diff --git a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/FantomEnhancerParserTest.java b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/FantomEnhancerParserTest.java index 2ddcdff40..5bd186798 100644 --- a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/FantomEnhancerParserTest.java +++ b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/FantomEnhancerParserTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2019 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,9 +21,7 @@ package org.monarchinitiative.exomiser.data.genome.model.parsers.genome; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; -import org.junitpioneer.jupiter.TempDirectory.TempDir; +import org.junit.jupiter.api.io.TempDir; import java.nio.file.Files; import java.nio.file.Path; @@ -39,7 +37,6 @@ public class FantomEnhancerParserTest { @Test - @ExtendWith(TempDirectory.class) public void parse(@TempDir Path tempDir) throws Exception { Path inputFile = Paths.get("src/test/resources/genome/fantom_enhancers.bed"); Path outputFile = tempDir.resolve("test_fantom_enhancers.pg"); diff --git a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/FantomEnhancerToBedConverterTest.java b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/FantomEnhancerToBedConverterTest.java index 5b77b606b..4ee74ec5c 100644 --- a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/FantomEnhancerToBedConverterTest.java +++ b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/FantomEnhancerToBedConverterTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2019 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,9 +21,7 @@ package org.monarchinitiative.exomiser.data.genome.model.parsers.genome.liftover; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; -import org.junitpioneer.jupiter.TempDirectory.TempDir; +import org.junit.jupiter.api.io.TempDir; import java.nio.file.Files; import java.nio.file.Path; @@ -39,7 +37,6 @@ public class FantomEnhancerToBedConverterTest { @Test - @ExtendWith(TempDirectory.class) public void run(@TempDir Path tempDir) throws Exception { Path inputFile = Paths.get("src/test/resources/genome/liftover"); Path expectedOutputFile = Paths.get("src/test/resources/genome/liftover/hg19_fantom_permissive_enhancer_usage.bed"); diff --git a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/TadHg38BedToPgConverterTest.java b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/TadHg38BedToPgConverterTest.java index 53362cbc4..59e09864f 100644 --- a/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/TadHg38BedToPgConverterTest.java +++ b/exomiser-data-genome/src/test/java/org/monarchinitiative/exomiser/data/genome/model/parsers/genome/liftover/TadHg38BedToPgConverterTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2019 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,9 +21,7 @@ package org.monarchinitiative.exomiser.data.genome.model.parsers.genome.liftover; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junitpioneer.jupiter.TempDirectory; -import org.junitpioneer.jupiter.TempDirectory.TempDir; +import org.junit.jupiter.api.io.TempDir; import java.nio.file.Files; import java.nio.file.Path; @@ -42,7 +40,6 @@ public class TadHg38BedToPgConverterTest { @Test - @ExtendWith(TempDirectory.class) public void testMerge(@TempDir Path tempDir) throws Exception { Path inputFile = Paths.get("src/test/resources/genome/liftover/test_split_tad.bed"); Path expectedOutputFile = Paths.get("src/test/resources/genome/liftover/test_expected_tad.bed"); diff --git a/exomiser-data-phenotype/README.md b/exomiser-data-phenotype/README.md index 821bc6e14..c5f141417 100644 --- a/exomiser-data-phenotype/README.md +++ b/exomiser-data-phenotype/README.md @@ -3,40 +3,29 @@ The Exomiser - Phenotype DB build This maven project is used to build the Exomiser phenotype database used by the Exomiser. -Currently the build relies on a preliminary OWLSim2 file build which in future versions will -be incorporated into this codebase: - -1. OWLTools: - ```git clone https://github.com/owlcollab/owltools.git``` or ```git pull``` - ```cd owltools/OWLTools-Parent - mvn clean install - cd ../../ - chmod +x owltools/OWLTools-Runner/bin/owltools - ``` - Add ```owltools/OWLTools-Oort/bin/ontology-release-runner``` and ```owltools/OWLTools-Runner/bin/owltools``` to path -2. Clone Monarch OwlSim: -```git clone https://github.com/monarch-initiative/monarch-owlsim-data or git pull``` -3. Clone the HPO: -```git clone https://github.com/obophenotype/human-phenotype-ontology/ or git pull``` -4. Clone the MPO: +N.B. Now all run from apocrita (home folder on login.hpc.qmul.ac.uk) and from owltools installation at /data/WHRI-Phenogenomics/software/opt/owltools/owltools. To install from scratch use + +```git clone https://github.com/owlcollab/owltools.git +cd owltools/OWLTools-Parent +mvn clean install +cd ../../ +chmod +x owltools/OWLTools-Runner/bin/owltools ``` - git clone https://github.com/obophenotype/mammalian-phenotype-ontology/ or git pull - cd mammalian-phenotype-ontology/src/ontology - make mp.owl - cd ../../../ - ``` -5. Clone uPheno: -```git clone https://github.com/obophenotype/upheno``` -6. Get ZPO: -```wget http://compbio.charite.de/jenkins/job/zp-owl/lastSuccessfulBuild/artifact/zp.owl``` -7. Replace