Table SI. Targets of berberine. Table SI. Continued. symbol Gene name Gene symbol Gene name ABL1 CHEK1 ABO CMA1 ACADM CRABP2 ACHE CTNNA1 ADAM17 CTSB ADAM33 CTSK ADH1C CTSS ADH5 CYP19A1 ADK CYP2C9 ADRB2 DAPK1 AKR1B1 DCK AKR1C1 DCPS AKR1C2 DHFR AKR1C3 DHODH AKT1 DPEP1 ALB DPP4 AMD1 DTYMK AMY2A DUSP6 ANXA5 DUT APAF1 EGFR APOA2 EIF4E APRT ELANE AR EPHB4 AURKA EPHX2 BACE1 ERBB4 BCAT2 ESR1 BCHE ESR2 BCL2L1 ESRRG BHMT F10 BIRC7 F2 BMP2 FABP3 BRAF FABP6 CA2 FABP7 CALM FDPS CASP1 FECH CASP3 FGFR1 CASP7 FGFR2 CCL5 FGG CCNA2 FKBP1A CDK2 FKBP1B CDK6 FKBP3 CES1 GC CFD GMPR Table SI. Continued. Table SI. Continued. Gene symbol Gene name Gene symbol Gene name GMPR2 MAPK14 GPI MAPKAPK2 GSK3B MET GSR METAP2 GSTA1 MME GSTA3 MMP12 GSTM1 MMP13 GSTM2 MMP2 GSTP1 MMP3 HADH MMP8 HCK MMP9 HDAC8 MTAP HINT1 MTHFD1 HMGCR NCOA2 HNF4G NGAL HNMT NMNAT1 HPGDS NOS2 HPRT1 NOS3 HRAS NQO1 HSD11B1 NQO2 HSD17B1 NR1A1 HSP90AA1 NR1B2 HSP90AB1 NR1H2 HSPA8 NR1H3 IGF1 NR1H4 IGF1R NR1I2 IGLV2-8 NR3C1 IL2 NR3C2 INSR OAT ITK OTC JAK2 PAH JAK3 PAPSS1 KAT2B PCK1 KCNH2 PDE10A KDR PDE3B KIF11 PDE4B KIT PDE4D PDE5A LSS PDK2 LTA4H PDPK1 MAOB PGF MAP2K1 PGR MAPK10 Pim1 Table SI. Continued. Table SI. Continued. Gene symbol Gene name Gene symbol Gene name PKLR SULT2A1 PLA2G2A TAP1 PNMT TEK PPARA TGFB2 PPARD TGFBR1 PPARG TGM3 PPIA THRB PPP1CC TPSB2 PPP5C TRAPPC3 PRKACA TTPA PRKCQ TTR PROCR TYMS PRSS1 VDR PTGS1 XIAP PTGS2 ZAP70 PTK2 PTPN1 PTPN11 PYGL RAP2A RARA RARG RBP4 REN RFK RORA RXRA RXRB S100A9 SCN5A SDS SEC14L2 SERPINA1 SETD7 SHBG SIRT5 SORD SPR Src STAT1 STS SULT1A1 SULT1E1 Table SII. differentially expressed in liver . Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TP73 ECHS1 ABL1 MUC1 AOX1 DAPK1 ENO1 ADH1B ABO SCAMP3 APOA1 DCK MASP2 GPC3 ACADM FDPS ARG1 DCPS ALDH4A1 ALB ADAM17 YY1AP1 CCT3 DHFR PLA2G2A BHMT ADH1C CCT3 CTSB DHODH ALPL PLG ADH5 HDGF CYP2C8 DPP4 RUNX3 VIM ADK CD5L FAH DTYMK STMN1 RGN ADRB2 APCS FGA DUSP6 SFN TF AKR1B1 CRP FGL1 DUT FCN3 FABP1 AKR1C1 COPA FTCD EGFR FAM76A HPD AKR1C2 NCSTN GHR EIF4E KHDRBS1 ACADSB AKR1C3 ITLN1 HSPB1 EPHB4 EIF3S2 CAT AKT1 ATF6 IGF2 EPHX2 FNDC5 MTHFD1 ALB RGS5 KRT8 ERBB4 PHC2 RPSA AMD1 GLUL NDRG1 ESR1 DNALI1 SLC22A1 ANXA5 PTGS2 S100A10 ESR2 YBX1 TDO2 APAF1 RGS1 SCP2 ESRRG CDC20 ADH4 APOA2 CFHR3 SELENBP1 F10 PRDX1 CP APRT UBE2T SULT2A1 F2 CDKN2C CYP2E1 AR CHI3L1 UBD FDPS SCP2 PCK1 AURKA KISS1 ACAA1 FGFR1 C8A