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immune_disease_genes.R
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##
## List of genes associated with immune diseases. (~/Documents/Stage/Data/disease_genes.xls)
##
## Saved data: data/immune_disease_genes
##
diabetes.1.genes <- c("AP4B1","BCAR1","C11orf21","C14orf64","C1QTNF6","C7orf71","CCDC101","CCR7","CD226","CDC37P1","CDK2","CLEC16A","CLECL1","CLN3","CSF3","CTLA4","CTSH","DOK6","EIF3C","EIF3CL","ENSG00000232530","ENSG00000241287","ENSG00000256582","ENSG00000257411","ENSG00000258511","ENSG00000261089","ENSG00000264198","ENSG00000266840","ERBB3","FKRP","GDF11","GSDMB","HLA.DMA","HLA.DQA1","HLA.DQB1","HLA.DQB1.AS1","HLA.DQB2","HLA.DRB5","HOTAIRM1","HOXA1","HOXA2","IKZF3","IL27","IL2RA","LIF","MIR320E","NPIPB6","NPIPB7","NPIPB8","NPIPB9","ORMDL3","PRKD2","PTPN2","RAB5B","RABEP2","RPS26","SBK1","SH2B1","SIRPG","SKAP2","STRN4","SULT1A1","SULT1A2","SUOX","TSPAN32","TYK2","ZPBP2")
celiac.genes <- c("AGER","ARHGAP31","BCL9L","C1orf106","CACNA1S","CCDC116","CCR1","CCR2","CCR3","CCRL2","CIITA","CPLX3","CSK","CXCR6","ELMO1","ENSG00000223552","ENSG00000236525","ENSG00000237058","ENSG00000238164","ENSG00000240310","ENSG00000241287","ENSG00000255422","ENSG00000259382","ENSG00000261606","ENSG00000263080","FLT1P1","GPR25","GPSM3","HLA.DMA","HLA.DQB1","HLA.DQB1.AS1","HLA.DRB5","ICOS","ICOSLG","IL18R1","IL1RL1","IRF4","KIAA1109","LMAN1L","LTF","MIR4513","MIR4772","MMEL1","PBX2","PLEK","PTPN2","RMI2","RNF5","THEMIS","TNFRSF14","TTC34","UBASH3A","UBE2L3","ULK3")
ibd.genes <- c("AAGAB","AAMP","ACO2","ACTR1A","ADO","AGAP5","ANKMY1","AP4B1","APEH","ARPC2","ATG16L1","BACH2","BSN","C10orf55","C17orf67","C20orf112","C5orf47","C7orf71","CACNA1S","CALM3","CAMK2G","CARD9","CAST","CCDC116","CCR5","CD226","CD40","CDH3","CEBPB","CELSR3","CISD1","CLN3","COMMD7","CPEB4","CRTC3","CSDC2","CTSW","CUL2","CXCL5","DACT3","DAG1","DENND1B","DESI1","DNLZ","DOCK7","DOK6","EDN3","EFCAB8","EFEMP2","EIF2S2P3","EIF3C","ENSG00000167807","ENSG00000170091","ENSG00000197146","ENSG00000202533","ENSG00000203999","ENSG00000213702","ENSG00000224276","ENSG00000224397","ENSG00000225331","ENSG00000225931","ENSG00000227598","ENSG00000228037","ENSG00000229299","ENSG00000229951","ENSG00000231858","ENSG00000231993","ENSG00000233077","ENSG00000234132","ENSG00000235582","ENSG00000236525","ENSG00000237604","ENSG00000238164","ENSG00000238280","ENSG00000242288","ENSG00000242687","ENSG00000243628","ENSG00000243696","ENSG00000247121","