New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Outdated GO terms for enrichment analysis #12

Open

mgalland opened this issue Jun 18, 2021 · 1 comment

Labels

Member

mgalland commented Jun 18, 2021

Apparently, the GO terms in the org.At.tair.db Bioconductor package (release 3.10) are outdated.

In this package, there are 27,416 Arabidopsis genes for a total of 4837 GO terms.

columns(org.At.tair.db)
 [1] "ARACYC"       "ARACYCENZYME" "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL" 
 [7] "GENENAME"     "GO"           "GOALL"        "ONTOLOGY"     "ONTOLOGYALL"  "PATH"        
[13] "PMID"         "REFSEQ"       "SYMBOL"       "TAIR"        

length(keys(org.At.tair.db, keytype = 'TAIR'))
[1] 27416

length(keys(org.At.tair.db, keytype = 'GO'))
[1] 4837

One solution would perhaps to use the official most up to date GO terms (available here) and perform the enrichment analysis manually.

The text was updated successfully, but these errors were encountered:

mgalland added the help wanted label

Member Author

mgalland commented Jun 18, 2021

Useful links:
https://davetang.org/muse/2017/08/08/getting-started-arabidopsis-thaliana-genomics/
https://davetang.org/muse/2010/11/10/gene-ontology-enrichment-analysis/

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment