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generate_known.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
It generates the list of allowed candidate fusion genes. This list is hard coded
inhere and it is manually curated from publications.
Author: Daniel Nicorici, Daniel.Nicorici@gmail.com
Copyright (c) 2009-2022 Daniel Nicorici
This file is part of FusionCatcher.
FusionCatcher is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
FusionCatcher 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with FusionCatcher (see file 'COPYING.txt'). If not, see
<http://www.gnu.org/licenses/>.
By default, FusionCatcher is running BLAT aligner
<http://users.soe.ucsc.edu/~kent/src/> but it offers also the option to disable
all its scripts which make use of BLAT aligner if you choose explicitly to do so.
BLAT's license does not allow to be used for commercial activities. If BLAT
license does not allow to be used in your case then you may still use
FusionCatcher by forcing not use the BLAT aligner by specifying the option
'--skip-blat'. Fore more information regarding BLAT please see its license.
Please, note that FusionCatcher does not require BLAT in order to find
candidate fusion genes!
This file is not running/executing/using BLAT.
"""
import sys
import os
import optparse
import symbols
if __name__ == '__main__':
#command line parsing
usage = "%prog [options]"
description = """It generates the list of allowed candidate fusion genes (which are manually curated from scientific articles)."""
version = "%prog 0.14 beta"
parser = optparse.OptionParser(usage=usage,description=description,version=version)
parser.add_option("--organism",
action = "store",
type = "string",
dest = "organism",
default = "homo_sapiens",
help="""The name of the organism for which the list of allowed candidate fusion genes is generated, e.g. homo_sapiens, mus_musculus, etc. Default is '%default'.""")
parser.add_option("--output",
action="store",
type="string",
dest="output_directory",
default = '.',
help="""The output directory where the list of allowed candidate fusion genes is generated. Default is '%default'.""")
parser.add_option("--skip-filter-overlap",
action="store_true",
dest="skip_filter_overlap",
default = False,
help="""If set then it filters out the known fusion genes where the (i) genes are fully overlapping, or (ii) the genes are partially overlapping and are on the same strand. Default is '%default'.""")
