Table 3 List of genes enriched within the gene sets differentially expressed between cases with retention and LOH of PTPRJ

Upregulated in RET cases

HSA03030_DNA_Polymerase

POLQ,PRIM1,POLD3,POLE3,POLK,POLE2,POLE4,POLS,REV1,POLA2,RFC5,POLD1,POLB,POLI,POLE

HSA04115_P53_Signaling_ pathway

CDC2,PTEN,TNFRSF10B,CHEK1,PMAIP1,CDK4,CDK2,SFN,PERP,P53AIP1,FAS,CCNB1,SERPINB5,CASP8,CCNB2,EI24,CCND2,TP53I3,CCNE2,RFWD2,CCNB3,MDM2

HSA03050_Proteasome

PSMB4,PSMA3,PSMA4,PSMA1,PSMB7,PSMD11,PSMD13,PSMD1,PSMC3,PSMA2,PSMA5,PSMD2,PSMA7,PSMA6

Upregulated in LOH cases

HSA04370_VEGF_signaling_pathway

MAPKAPK2,PLA2G10,PXN,PLA2G6,PLA2G2F,MAP2K1,MAP2K2,RAF1,PRKCG,PIK3R1,PLA2G1B,MAPK3,MAPK12,SPHK2,AKT3,PLA2G2A,BAD,RAC1,PLA2G5,PIK3CD,NFATC3,PRKCA,PIK3CG

HSA05218_Melanoma

FGF9,CCND1,MET,FGF17,FGF22,MAP2K1,MAP2K2,IGF1,RAF1,PIK3R1,MAPK3,CDK6,AKT3,FGF8,BAD,FGF23,ARAF,FGF12,FGFR1,PIK3CD,PDGFRA,PDGFD,FGF7,PIK3CG

HSA04012_ERBB_signaling_pathway

CAMK2G,SHC4,MAP2K1,MAP2K2,RAF1,STAT5B,PRKCG,PAK2,NRG3,RPS6KB2,CAMK2B,PIK3R1,PAK4,NRG1,MAPK3,ERBB2,AKT3,TGFA,BAD,ARAF,CBL,ERBB3,PIK3CD,PRKCA,PIK3CG, PAK3

HSA04020_Calcium_ signaling_pathway

GNA11,HTR4,CCKBR,CHP,ADRA1D,ITPR1,RYR2,SLC25A5,PHKA1,NOS1,PHKA2,SLC8A2,CACNA1C,ATP2B1,MYLK,AGTR1,CAMK2G,CHRNA7,CAMK4,MYLK2,PRKCG,CAMK2B,GRM5,BDKRB1,ADCY8,RYR1,ERBB2,SPHK2,TRHR,CALM3,PRKACG,ADORA2A,PLN,GNA14,TBXA2R,PTAFR,ERBB3,ADCY9,P2RXL1,TACR2,CACNA1D,PDGFRA,HRH1,NTSR1,PLCB4,HTR2B,PRKCA, CACNA1I,SLC25A6,PTGER3,ITPKB

HSA04664_FC_epsilon_RI_ signaling_pathway

PLA2G2F,VAV3,MAP2K1,MAP2K2,RAF1,PIK3R1,PLA2G1B,MAPK3,MAPK12,AKT3,PLA2G2A,RAC1,IL4,PLA2G5,PIK3CD,IL5, PDK1,PRKCA,PIK3CG

HSA04010_MAPK_signaling_pathway

DUSP8,MAP2K7,FGF21,CACNA2D3,MEF2C,FGF5,RPS6KA3,CACNA2D1,TGFBR2,TAOK2,CACNA2D2,RAC3,NFKB2,CHP,FLNA,SRF,FGF9,DAXX,RPS6KA6,RRAS,MAPKAPK2,PLA2G10,NTRK1,CACNA1C,PLA2G6,FGF17,FGF22,RAP1A,FLNC,MAP3K14,PLA2G2F,CACNB4,MAP2K1,GADD45A,RPS6KA1,NF1,MAP2K2,RPS6KA5,RAF1,PRKCG,PAK2,TAOK3,MOS,MAPK8IP3,PLA2G1B, MAPK3,MAPK12,RRAS2,PRKACG,GADD45G,AKT3,NTF5,FGF8, PLA2G2A,FLNB,RAC1,FGF23,FGF12,RASGRF2,FGFR1,PLA2G5,MAP3K8NLK PTPN5 CACNA1D IL1R1 PDGFRA ARRB2 MAP3K10 RPS6KA4 PPP5C FGF7 GNA12 CACNG5 MAP3K13 DUSP7 PRKCA MAP2K5 CACNA1I MAPK8IP2

HSA04150_MTOR_signaling_pathway

VEGFB,RICTOR,PGF,AKT1,PRKAA1,RPS6KA3,RPS6KA6,RPS6KA1,IGF1,RPS6KB2,PIK3R1,EIF4B,MAPK3,VEGFC,AKT3,FIGF, PIK3CD,PIK3CG

HSA05221_Acute_myeloid_ leukemia

PIM2,NFKB2,STAT3,CCND1,FLT3,MAP2K1,CEBPA,MAP2K2,RAF1,RPS6KB2,JUP,MAPK3,TCF7,AKT3,BAD,ARAF,PIK3CD, PIK3CG,KIT