ENSG00000248636","ENSG00000249141","ENSG00000251572","ENSG00000254275","ENSG00000256428","ENSG00000256914","ENSG00000257582","ENSG00000261089","ENSG00000261338","ENSG00000261662","ENSG00000262820","ENSG00000266786","ENSG00000266840","ENSG00000267607","ENSG00000268810","ENSG00000269151","ENSG00000269292","ENSG00000269636","ERAP1","ERAP2","ERGIC1","FADS1","FADS2","FEN1","FIBP","FOXR1","FUT2","GNA12","GNG8","GPBAR1","GPR25","GSDMB","HLA.DRB5","HLA.DRB6","HOTAIRM1","HOXA1","HOXA2","ICAM1","ICAM4","ICAM5","ICOSLG","IL18R1","IL1RL1","IL23R","IL27","IL6ST","INPP5D","IP6K2","IPMK","IRF5","IRGM","ITGAL","ITIH4","ITM2BP1","KIF11","KIR2DL1","KIR3DL1","KIR3DL2","KSR1","LIME1","LNPEP","LRRK2","LY75","LY75.CD302","MAP3K8","MAPRE1","MEI1","MIR1908","MIR3939","MIR4772","MIR611","MMEL1","MRPL20","MRPL23","MST1","MUS81","MXRA8","MYRF","NDFIP1","NFATC1","NFKB1","NKX2.3","NOTCH2","NPIPB6","NPIPB7","NPIPB8","NPIPB9","NTN5","ORMDL3","P4HA2","PARK7","PEBP1P3","PF4","PFKFB4","PLAU","PLCH2","PLCL1","PMM1","POLR3H","PPP5C","PPP5D1","PRKAB1","PRKCB","PSMB8","PSMB9","PTGIR","PTGS2","PTPN2","PTPRC","RASGRP1","RBM22","REG4","RFTN2","RIPK2","RN7SL657P","RNASET2","RNF145","RNFT1","RPL9P29","RPS6KA2","SAG","SCNN1D","SEC1P","SKAP2","SLC22A5","SLC25A20","SLC26A6","SLC2A4RG","SLC35C2","SLC35D1","SLMO2","SMIM3","SMURF1","SNAPC4","SP140","SUFU","SULT1A2","SYNGR1","TEF","TM9SF4","TMBIM1","TMEM180","TMEM258","TNFRSF14","TNFSF8","TOB2","TSPAN14","TYK2","UBE2L3","UBQLN4","USP36","ZBTB38","ZBTB46","ZFP90","ZGLP1","ZGPAT","ZNF300P1","ZNF831","ZPBP2")
rheuma.genes <- c("ACSL6","AFF3","AHNAK2","ALS2CR12","ANKRD55","AP4B1","ARAP1","ARAP1-AS2","ARID5B","ATG5","BCL9L","BLK","CCDC157","CCR6","CD226 ","CD40","CD5","CFLAR","CTLA4","DDX6","ENSG00000228403","ENSG00000230955","ENSG00000237058","ENSG00000238164","ENSG00000254275","ENSG00000254774","ENSG00000255354","ENSG00000255518","ENSG00000256914","ENSG00000262211","ENSG00000264198","ENSG00000266840","ENSG00000267520","ENSG00000269468","ENSG00000269954","ERBB3","FADS1","FADS2","FAM167A","GPSM3","GSDMB","HLA-DQA1","HLA-DQA2","HLA-DRB1","HLA-DRB5","HLA-DRB6","HLA-DRB9","IFNAR1","IL6R","IL6ST","INPP5B","IRF5","JAZF1","KCTD20","MED1","MMEL1","MYRF","NOTCH4","ORMDL3","PADI4","PAM","PBX2","PDE2A","PHF19","PSMD5","RPS26","RTKN2","SHE","SLC35C2","SPRED2","SUOX","SYNGR1","TBC1D10A","TNFRSF14","TRAF1","TTC34","UBASH3A","UTS2","VPS37C","ZPBP2")
save(diabetes.1.genes, celiac.genes, ibd.genes, rheuma.genes, file = "data/immune_disease_genes")