(options,args) = parser.parse_args()
# validate options
if not (options.output_directory
):
parser.print_help()
sys.exit(1)
#
#
#
print "Generating the list of allowed/known fusion genes..."
fusions = dict()
# manual curation from papers
fusions['rattus_norvegicus'] = []
fusions['mus_musculus'] = []
fusions['canis_lupus_familiaris'] = []
fusions['homo_sapiens'] = [
['A121','VEGF'],
['A1BG-AS1','APOA2'],
['A20','K20'],
['A20','TNFAIP3'],
['A2M','ALK'],
['A2M','NOL10'],
['AAC1','AAC2'],
['AACSP1','ZNF354A'],
['AADACL2','ENSA'],
['AADACL2','SLC45A3'],
['EWSR1','SSX2'],
['AADAT','TPT1'],
['AAK1','ARNT2'],
['AAK1','C2ORF42'],
['AAK1','LHX2'],
['AAK1','RPL36A'],
['AAK1','TEX261'],
['AAK1','WFDC10B'],
['AAK1','WFDC13'],
['AAMDC','SLC12A7'],
['AARSD1','MAP2K6'],
['AARSD1','NF1'],
['AASDH','LRRC66'],
['AASDH','PPAT'],
['TNIP1','PDGFRB'],
['PCM1','FGFR1'],
['FYCO1','RAF1'],
['CTTNBP2','BRAF'],
['SLC44A1','BRAF'],
['KIAA1549','BRAF'],
['TBLR1','RARA'],
['AATF','TADA2A'],
['AATF','ZMYND11'],
['ABAT','NAT10'],
['ABCA2','FYTTD1'],
['ABCA4','BCAR3'],
['PGR','NR4A3'],
['UBR5','PGR'],
['ABCA5','PPP4R1L'],
['ABCA5','UNK'],
['ABCA8','TTC37'],
['ABCA9','MED13'],
['ABCB1','DMTF1'],
['ABCB1','SEMA3D'],
['ABCB1','SLC25A40'],
['ABCB11','LRP2'],
['ABCB9','ZDHHC7'],
['ABCC1','C16ORF45'],
['ABCC1','MPV17L'],
['ABCC1','MRP1'],
['ABCC1','TP53'],
['ABCC3','MRP3'],
['ABCC4','ETV4'],
['ABCC8','VCL'],
['ABCD3','C1ORF123'],
['ABCD3','CPOX'],
['ABCF1','PLVAP'],
['ABCG1','SLC37A1'],
['ABCG2','BCRP'],
['ABCG8','EPCAM'],
['ABHD11','BAZ1B'],
['ABHD12','CRTC1'],
['ABHD12','ZNF337'],
['ABHD12B','PYGL'],
['ABHD12B','RCC1'],
['ABHD12B','SAV1'],
['ABHD14B','DHX30'],
['ABHD15','TAOK1'],
['MEIS1','NCOA1'],
['KMT2A','AFDN'],
['ZNF532','NUTM1'],
['PGAP3','SRPK1'],
['CTNNBIP1','CLSTN1'],
['GHR','ALK'],
['HOOK3','FGFR1'],
['GOLGA4','JAK2'],
['PGAP3','SRPK1'],
['CD63','BCAR4'],
['PAFAH1B1','USP6'],
['CTNNBIP1','CLSTN1'],
['ABHD3','ESCO1'],
['ABHD3','ROCK1'],
['ABI1','BMI1'],
['ABI1','KMT2A'],
['ABI1','MLL'],
['ABI1','PDSS1'],
['ABI2','KMT2A'],
['ABI2','MLL'],
['ABI2','MTA3'],
['ABL','BCR'],
['ABL','ETV6'],
['ABL','HOXA9'],
['ABL','MYC'],
['ABL','NUP214'],
['ABL','PDGFRA'],
['ABL','PDGFRB'],
['ABL1','ADAMTSL2'],
['ABL1','AIF1L'],
['ABL1','ANXA4'],
['ABL1','ARNT'],
['ABL1','BCR'],
['ABL1','CBFB'],
['ABL1','CDX2'],
['ABL1','CENPC'],
['ABL1','CENPC1'],
['ABL1','CHIC2'],
['ABL1','CNTRL'],
['ABL1','DEK'],
['ABL1','EML1'],
['ABL1','ETV6'],