human phenotype annotation files in Monarch git repo as these include common disease and merge together some + +Add ```owltools/OWLTools-Oort/bin/ontology-release-runner``` and ```owltools/OWLTools-Runner/bin/owltools``` to path + +1. ```git clone https://github.com/obophenotype/upheno``` or ```git pull``` +2. ```wget http://purl.obolibrary.org/obo/mp.owl``` +3. ```wget http://purl.obolibrary.org/obo/hp.owl``` +4. ```wget http://purl.obolibrary.org/obo/zp.owl``` +5. Replace human phenotype annotation files in Monarch git repo as these include common disease and merge together some OMIM and Orphanet entries in a way that does not represent the data in our db. Requires logic like: ```perl -system("wget http://purl.obolibrary.org/obo/hp/hpoa/phenotype_annotation.tab:"); +system("wget http://purl.obolibrary.org/obo/hp/hpoa/phenotype_annotation.tab"); open(IN,"phenotype_annotation.tab"); -open(OUT1,">monarch-owlsim-data/data/Homo_sapiens/Hs_disease_phenotype.txt"); -open(OUT2,">monarch-owlsim-data/data/Homo_sapiens/Hs_disease_labels.txt"); +open(OUT1,">Hs_disease_phenotype.txt"); +open(OUT2,">Hs_disease_labels.txt"); my %data; while (my $line = ){ my @line = split(/\t/,$line); @@ -60,29 +49,27 @@ close OUT1; close OUT2; ``` -8. Run owltools commands: - -TODO: switch to using archive monarch data for all builds +6. ```wget https://archive.monarchinitiative.org/latest/owlsim/data/Mus_musculus/Mm_gene_phenotype.txt``` +7. ```wget https://archive.monarchinitiative.org/latest/owlsim/data/Mus_musculus/Mm_gene_labels.txt``` +8. ```wget wget https://archive.monarchinitiative.org/latest/owlsim/data/Danio_rerio/Dr_gene_phenotype.txt``` +9. ```wget wget https://archive.monarchinitiative.org/latest/owlsim/data/Danio_rerio/Dr_gene_labels.txt``` +10. Run owltools commands: ``` +owltools --catalog-xml upheno/catalog-v001.xml mp.owl hp.owl zp.owl Mm_gene_phenotype.txt Hs_disease_phenotype.txt Dr_gene_phenotype.txt --merge-imports-closure --load-instances Mm_gene_phenotype.txt --load-labels Mm_gene_labels.txt --merge-support-ontologies -o Mus_musculus-all.owl -wget https://archive.monarchinitiative.org/latest/owlsim/data/Mus_musculus/Mm_gene_phenotype.txt -wget https://archive.monarchinitiative.org/latest/owlsim/data/Mus_musculus/Mm_gene_labels.txt - +owltools --catalog-xml upheno/catalog-v001.xml mp.owl hp.owl zp.owl Mm_gene_phenotype.txt Hs_disease_phenotype.txt Dr_gene_phenotype.txt --merge-imports-closure --load-instances Hs_disease_phenotype.txt --load-labels Hs_disease_labels.txt --merge-support-ontologies -o Homo_sapiens-all.owl -owltools --catalog-xml upheno/catalog-v001.xml mammalian-phenotype-ontology/src/ontology/mp.owl human-phenotype-ontology/hp.owl zp.owl Mm_gene_phenotype.txt monarch-owlsim-data/data/Homo_sapiens/Hs_disease_phenotype.txt monarch-owlsim-data/data/Danio_rerio/Dr_gene_phenotype.txt --merge-imports-closure --load-instances Mm_gene_phenotype.txt --load-labels Mm_gene_labels.txt --merge-support-ontologies -o Mus_musculus-all.owl - -owltools --catalog-xml upheno/catalog-v001.xml mammalian-phenotype-ontology/src/ontology/mp.owl human-phenotype-ontology/hp.owl zp.owl Mm_gene_phenotype.txt monarch-owlsim-data/data/Homo_sapiens/Hs_disease_phenotype.txt monarch-owlsim-data/data/Danio_rerio/Dr_gene_phenotype.txt --merge-imports-closure --load-instances monarch-owlsim-data/data/Homo_sapiens/Hs_disease_phenotype.txt --load-labels monarch-owlsim-data/data/Homo_sapiens/Hs_disease_labels.txt --merge-support-ontologies -o Homo_sapiens-all.owl - -owltools --catalog-xml upheno/catalog-v001.xml upheno/vertebrate.owl mammalian-phenotype-ontology/src/ontology/mp.owl human-phenotype-ontology/hp.owl zp.owl Mm_gene_phenotype.txt monarch-owlsim-data/data/Homo_sapiens/Hs_disease_phenotype.txt monarch-owlsim-data/data/Danio_rerio/Dr_gene_phenotype.txt --load-instances monarch-owlsim-data/data/Danio_rerio/Dr_gene_phenotype.txt --load-labels monarch-owlsim-data/data/Danio_rerio/Dr_gene_labels.txt --load-instances monarch-owlsim-data/data/Homo_sapiens/Hs_disease_phenotype.txt --load-labels monarch-owlsim-data/data/Homo_sapiens/Hs_disease_labels.txt --merge-support-ontologies --merge-imports-closure --remove-disjoints --remove-equivalent-to-nothing-axioms --run-reasoner -r elk --assert-implied --make-super-slim HP,ZP -o hp-zp-all.owl +owltools --catalog-xml upheno/catalog-v001.xml upheno/vertebrate.owl mp.owl hp.owl zp.owl Mm_gene_phenotype.txt Hs_disease_phenotype.txt Dr_gene_phenotype.txt --load-instances Dr_gene_phenotype.txt --load-labels Dr_gene_labels.txt --load-instances Hs_disease_phenotype.txt --load-labels Hs_disease_labels.txt --merge-support-ontologies --merge-imports-closure --remove-disjoints --remove-equivalent-to-nothing-axioms --run-reasoner -r elk --assert-implied --make-super-slim HP,ZP -o hp-zp-all.owl owltools Homo_sapiens-all.owl --merge-import-closure --remove-disjoints --remove-equivalent-to-nothing-axioms -o Homo_sapiens-all-merged.owl + owltools Mus_musculus-all.owl --merge-import-closure --remove-disjoints --remove-equivalent-to-nothing-axioms -o Mus_musculus-all-merged.owl -owltools hp-zp-all.owl --merge-import-closure --remove-disjoints --remove-equivalent-to-nothing-axioms -o hp-zp-all-merged.owl +owltools hp-zp-all.owl --merge-import-closure --remove-disjoints --remove-equivalent-to-nothing-axioms -o hp-zp-all-merged.owl ``` -9. Run final commands on high mem machines on apocrita after scp *-merged.owl and upheno/hp-mp/mp_hp-align-equiv.owl to aprocrita (home folder on login.hpc.qmul.ac.uk) +12. Run final commands on high mem machines on apocrita (home folder on login.hpc.qmul.ac.uk) ``` qsub owltools_hp_hp.sh @@ -91,14 +78,14 @@ qsub owltools_hp_zp.sh ``` -10. Running the build. More detail below but essentially +13. Running the build. More detail below but essentially ``` gzip hp-*-mapping-cache.txt cd /data/WHRI-Phenogenomics/projects/Damian/ mkdir -p 2109-phenotype-build/resources cp ~/hp-*cache.txt.gz 2109-phenotype-build/resources -java -jar exomiser-data-phenotype-13.0.0-SNAPSHOT.jar --phenotype.build-version=2109 --phenotype.build-dir=/data/WHRI-phenogemonics/projects/Damian/2109-phenotype-build +java -Djava.io.tmpdir=/data/WHRI-Phenogenomics/projects/Damian -jar exomiser-data-phenotype-13.0.0-SNAPSHOT.jar --phenotype.build-version=2109 --phenotype.build-dir=/data/WHRI-Phenogenomics/projects/Damian/2109-phenotype-build ``` diff --git a/exomiser-data-phenotype/pom.xml b/exomiser-data-phenotype/pom.xml index 35e06b156..74d479195 100644 --- a/exomiser-data-phenotype/pom.xml +++ b/exomiser-data-phenotype/pom.xml @@ -31,7 +31,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 diff --git a/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneMoiComparisonStepTest.java b/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneMoiComparisonStepTest.java index 688d25ba5..c1037b608 100644 --- a/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneMoiComparisonStepTest.java +++ b/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneMoiComparisonStepTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -21,9 +21,7 @@ package org.monarchinitiative.exomiser.data.phenotype.processors.steps.disease; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; -import org.junitpioneer.jupiter.TempDirectory; import org.monarchinitiative.exomiser.data.phenotype.processors.Resource; import org.monarchinitiative.exomiser.data.phenotype.processors.model.disease.DiseaseGeneMoiComparison; import org.monarchinitiative.exomiser.data.phenotype.processors.writers.OutputLineWriter; @@ -35,7 +33,6 @@ /** * @author Jules Jacobsen */ -@ExtendWith(TempDirectory.class) class DiseaseGeneMoiComparisonStepTest { @Test diff --git a/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneStepTest.java b/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneStepTest.java index 17bef458a..3a8c1ea83 100644 --- a/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneStepTest.java +++ b/exomiser-data-phenotype/src/test/java/org/monarchinitiative/exomiser/data/phenotype/processors/steps/disease/DiseaseGeneStepTest.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2020 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -22,9 +22,7 @@ import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; -import org.junitpioneer.jupiter.TempDirectory; import org.monarchinitiative.exomiser.data.phenotype.processors.Resource; import org.monarchinitiative.exomiser.data.phenotype.processors.model.disease.DiseaseGene; import org.monarchinitiative.exomiser.data.phenotype.processors.writers.OutputLineWriter; @@ -37,18 +35,17 @@ /** * @author Jules Jacobsen */ -@ExtendWith(TempDirectory.class) class DiseaseGeneStepTest { @Disabled @Test void testRun(@TempDir Path tempDir) { Path dataDir = Path.of("src/test/resources/data"); - Resource phenotypeAnnotationsResource = Resource.of(dataDir, "phenotype_annotation.tab"); + Resource phenotypeAnnotationsResource = Resource.of(dataDir, "phenotype_annotation_test.tab"); Resource geneMap2Resource = Resource.of(dataDir, "genemap2.txt"); - Resource mimToGeneResource = Resource.of(dataDir, "mim2gene.txt"); + Resource mimToGeneResource = Resource.of(dataDir, "mim2gene_test.txt"); Resource product1Resource = Resource.of(dataDir, "en_product1_test.xml"); - Resource product6Resource = Resource.of(dataDir, "en_product6.xml"); + Resource product6Resource = Resource.of(dataDir, "en_product6_test.xml"); Resource product9Resource = Resource.of(dataDir, "en_product9_ages.xml"); Path diseasePg = tempDir.resolve("disease.pg"); diff --git a/exomiser-rest-prioritiser/pom.xml b/exomiser-rest-prioritiser/pom.xml index dad8d027e..1e6c5ef42 100644 --- a/exomiser-rest-prioritiser/pom.xml +++ b/exomiser-rest-prioritiser/pom.xml @@ -27,7 +27,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 exomiser-rest-prioritiser diff --git a/exomiser-spring-boot-autoconfigure/pom.xml b/exomiser-spring-boot-autoconfigure/pom.xml index c6a3e5b70..2a6639ac8 100644 --- a/exomiser-spring-boot-autoconfigure/pom.xml +++ b/exomiser-spring-boot-autoconfigure/pom.xml @@ -35,7 +35,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 diff --git a/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfiguration.java b/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfiguration.java index 2025480cb..64c955362 100644 --- a/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfiguration.java +++ b/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfiguration.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2018 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -37,6 +37,7 @@ @ConditionalOnClass({Exomiser.class, AnalysisFactory.class}) @EnableConfigurationProperties({ExomiserProperties.class}) @Import({ + ExomiserConfigReporter.class, PrioritiserAutoConfiguration.class, GenomeAnalysisServiceAutoConfiguration.class }) diff --git a/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserConfigReporter.java b/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserConfigReporter.java new file mode 100644 index 000000000..89a1fdab4 --- /dev/null +++ b/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserConfigReporter.java @@ -0,0 +1,60 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2022 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.autoconfigure; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.core.env.Environment; +import org.springframework.stereotype.Component; + +@Component +public class ExomiserConfigReporter { + + private static final Logger logger = LoggerFactory.getLogger(ExomiserConfigReporter.class); + + public ExomiserConfigReporter(ExomiserProperties exomiserProperties, Environment environment) { + + var dataDir = propertyOrDefault(exomiserProperties.getDataDirectory(), "-"); + logger.info("exomiser.data-directory: {}", dataDir); + + var hg19Properties = exomiserProperties.getHg19(); + var hg19DataVersion = propertyOrDefault(hg19Properties.getDataVersion(), "-"); + logger.info("exomiser.hg19.data-version: {}", hg19DataVersion); + + var hg38Properties = exomiserProperties.getHg38(); + var hg38DataVersion = propertyOrDefault(hg38Properties.getDataVersion(), "-"); + logger.info("exomiser.hg38.data-version: {}", hg38DataVersion); + + var phenoProperties = exomiserProperties.getPhenotype(); + var phenoDataVersion = propertyOrDefault(phenoProperties.getDataVersion(), "-"); + logger.info("exomiser.phenotype.data-version: {}", phenoDataVersion); + + String cacheType = environment.getProperty("spring.cache.type"); + if (cacheType != null && !cacheType.equals("none")) { + logger.info("spring.cache.type: {}", cacheType); + } + } + + private String propertyOrDefault(String property, String defaultValue) { + return property.isEmpty() ? defaultValue : property; + } + +} diff --git a/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.java b/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.java index 15311599e..8243b5604 100644 --- a/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.java +++ b/exomiser-spring-boot-autoconfigure/src/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2017 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -48,6 +48,9 @@ public class GenomeAnalysisServiceAutoConfiguration { public GenomeAnalysisServiceProvider genomeAnalysisServiceProvider(GenomeAnalysisService... genomeAnalysisServices) { Arrays.stream(genomeAnalysisServices) .forEach(service -> logger.info("Configured {} genome analysis service", service.getGenomeAssembly())); + if (genomeAnalysisServices.length == 0) { + throw new IllegalStateException("No " + GenomeAnalysisService.class.getName() + " instance provided! You must specify at least one exomiser genome assembly data version in the application.properties file."); + } return new GenomeAnalysisServiceProvider(genomeAnalysisServices); } diff --git a/exomiser-spring-boot-autoconfigure/src/test/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfigurationTest.java b/exomiser-spring-boot-autoconfigure/src/test/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfigurationTest.java new file mode 100644 index 000000000..a8b843bfa --- /dev/null +++ b/exomiser-spring-boot-autoconfigure/src/test/java/org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfigurationTest.java @@ -0,0 +1,80 @@ +/* + * The Exomiser - A tool to annotate and prioritize genomic variants + * + * Copyright (c) 2016-2022 Queen Mary University of London. + * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +package org.monarchinitiative.exomiser.autoconfigure.genome; + +import org.junit.jupiter.api.Test; +import org.monarchinitiative.exomiser.autoconfigure.AbstractAutoConfigurationTest; +import org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider; +import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; +import org.springframework.beans.factory.BeanCreationException; +import org.springframework.boot.autoconfigure.ImportAutoConfiguration; +import org.springframework.cache.CacheManager; +import org.springframework.cache.support.NoOpCacheManager; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.util.Set; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.junit.jupiter.api.Assertions.assertThrows; + +public class GenomeAnalysisServiceAutoConfigurationTest extends AbstractAutoConfigurationTest { + + @Test + public void genomeAnalysisServiceProviderFailsWithNoGenomeAnalysisServiceSpecified() { + BeanCreationException result = assertThrows(BeanCreationException.class, () -> load(EmptyConfiguration.class, TEST_DATA_ENV)); + assertThat(result.getRootCause().getMessage(), equalTo("No org.monarchinitiative.exomiser.core.genome.GenomeAnalysisService instance provided! You must specify at least one exomiser genome assembly data