['ABL1','EVI1'],
['ABL1','EXOSC2'],
['ABL1','FACL6'],
['ABL1','FGFR1'],
['ABL1','FGFR3'],
['ABL1','FOXP1'],
['ABL1','GAB1'],
['ABL1','HLXB9'],
['ABL1','INPP5D'],
['ABL1','JAK2'],
['ABL1','KIAA1671'],
['ABL1','LSM14A'],
['ABL1','MDS2'],
['ABL1','MN1'],
['ASAP1','USP6'],
['FAT1','USP6'],
['SAR1A','USP6'],
['TNC','USP6'],
['ABL1','NUP153'],
['ABL1','NUP214'],
['ABL1','PAX5'],
['ABL1','PER1'],
['ABL1','PRDM12'],
['ABL1','RALGPS1'],
['GOLGA4','JAK2'],
['ABL1','RANBP2'],
['ABL1','RCSD1'],
['ABL1','RNF213'],
['ABL1','SEPT9'],
['ABL1','SFPQ'],
['ABL1','SNX2'],
['ABL1','SPTAN1'],
['ABL1','STL'],
['ABL1','SYK'],
['ABL1','TEL'],
['ABL1','TNRC6B'],
['ABL1','TTL'],
['ABL1','ZBTB16'],
['ABL1','ZMIZ1'],
['ABL2','ETV6'],
['ABL2','GAB2'],
['ABL2','KMT2A'],
['ABL2','PAG1'],
['ABL2','RCSD1'],
['ABL2','SLC38A2'],
['ABL2','ZC3HAV1'],
['ABLIM1','PDZD8'],
['ABLIM2','DIP2C'],
['ABR','CLUH'],
['ABR','FAM76A'],
['PTBP1','MAML2'],
['ABR','GAS7'],
['ABR','KCNK1'],
['ABR','STAP2'],
['ABR','YWHAE'],
['ABRACL','MAP3K5'],
['AC004066.1','PPA2'],
['AC004870.4','EGFR'],
['AC005262.1','AES'],
['AC006372.2','KMT2C'],
['AC011523.1','KDM4A'],
['AC011523.1','KDM4B'],
['AC011997.1','PLCB1'],
['AC012314.2','TRPC5'],
['AC012354.6','SIX3'],
['AC015849.2','TAF15'],
['AC016582.1','TP53'],
['AC019197.1','SCN2A'],
['AC025048.2','TP53'],
['AC027612.3','MRPS6'],
['AC079780.1','THADA'],
['AC083837.1','IL7'],
['AC090627.1','THRA'],
['AC090987.1','PVT1'],
['AC091132.4','KANSL1'],
['AC099850.1','TMEM49'],
['AC099850.1','VMP1'],
['AC117386.2','OLFM1'],
['AC126544.2','EPOR'],
['AC138031.1','ADRB2'],
['AC141586.5','KCTD5'],
['AC243829.2','TP53'],
['AC245884.1','EPOR'],
['ACA11','WHSC1'],
['ACACA','C20ORF72'],
['ACACA','DDX52'],
['ACACA','ERBB2'],
['ACACA','HTRA4'],
['ACACA','KMT2A'],
['ACACA','MLL'],
['ACACA','MSI2'],
['ACACA','STAC2'],
['ACACA','UTP18'],
['ACAD10','MAPKAPK5'],
['ACAD11','CPNE4'],
['ACAD8','GLB1L3'],
['ACAD9','C3ORF46'],
['ACADSB','FGFR2'],
['ACADVL','FXR2'],
['ACAT1','TESK1'],
['ACBD3','ESRRG'],
['ACBD5','RET'],
['ACBD6','IGF1R'],
['ACBD6','RRP15'],
['ACCN1','NF1'],
['ACCS','BCL7A'],
['ACCS','EXT2'],
['ACCS','KAT6A'],
['ACE','KPNB1'],
['ACE2','PIR'],
['ACER1','MLL'],
['ACER3','CALCOCO2'],
['ACER3','PAK1'],
['ACER3','TAOK1'],
['ACIN1','NUTM1'],
['ACKR2','KRBOX1'],
['ACLY','ERBB2'],
['ACLY','NTN1'],
['ACO1','GNRHR2P1'],
['ACO2','ARHGEF17'],
['ACOT11','BLK'],
['ACOT2','RXFP1'],
['ACOT7','RERE'],
['ACOT9','APOO'],
['ACOT9','DMD'],
['ACOT9','SCHIP1'],
['ACP6','AHCTF1'],
['ACP6','CNOT2'],
['ACPL2','RASA2'],
['ACPP','AXL'],
['ACPP','CD200'],
['ACPP','ETV1'],
['ACPP','FGFR1'],
['ACPP','PIK3CB'],
['ACPP','SEC13'],
['ACPP','SKIL'],
['ACRBP','ENO2'],
['ACS2','ETV6'],
['ACSF2','MED1'],
['ACSF3','CBFA2T3'],
['ACSL3','C15ORF21'],
['ACSL3','COL4A3'],
['ACSL3','ETV1'],
['ACSL3','MOGAT1'],
['ACSL4','DCAF6'],
['ACSL5','FGFR2'],
['ACSL5','GUCY2GP'],
['ACSL6','ETV6'],
['ACSM1','IKBKE'],
['ACSM3','EEF2K'],
['ACSS1','C20ORF3'],
['ACSS1','RARA'],
['ACSS3','PITPNM2'],
['ACTA1','CARD11'],
['ACTA2','PLAG1'],
['ACTB','COL1A1'],
['ACTB','FOSB'],
['ACTB','GLI1'],
['ACTB','MAP7D1'],
['ACTB','MITF'],
['ACTB','OXSR1'],
['ACTB','TFEB'],
['ACTG1','MITF'],
['ACTG1','PDLIM5'],
['ACTG2','ALK'],
['ACTG2','DGUOK'],
['ACTG2','UFM1'],
['ACTL6A','WWTR1'],
['ACTN1','MYBL1'],
['ACTN2','TBCE'],
['ACTN4','AKT2'],
['ACTN4','C19ORF10'],
['ACTN4','COQ8B'],
['ACTN4','EIF3K'],
['ACTN4','KMT2A'],
['ACTN4','MLL'],
['ACTR10','ARID4A'],
['ACTR1B','ERVW-1'],
['ACTR3','RPS15'],
['ACTR3B','DPP6'],
['ACTR3B','MLL3'],
['ACTR8','IL17RB'],
['ACVR1','NFATC1'],
['ACVR1B','BAZ2A'],
['ACVR1B','PGC'],
['ACVR1C','CHN1'],
['ACVR2A','AKT3'],
['ACVR2A','CASP8'],
['ACVR2A','FN1'],
['ACVR2A','IGF2R'],
['ACVR2A','SUMO1'],
['ACVR2B','XYLB'],
['ADAM10','NUP37'],
['ADAM12','AFF1'],
['ADAM17','SLC23A3'],
['ADAM17','YWHAQ'],
['ADAM18','FGFR1'],
['ADAM28','BCR'],
['ADAM29','RBMY1J'],
['ADAM9','ANK1'],
['ADAM9','ASAH1'],
['ADAM9','NRG1'],
['ADAM9','PLEKHA2'],
['ADAM9','TM2D2'],
['ADAMTS12','PXDNL'],
['ADAMTS12','TRIO'],
['ADAMTS13','LHX2'],
['ADAMTS14','SNHG11'],
['ADAMTS17','ADAMTSL3'],
['ADAMTS17','LRRK1'],
['ADAMTS17','PML'],
['ADAMTS17','RARA'],
['ADAMTS19','RUNX1'],
['ADAMTS19','SLC27A6'],
['ADAMTS6','ARID1B'],
['ADAMTSL1','DENND4C'],
['ADAMTSL3','MAP2K5'],
['ADAP1','SUN1'],
['ADAP2','TTC28-AS1'],
['ADAR','TPM3'],
['ADARB1','PCBP3'],
['ADAT3','SPRY4'],
['ADC','SASS6'],
['ADCK1','KCNQ2'],
['ADCK1','OSBPL2'],
['ADCK1','TMC1'],
['ADCK2','HIPK2'],
['ADCK2','TBXAS1'],
['ADCK3','CYP2E1'],
['ADCK3','EPHX1'],
['ADCK3','KCNT2'],
['ADCK3','NEK7'],
['ADCK3','SPRN'],
['ADCK4','AKAP8'],
['ADCK4','NUMBL'],
['ADCK4','PPM1A'],
['ADCY3','SOS1'],
['ADCY4','RABGGTA'],
['ADCY7','NKD1'],
['ADCY8','ASAP1'],
['ADCY9','CDK12'],
['ADCY9','PRKCB'],
['ADCYAP1','CASP9'],
['ADD1','FGFR3'],
['ADD1','HTT'],
['ADD1','POMC'],
['ADD2','EXOC6B'],
['ADD3','NUP98'],
['ADGRF5','THBS1'],
['ADGRG6','ROS1'],
['ADGRG7','TFG'],
['ADH7','CNOT2'],
['ADIPOR2','NINJ2'],
['ADK','C10ORF11'],
['ADK','CD133'],
['ADK','DLG5'],
['ADK','EIF3A'],
['ADK','KAT6B'],
['ADK','PI4K2A'],
['ADK','SAMD8'],
['ADK','VCL'],
['ADNP','C20ORF132'],
['ADNP2','ITGB3BP'],
['ADORA2B','TTC19'],
['ADPRHL1','ZP4'],
['ADRA1A','GUF1'],
['ADRA1A','YIPF7'],
['ADRB3','DIS3'],
['ADRBK1','BAIAP2'],
['ADRBK1','CHGA'],
['ADRBK1','IGH@'],
['ADRBK1','IGHMBP2'],
['ADRBK1','POLD4'],
['ADRBK2','AP1B1'],
['ADRBK2','EHD1'],
['ADRBK2','EP300'],
['ADRBK2','RHBDL3'],
['ADRBK2','SF3A1'],
['ADRBK2','SGSM3'],
['ADRBK2','WWC1'],
['AE1','AE3'],
['AEBP2','PVT1'],
['AEBP2','VPS4B'],
['AES','FGFR3'],
['AF10','AF17'],
['AF10','CALM'],
['AF10','HEAB'],
['AF10','MLL'],
['AF10','MLLT10'],
['AF10','PICALM'],
['AF127577.4','NRIP1'],
['AF127936.2','NRIP1'],
['AF15Q14','MLL'],
['AF17','KMT2A'],
['AF17','MLL'],
['AF17','MLLT6'],
['AF186192.5','AGAP5'],
['AF1P','EPS15'],
['AF1P','MLL'],
['AF1Q','ARHGEF12'],
['AF1Q','CBFA2T1'],
['AF1Q','CREBBP'],
['AF1Q','ELL'],
['AF1Q','EP300'],
['AF1Q','FNBP1'],
['AF1Q','FOXO3A'],
['AF1Q','GAS7'],
['AF1Q','GMPS'],
['AF1Q','GPHN'],
['AF1Q','GRAF'],
['AF1Q','HEAB'],
['AF1Q','LAF4'],
['AF1Q','LCX'],
['AF1Q','LPP'],
['AF1Q','MLL'],
['AF1Q','MSF'],
['AF1Q','PICALM'],
['AF1Q','PNUTL1'],
['AF1Q','SEPT6'],
['AF1Q','SH3GL1'],
['AF1Q','SSH3BP1'],
['AF3P21','MLL'],
['AF4','AF9'],
['AF4','AFF1'],
['AF4','FMR2'],
['AF4','KMT2A'],
['AF4','MLL'],
['AF4','NOL4L'],
['AF5Q31','MLL'],
['AF6','MLL'],
['AF6','MLLT4'],
['AF9','DOT1L'],
['AF9','KMT2A'],
['AF9','MLL'],
['AF9','MLLT3'],
['AFAP','NTRK2'],
['AFAP1','NTRK1'],
['AFAP1','NTRK2'],
['AFAP1','NTRK3'],
['AFAP1L1','PDGFRB'],
['AFAP1L2','RET'],
['AFDN','KMT2A'],
['AFF1','ARHGAP17'],
['AFF1','C1QTNF1'],
['AFF1','DOM'],
['AFF1','DSCAML1'],
['AFF1','ELF2'],
['AFF1','FXYD6'],
['AFF1','GAS7'],
['AFF1','HOXA13'],
['AFF1','IL10RB'],
['AFF1','KMT2A'],
['AFF1','LYZ'],
['AFF1','MLL'],
['AFF1','MYC'],
['AFF1','PAIP2'],
['AFF1','PBX1'],
['AFF1','PHACTR2'],
['AFF1','PIM1'],
['AFF1','PTPN13'],
['AFF1','RABGAP1L'],
['AFF1','RAD51B'],
['AFF1','SRSF11'],
['AFF1','TRIM33'],
['AFF1','UBE2D3'],
['AFF2','DEK'],
['AFF2','FMR2'],
['AFF3','BCL2'],
['AFF3','FGFR2'],
['AFF3','KMT2A'],
['AFF3','LAF4'],
['AFF3','MAP4K4'],
['AFF3','MLL'],
['AFF3','PHF1'],
['AFF3','RUNX1'],
['AFF4','FGFR2'],
['AFF4','KMT2A'],
['AFF4','MLL'],
['AFF4','SEPT8'],
['AFF4','SLC38A4'],
['AFM','ALB'],
['AFM','FBF1'],
['AFP','ALB'],
['AFP','CUX1'],
['AFTPH','PRKCE'],