version in the application.properties file.")); + } + + @Test + public void genomeAnalysisServiceProviderHg19Only() { + load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710"); + + GenomeAnalysisServiceProvider genomeAnalysisServiceProvider = (GenomeAnalysisServiceProvider) context.getBean("genomeAnalysisServiceProvider"); + assertThat(genomeAnalysisServiceProvider.getProvidedAssemblies(), equalTo(Set.of(GenomeAssembly.HG19))); + } + + @Test + public void genomeAnalysisServiceProviderHg38Only() { + load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg38.data-version=1710"); + + GenomeAnalysisServiceProvider genomeAnalysisServiceProvider = (GenomeAnalysisServiceProvider) context.getBean("genomeAnalysisServiceProvider"); + assertThat(genomeAnalysisServiceProvider.getProvidedAssemblies(), equalTo(Set.of(GenomeAssembly.HG38))); + } + + @Test + public void genomeAnalysisServiceProviderAllAssemblies() { + load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710", "exomiser.hg38.data-version=1710"); + + GenomeAnalysisServiceProvider genomeAnalysisServiceProvider = (GenomeAnalysisServiceProvider) context.getBean("genomeAnalysisServiceProvider"); + assertThat(genomeAnalysisServiceProvider.getProvidedAssemblies(), equalTo(Set.of(GenomeAssembly.HG19, GenomeAssembly.HG38))); + } + + @Configuration + @ImportAutoConfiguration(value = GenomeAnalysisServiceAutoConfiguration.class) + protected static class EmptyConfiguration { + @Bean + public CacheManager cacheManager() { + return new NoOpCacheManager(); + } + } +} \ No newline at end of file diff --git a/exomiser-spring-boot-starter/pom.xml b/exomiser-spring-boot-starter/pom.xml index 803f417be..c0dfe95bf 100644 --- a/exomiser-spring-boot-starter/pom.xml +++ b/exomiser-spring-boot-starter/pom.xml @@ -28,7 +28,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 exomiser-spring-boot-starter diff --git a/exomiser-spring-boot-test/pom.xml b/exomiser-spring-boot-test/pom.xml index cd4c574c4..152e92846 100644 --- a/exomiser-spring-boot-test/pom.xml +++ b/exomiser-spring-boot-test/pom.xml @@ -27,7 +27,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 exomiser-spring-boot-test diff --git a/exomiser-web/README.md b/exomiser-web/README.md index 823fe9c72..6e7aebde4 100644 --- a/exomiser-web/README.md +++ b/exomiser-web/README.md @@ -50,8 +50,68 @@ If the instance *is* running in a clinically-compliant setting, the banner can b ```properties exomiser.web.clinical-instance=true ``` + or override this by launching the application using the command-line option ```shell --exomiser.web.clinical-instance=true -``` \ No newline at end of file +``` + +## Running the Docker image + +To run the image you will need the standard exomiser directory layout to mount as separate volumes and supply +an `application.properties` file or environmental variables to point to the data required _e.g._ + +```shell +docker run \ +-v "/data/exomiser-data:/exomiser-data" \ +-v "/opt/exomiser/exomiser-config/:/exomiser" \ +-p 8080:8080 \ +exomiser/exomiser-web:latest \ +--spring.config.location=/exomiser/application.properties +``` + +or using Spring configuration arguments instead of the `application.properties`: + +```shell +docker run -v "/data/exomiser-data:/exomiser-data" \ +-p 8080:8080 \ +exomiser/exomiser-web:latest \ +--exomiser.data-directory=/exomiser-data \ +--exomiser.hg19.data-version=2109 \ +--exomiser.hg19.variant-white-list-path=2109_hg19_clinvar_whitelist.tsv.gz \ +--exomiser.phenotype.data-version=2109 +``` + +Here the contents of `/opt/exomiser/exomiser-config` is simply the `application.properties` file. + +```shell +$ tree /opt/exomiser/exomiser-config/ +exomiser-config/ +└──application.properties +``` + +and the `application.properties` contents for hg38: + +```yaml +exomiser.data-directory=/exomiser-data + +## hg38 config +exomiser.hg38.data-version=2109 +#exomiser.hg38.remm-path=${exomiser.data-directory}/remm/ReMM.v0.3.1.post1.hg38.tsv.gz +#exomiser.hg38.local-frequency-path=${exomiser.data-directory}/local/local_frequency_test_hg38.tsv.gz +exomiser.hg38.variant-white-list-path=${exomiser.hg38.data-version}_hg38_clinvar_whitelist.tsv.gz + +## phenotype config +exomiser.phenotype.data-version=2109 +``` + +Resizing the JVM +----------------------- + +Running a WGS analysis can take a few GB of RAM, depending on the size of the sample in question. If you need to +increase the max memory of the JVM, include the following environment variable: + +```shell +-e JAVA_TOOL_OPTIONS="-Xmx8G" +``` diff --git a/exomiser-web/pom.xml b/exomiser-web/pom.xml index de7c66349..4b2a1d242 100644 --- a/exomiser-web/pom.xml +++ b/exomiser-web/pom.xml @@ -31,7 +31,7 @@ org.monarchinitiative.exomiser exomiser - 13.0.1 + 13.1.0 @@ -140,6 +140,43 @@ + + com.google.cloud.tools + jib-maven-plugin + 3.2.0 + + + install + + buildTar + + + + + + ${docker.base.image} + + + amd64 + linux + + + + + ${project.artifactId}:${project.parent.version} + + ${project.parent.version} + latest + + + + + /exomiser-data + /exomiser + + + + diff --git a/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/ExomiserWebApp.java b/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/ExomiserWebApp.java index 0cb278bb6..f1f185c16 100644 --- a/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/ExomiserWebApp.java +++ b/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/ExomiserWebApp.java @@ -1,7 +1,7 @@ /* * The Exomiser - A tool to annotate and prioritize genomic variants * - * Copyright (c) 2016-2017 Queen Mary University of London. + * Copyright (c) 2016-2022 Queen Mary University of London. * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. * * This program is free software: you can redistribute it and/or modify @@ -22,11 +22,12 @@ import org.springframework.boot.SpringApplication; import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration; /** * @author Jules Jacobsen */ -@SpringBootApplication +@SpringBootApplication(exclude = {DataSourceAutoConfiguration.class}) public class ExomiserWebApp { public static void main(String[] args) { diff --git a/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/controller/SubmitJobController.java b/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/controller/SubmitJobController.java index 1af1e87c2..aef912b26 100644 --- a/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/controller/SubmitJobController.java +++ b/exomiser-web/src/main/java/org/monarchinitiative/exomiser/web/controller/SubmitJobController.java @@ -38,10 +38,7 @@ import org.monarchinitiative.exomiser.core.filters.FilterReport; import org.monarchinitiative.exomiser.core.genome.GenomeAssembly; import org.monarchinitiative.exomiser.core.genome.VcfFiles; -import org.monarchinitiative.exomiser.core.model.Gene; -import org.monarchinitiative.exomiser.core.model.GeneticInterval; -import org.monarchinitiative.exomiser.core.model.Pedigree; -import org.monarchinitiative.exomiser.core.model.VariantEvaluation; +import org.monarchinitiative.exomiser.core.model.*; import org.monarchinitiative.exomiser.core.model.frequency.FrequencySource; import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource; import org.monarchinitiative.exomiser.core.prioritisers.PriorityType; @@ -64,6 +61,7 @@ import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.text.DecimalFormat; import java.util.*; import static org.monarchinitiative.exomiser.core.prioritisers.PriorityType.*; @@ -314,12 +312,28 @@ private void buildResultsModel(Model model, Analysis analysis, AnalysisResults a List passedGenes = ResultsWriterUtils.getMaxPassedGenes(sampleGenes, maxGenes); model.addAttribute("genes", passedGenes); - //this will change the links to the relevant resource. +//this will change the links to the relevant resource. // For the time being we're going to maintain the original behaviour (UCSC) // Need to wire it up through the system or it might be easiest to autodetect this from the transcripts of passed variants. // One of UCSC, ENSEMBL or REFSEQ - model.addAttribute("transcriptDb", "UCSC"); + var transcriptDb = analysisResults.getContributingVariants().stream() + .flatMap(variantEvaluation -> variantEvaluation.getTranscriptAnnotations().stream()) + .findFirst() + .map(TranscriptAnnotation::getAccession) + .map(value -> { + if (value.startsWith("ENST")) { + return "ENSEMBL"; + } else if (value.startsWith("uc")) { + return "UCSC"; + } else if (value.startsWith("NM") || value.startsWith("NR") || value.startsWith("XM") || value.startsWith("XR")) { + return "REFSEQ"; + } + return ""; + }) + .orElse("ENSEMBL"); + model.addAttribute("transcriptDb", transcriptDb); model.addAttribute("variantRankComparator", new VariantEvaluation.RankBasedComparator()); + model.addAttribute("pValueFormatter", new DecimalFormat("0.0E0")); } private int numGenesPassedFilters(List genes) { diff --git a/exomiser-web/src/main/resources/application.properties b/exomiser-web/src/main/resources/application.properties index 922765be8..167a386d7 100644 --- a/exomiser-web/src/main/resources/application.properties +++ b/exomiser-web/src/main/resources/application.properties @@ -1,8 +1,8 @@ # # The Exomiser - A tool to annotate and prioritize genomic variants # -# Copyright (c) 2016-2021 Queen Mary University of London. -# Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. +# Copyright (c) 2016-2022 Queen Mary University of London. +# Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd. # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as @@ -42,6 +42,9 @@ exomiser.web.max-genes=30 #If this instance is running on hardware located in a clinical setting where patient data is #protected according to local policy, this can be set to true to disable the warning on the analysis submission page. exomiser.web.clinical-instance=false - +# Configure the Exomiser properties - use the exomiser-cli application.properties as a template exomiser.data-directory=${data.dir} +#exomiser.hg19.data-version=2109 +#exomiser.hg19.variant-white-list-path=${exomiser.hg19.data-version}_hg19_clinvar_whitelist.tsv.gz +#exomiser.phenotype.data-version=2109 exomiser.phenotype.random-walk-preload=true \ No newline at end of file diff --git a/exomiser-web/src/main/resources/templates/results.html b/exomiser-web/src/main/resources/templates/results.html index 5783f9a2e..ed272fe59 100644 --- a/exomiser-web/src/main/resources/templates/results.html +++ b/exomiser-web/src/main/resources/templates/results.html @@ -128,8 +128,8 @@