['AFX','PAX3'],
['AFX1','FOXO4'],
['AGAP1','IGFBP2'],
['AGAP2','CYP27B1'],
['AGAP2','MARS'],
['AGAP2','TIE1'],
['AGAP2','TMEM67'],
['AGAP2','TSFM'],
['AGAP3','BRAF'],
['AGAP3','HOXD11'],
['AGAP3','JAZF1'],
['AGAP5','BMS1P4'],
['AGBL1','MAGI1'],
['AGBL1','NTRK3'],
['AGBL3','SLC6A3'],
['AGBL4','NTRK1'],
['AGBL4','NTRK2'],
['AGBL4','NTRK3'],
['AGFG1','NTRK1'],
['AGGF1','PDGFRB'],
['AGGF1','RAF1'],
['AGK','BRAF'],
['AGK','KIAA1147'],
['AGK','WDR60'],
['AGL','C9ORF25'],
['AGMO','MAP3K1'],
['AGO2','PTK2'],
['AGO3','SPDYA'],
['AGPAT5','MCPH1'],
['AGPAT5','MSRA'],
['AGT','CLU'],
['AGTPBP1','DAPK1'],
['AGTPBP1','NAA35'],
['AGTRAP','BRAF'],
['AGXT2L2','CYB5R1'],
['AHCTF1','NAAA'],
['AHCY','ITCH'],
['AHCY','TAX1BP1'],
['AHCYL1','FGFR2'],
['AHCYL1','KDM5B'],
['AHCYL1','RAD51C'],
['AHCYL2','MKLN1'],
['AHCYL2','PAX5'],
['AHCYL2','TMEM178B'],
['AHDC1','MACF1'],
['SS18L1','SSX1'],
['EWSR1','SSX1'],
['SS18','SSX2'],
['MN1','SSX1'],
['AHDC1','MAP3K6'],
['AHDC1','WDFY3'],
['AHI1','HBS1L'],
['AHI1','MYB'],
['AHI1','TRB@'],
['AHNAK','HNRNPUL2'],
['AHNAK','KAT5'],
['AHNAK','MALAT1'],
['AHNAK','NXF1'],
['AHNAK','RPS6KA4'],
['AHNAK2','PLD4'],
['AHRR','ETV4'],
['AHRR','NCOA2'],
['AHRR','NCOA3'],
['AHSG','PARP15'],
['AHSG','SERPINA1'],
['AIDA','KCNH1'],
['AIF1','CD163'],
['AIF1L','ETV6'],
['AIFM1','FGF13'],
['AIG1','GOSR1'],
['AIG1','NFIB'],
['AIM1','SOBP'],
['AIP','ATE1'],
['AK125726','ETV6'],
['AK2','AK8'],
['AK2','CD274'],
['AK2','PDCD1LG2'],
['AK7','CREBRF'],
['AK7','EXOC2'],
['AK7','PAPOLA'],
['AKAP1','RNF43'],
['AKAP11','MRPS31'],
['AKAP12','ESR1'],
['AKAP13','GSN'],
['AKAP13','IGF1R'],
['AKAP13','NEDD4'],
['AKAP13','NRG1'],
['AKAP13','NTRK3'],
['AKAP13','PDE8A'],
['AKAP13','PLDN'],
['AKAP13','RET'],
['AKAP6','EGLN3'],
['AKAP6','ERBB4'],
['AKAP6','LEPR'],
['AKAP6','NPAS3'],
['AKAP6','PRKD1'],
['AKAP7','ESR1'],
['AKAP8','BRD4'],
['AKAP8','CACNA1A'],
['AKAP8L','BRD4'],
['AKAP8L','ENO1'],
['CSF1','CD96'],
['RAB3IP','HMGA2'],
['SEC16A','KMT2A'],
['PAX5','KIDINS220'],
['LAMTOR1','AKT1'],
['NRIP1','MIR99AHG'],
['SPON1','TRIM29'],
['MYB','TYK2'],
['EWSR1','CTBP1'],
['MALAT1','GLI1'],
['SPON1','TRIM29'],
['CTLA4','CD28'],
['AGK','BRAF'],
['ZNF532','NUTM1'],
['TBLR1','RARA'],
['AKAP8L','FGFR1'],
['AKAP9','ANKIB1'],
['AKAP9','BRAF'],
['AKAP9','CDK6'],
['AKAP9','KIAA1549'],
['AKAP9','LSM14A'],
['AKAP9','PON2'],
['AKAP9','RUNX1'],
['AKAP9','SHFM1'],
['AKIRIN1','MACF1'],
['AKR1A1','PRDX1'],
['AKR1C6P','B4GALT5'],