MISSENSE - - chr10:g.123256215T>G [0/1] + chr10:g.123256215T>G [0/1] + 10 Mb rs141235720 @@ -177,12 +177,155 @@

Analyzed samples

class="alert-link">download from the FTP site.
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-

+

FGFR2 @@ -195,16 +338,15 @@

Analyzed samples

-

Exomiser Score: 1.005 +

Exomiser Score: 1.00 + (p=0.1e-4)

-

Phenotype Score: 1.005 -

+

Phenotype Score: 1.00

-

Variant Score: 1.005 -

+

Variant Score: 1.00

@@ -222,104 +364,355 @@

Variant Score: -
-
- Top ranked variants: -
-
+
+ th:unless="${#sets.isEmpty(gene.getCompatibleInheritanceModes())}">
- MISSENSE - - chr10:g.123256215T>G [0/1] - - rs141235720 - - + Gene scores under compatible inheritance modes:
-
- ClinVar: - - BENIGN - BENIGN_OR_LIKELY_BENIGN - LIKELY_BENIGN - LIKELY_PATHOGENIC - PATHOGENIC_OR_LIKELY_PATHOGENIC - PATHOGENIC - UNCERTAIN_SIGNIFICANCE - - (criteria_provided,_single_submitter) - - +
+ +
+ + +
+
+
+