['AKR1D1','BEND7'],
['AKR1D1','RIOK1'],
['AKR1E2','CCT4P1'],
['AKR7A2','LMBRD2'],
['AKT1','CPSF2'],
['AKT1','LAMTOR1'],
['AKT1','PGC'],
['AKT1','PHRF1'],
['AKT1','PRKACA'],
['AKT2','ART3'],
['AKT2','BCAM'],
['AKT2','C19ORF12'],
['AKT2','C19ORF47'],
['AKT2','CXCL11'],
['AKT2','PAK4'],
['AKT2','PRKACA'],
['AKT2','SRRM5'],
['AKT2','TSHZ3'],
['AKT2','YIF1B'],
['AKT2','ZNF576'],
['AKT3','ARHGAP30'],
['AKT3','C1ORF150'],
['AKT3','CEP170'],
['AKT3','CNOT6L'],
['AKT3','MAGI3'],
['AKT3','PHIP'],
['AKT3','PLD5'],
['AKT3','PVT1'],
['AKT3','SMYD3'],
['AKT3','SSH2'],
['AKT3','TAF6L'],
['AKT3','XPNPEP1'],
['AKT3','ZEB2'],
['AL034550.1','PAX5'],
['AL035685.1','CSE1L'],
['AL121790.1','TTC6'],
['AL135923.2','DMAC1'],
['AL445647.1','MIR4500HG'],
['AL672183.2','CD55'],
['AL672183.2','IRF2BP2'],
['ALB','APOA2'],
['ALB','H19'],
['ALB','IGF2'],
['ALB','SEPP1'],
['ALCAM','RAF1'],
['ALDH16A1','PLEKHG5'],
['ALDH18A1','DEPDC5'],
['ALDH1A3','PTPRG'],
['ALDH2','CCNB1IP1'],
['ALDH2','CMKOR1'],
['ALDH2','EBF1'],
['ALDH2','FHIT'],
['ALDH2','HMGA2'],
['ALDH2','HMGIC'],
['ALDH2','WIF1'],
['ALDH7A1','SLC9A7'],
['ALDOB','KNG1'],
['ALG14','BCAR3'],
['ALG14','CNN3'],
['ALG5','PIGU'],
['ALG5','POSTN'],
['ALG6','ERBB2'],
['ALG8','KHDC1'],
['ALG9','PPP2R1B'],
['ALK','ALO17'],
['ALK','AMBRA1'],
['ALK','ANK1'],
['ALK','ATG16L1'],
['ALK','ATIC'],
['ALK','ATRNL1'],
['ALK','BCL11A'],
['ALK','BEND5'],
['ALK','BIRC6'],
['ALK','C2ORF22'],
['ALK','C2ORF34'],
['ALK','C2ORF44'],
['ALK','CAD'],
['ALK','CARS'],
['ALK','CCDC6'],
['ALK','CCDC61'],
['ALK','CCDC88A'],
['ALK','CDK15'],
['ALK','CEBPZ'],
['ALK','CHRNA7'],
['ALK','CLIP2'],
['ALK','CLTA'],
['ALK','CLTC'],
['ALK','CLTCL'],
['ALK','CLTCL1'],
['ALK','CMTR1'],
['ALK','COL1A2'],
['ALK','CTLC'],
['ALK','CTNNA1'],
['ALK','CUX1'],
['ALK','DCTN1'],
['ALK','DDX6'],
['ALK','DES'],
['ALK','DIAPH2'],
['ALK','DYSF'],
['ALK','EEF1G'],
['ALK','EEF2'],
['ALK','EGFR'],
['ALK','EIF2AK3'],
['ALK','EIF2AK4'],
['ALK','EML4'],
['ALK','ERC1'],
['ALK','ETV6'],
['ALK','FN1'],
['ALK','GALM'],
['ALK','GALNT17'],
['ALK','GCC2'],
['ALK','GFPT1'],
['ALK','GPC1'],
['ALK','GTF2IRD1'],
['ALK','HIP'],
['ALK','HIP1'],
['ALK','HNRNPA1'],
['ALK','HNRNPH3'],
['ALK','HOOK1'],
['ALK','HPCAL1'],
['ALK','IGFBP5'],
['ALK','IKBKG'],
['ALK','ITGAV'],
['ALK','KANK1'],
['ALK','KANK2'],
['ALK','KCNQ1'],
['ALK','KCNQ5'],
['ALK','KIAA1618'],
['ALK','KIF5B'],
['ALK','KLC1'],
['ALK','KMT2A'],
['ALK','KRAS'],
['ALK','KTN1'],
['ALK','LINC00211'],