+ AUTOSOMAL_DOMINANT + + + + + + + +

+
+
+

Exomiser Score: + 1.005 + (p=0.1e-4) +

+
+
+

Phenotype Score: 1.005 +

+
+
+

Variant Score: 1.005 +

+
+
-
- Variant - score: 0.600 - CONTRIBUTING VARIANT -
-
Transcripts:
-
- FGFR2:uc001lfg.4:c.518A>C:p.E173A - FGFR2:ENST00000429361.1:c.518A>C:p.E173A - FGFR2:NM_000141:c.518A>C:p.E173A -
-
+
+
+
+ + No phenotype matches to diseases with this MOI. + +
+ +
+ Phenotype matches to diseases consistent with this MOI: +
+ + + + + +
+ Phenotypic similarity 0.957 to OMIM:101600 APERT SYNDROME +
+ +
+
+
-
- -
-
Pathogenicity Data:
-
- 1.00 -
-
No - pathogenicity data -
-
Mutation Taster: 0.999 (P) -
-
+
+
+
+ Variants contributing to score: +
+
+
+
+ MISSENSE + SNV + chr10:g.123256215T>G [0/1] + 10 Mb + + rs141235720 + + esv3097123 + + nsv819538 + + dgv1891n106 + + 12345 + + +
+
+ Exomiser ACMG: + + BENIGN + LIKELY_BENIGN + LIKELY_PATHOGENIC + PATHOGENIC + UNCERTAIN_SIGNIFICANCE + NOT_AVAILABLE + + [PVS1, BP2] + + +
+
+ ClinVar: + + BENIGN + BENIGN_OR_LIKELY_BENIGN + LIKELY_BENIGN + LIKELY_PATHOGENIC + PATHOGENIC_OR_LIKELY_PATHOGENIC + PATHOGENIC + UNCERTAIN_SIGNIFICANCE + + (criteria_provided,_single_submitter) + + +
+
+ Variant + score: 0.600 + CONTRIBUTING VARIANT + WHITELIST VARIANT +
+
Transcripts:
+
+ FGFR2:uc001lfg.4:c.518A>C:p.E173A + FGFR2:ENST00000429361.1:c.518A>C:p.E173A + FGFR2:NM_000141:c.518A>C:p.E173A +
+
+
+
+ +
+
Pathogenicity Data:
+
1.00 +
+
No + pathogenicity data +
+
Mutation Taster: 0.999 (P) +
+
+
+
+ +
+
Frequency Data:
+
No frequency data
+
+ 1000Genomes: 0.02% +
+
+
+
+
+ +
+ +
+
+ Other passed variants: +
-
- -
-
Frequency Data:
-
No frequency - data -
-
- 1000Genomes: 0.02% -
-
+
+
+ MISSENSE + SNV + chr10:g.123256215T>G [0/1] + 10 Mb + + rs141235720 + + esv3097123 + + nsv819538 + + dgv1891n106 + + 12345 + + +
+ + + + + + + + + + + + + + + + + + + + + + +
+ ClinVar: + + BENIGN + BENIGN_OR_LIKELY_BENIGN + LIKELY_BENIGN + LIKELY_PATHOGENIC + PATHOGENIC_OR_LIKELY_PATHOGENIC + PATHOGENIC + UNCERTAIN_SIGNIFICANCE + + (criteria_provided,_single_submitter) + + +
+
+ Variant + score: 0.600 + WHITELIST VARIANT +
+
Transcripts:
+
+ FGFR2:uc001lfg.4:c.518A>C:p.E173A + FGFR2:ENST00000429361.1:c.518A>C:p.E173A + FGFR2:NM_000141:c.518A>C:p.E173A +
+
+
+
+ +
+
Pathogenicity Data:
+
1.00 +
+
No + pathogenicity data +
+
Mutation Taster: 0.999 (P) +
+
+
+
+ +
+
Frequency Data:
+
No frequency data
+
+ 1000Genomes: 0.02% +
+
+
-
+
-

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diff --git a/pom.xml b/pom.xml index 01c478258..308491886 100644 --- a/pom.xml +++ b/pom.xml @@ -2,7 +2,7 @@ org.mockito @@ -253,26 +250,6 @@ - - - - - - - - - - - - - - - - - - - - org.sonarsource.scanner.maven sonar-maven-plugin