['ALK','LMNA'],
['ALK','LRRFIP1'],
['ALK','MAD1L1'],
['ALK','MALAT1'],
['ALK','MAP2'],
['ALK','MCFD2'],
['ALK','MET'],
['ALK','MIR4432'],
['ALK','MLF1'],
['ALK','MLPH'],
['ALK','MPRIP'],
['ALK','MSI2'],
['ALK','MSN'],
['ALK','MYH9'],
['ALK','MYO5A'],
['ALK','MZT2B'],
['ALK','NCK2'],
['ALK','NCOA1'],
['ALK','NPM'],
['ALK','NPM1'],
['ALK','NSF'],
['ALK','NTRK1'],
['ALK','PARD3'],
['ALK','PICALM'],
['ALK','PLB1'],
['ALK','PLEKHA7'],
['ALK','PLEKHH2'],
['ALK','PLEKHM2'],
['ALK','PPFIBP1'],
['ALK','PPM1B'],
['ALK','PPP1CB'],
['ALK','PPP4R3B'],
['ALK','PQLC3'],
['ALK','PRKAR1A'],
['ALK','PRKAR2A'],
['ALK','PRRC2B'],
['ALK','PTPN3'],
['ALK','RAB10'],
['ALK','RANBP1'],
['ALK','RANBP2'],
['ALK','RARA'],
['ALK','RET'],
['ALK','RNF213'],
['ALK','RNPC3'],
['ALK','ROS1'],
['ALK','RPA1'],
['ALK','RRBP1'],
['ALK','SEC31A'],
['ALK','SEC31L1'],
['ALK','SLMAP'],
['ALK','SMEK2'],
['ALK','SMPD3'],
['ALK','SOCS5'],
['ALK','SOS1'],
['ALK','SPDYA'],
['ALK','SPECC1L'],
['ALK','SPTBN1'],
['ALK','SQSTM1'],
['ALK','SRBD1'],
['ALK','SRD5A2'],
['ALK','STK32B'],
['ALK','STPG4'],
['ALK','STRN'],
['ALK','SYN3'],
['ALK','SYNDIG1L'],
['ALK','TACR1'],
['ALK','TERT'],
['ALK','TFE3'],
['ALK','TFG'],
['ALK','TGFB1'],
['ALK','THBS1'],
['ALK','TIMP3'],
['ALK','TMED2'],
['ALK','TMP3'],
['ALK','TMP4'],
['ALK','TNIP2'],
['ALK','TNS1'],
['ALK','TP53'],
['ALK','TPM1'],
['ALK','TPM3'],
['ALK','TPM4'],
['ALK','TPR'],
['ALK','TRAF1'],
['ALK','TRIM33'],
['ALK','TRMT61B'],
['ALK','VCL'],
['ALK','VIT'],
['ALK','WDPCP'],
['ALK','ZC3H7A'],
['ALK','ZEB2'],
['ALK5','TFG'],
['ALKBH5','LLGL1'],
['ALMS1','MRTFB'],
['ALO17','MYC'],
['ALO17','RNF213'],
['ALOX12','MINK1'],
['ALOX15B','ETV1'],
['ALOXE3','ETV6'],
['ALOXE3','TP53'],
['ALPK1','ANK2'],
['ALPK2','PRKCH'],
['ALS2CL','ITGB4'],
['ALS2CR16','ALS2CR8'],
['ALX3','RECK'],
['AMACR','ERG'],
['AMACR','FGFR1'],
['AMACR','SDK1'],
['AMACR','SLC45A2'],
['AMD1','CDK19'],
['AMD1','KIAA1919'],
['AMDHD2','ATP6V0C'],
['AMDHD2','TRIM77'],
['AMER3','ANKRD42'],
['AMFR','IGF2BP2'],
['AMH','SF3A2'],
['AML1','CBFA2T3'],
['AML1','CLCA2'],
['AML1','EAP'],
['AML1','ETO'],
['AML1','ETV6'],
['AML1','EVI1'],
['AML1','FOG2'],
['AML1','JAK2'],
['AML1','LAF4'],
['AML1','LRP16'],
['AML1','MDS1'],
['AML1','MTG16'],
['AML1','MTG8'],
['AML1','PRDM16'],
['AML1','PRDX4'],
['AML1','PRPF38A'],
['AML1','RUNX1'],
['AML1','TEL'],
['AML1','USP25'],
['AMN1','C12ORF35'],
['AMOTL2','NTRK1'],
['AMPD1','BCAS3'],
['AMPD2','FGFR2'],