SPARC BCAT2 CD34 ACAA2 FGFR2 CACHD1 ACSL1 BCHE PPP2R5A AFP FGG LEPR ALDH1L1 BCL2L1 PARP1 ALDH2 FKBP1A IL12RB2 ALDH4A1 BHMT MTR ANXA2 FKBP3 BCL10 ALDOB BMP2 ADAM17 BUB1 GC CYR61 CPS1 BRAF RRM2 CLIC1 GMPR GNAI3 CYB5A CA2 RHOB COL1A2 GMPR2 RHOC CYP2C9 CASP1 DNMT3A COMT GPI SYCP1 FGB CASP3 KHK CYP2B6 GSR HAO2 FGG CASP7 EHD3 DCXR GSTA1 HMGCS2 GAPDH CCL5 HAAO DNASE1L3 GSTA3 FAM72B HRSP12 CCNA2 TACSTD1 FEN1 GSTM1 ECM1 HSD17B10 CDK2 GPR75 FN1 GSTM2 MCL1 HSPA5 CDK6 RTN4 GLUL GSTP1 PSMD4 IGFBP3 CES1 XPO1 HMMR HADH SNX27 PCK2 CHEK1 UGP2 HNRNPA2B1 HINT1 S100A9 PDIA3 CRABP2 TGFA HSP90B1 HMGCR ILF2 SERPINA1 CTNNA1 REG1A ITIH4 HNF4G JTB TTR CTSB REG3A KHK HNMT SHC1 AGXT CTSS MAT2A MT2A HPRT1 EFNA1 AKR1B10 CYP2C9 FABP1 NNMT HSD11B1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) IL18RAP NPM1 HSD17B1 PDGFRA HAAO PKLR STEAP3 PCSK6 HSP90AA1 UGT2B4 HDGF PLA2G2A PGK1 HSP90AB1 IGJ HGD PNMT CD302 PPIB IGF1 DCK HMGCS2 PPARA ITGA6 PRDX6 IGF1R SLC4A4 HSD17B4 PPARD HSPD1 RFC4 IL2 ALB HSPA1B PPARG CPS1 SLC2A2 INSR AFP HSPA8 PPIA ERBB4 SNRPE JAK2 AFM IGKC PPP1CC FN1 STMN1 KAT2B CXCL2 ISG15 PRKACA TUBA1 TOP2A KDR PLAC8 KNG1 PROCR SPP2 A2M KIF11 HPSE LAMP2 PRSS1 AGXT ACAT1 KIT PTPN13 MAT1A PTGS2 RAF1 ACY1 LCK SPARCL1 MCM2 PTK2 XPC ALDH1A1 MAOB SPP1 MMP9 PTPN1 TGFBR2 APOC3 MAP2K1 ABCG2 NME1 PTPN11 ACAA1 ARID3A MAPK14 ADH4 PCNA PYGL RPSAP15 ASS1 MET BDH2 PEMT RAP2A CTNNB1 C6 MME EGF PGRMC1 RBP4 VIPR1 C9 MMP12 MAD2L1 PKM2 REN CDC25A CA2 MMP13 ANXA5 PON3 RORA COL7A1 CAP2 MMP2 CCNA2 QDPR RXRA SEMA3B CCT5 MMP3 IL2 RBP1 RXRB RASSF1 CD14 MMP9 FGF2 RDBP SDS ZMYND10 CD24 MTAP EDNRA SCAMP3 SEC14L2 ACY1 CDK4 MTHFD1 FGB SERPING1 SERPINA1 DNASE1L3 CDKN1A NCOA2 FGA SOD1 SHBG FHIT CES1 NMNAT1 FGG TST SIRT5 ROBO1 CES2 NOS2 TDO2 TUBB SORD TMEM45A CLU NQO1 ANXA10 VTN SPR MUC13 COL1A1 NQO2 MFAP3L ACADVL Src ALDH1L1 CPB2 NR1H4 GPM6A ACTB STAT1 TF CTGF NR1I2 VEGFC ADH1C SULT1A1 MME CYP27A1 NR3C1 CASP3 ADH6 SULT1E1 SMC4 CYP2J2 OAT ACSL1 AKR1C2 SULT2A1 TNFSF10 CYP3A4 OTC KLKB1 ALAS1 TAP1 PIK3CA EFNA1 PAH VPS53 ALDH1B1 TGFB2 TFRC EPHX1 PAPSS1 NP_001001870.1 ALDH3A2 THRB FGFR3 ETS2 PCK1 SERPINF2 ALDOA TTPA HGFAC FABP5 PDK2 DERL2 B2M TTR S100P FH PDPK1 CENTB1 BNIP3 TYMS GPR78 GC PGF SHBG C1R XIAP LAP3 GNMT Pim1 TP53 C5orf13 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) NP_001004313.1 C8A GPC3 PC SHMT1 CAPG F9 PEG10 MFAP4 CBX1 SPANXC PGM1 NOS2A CFH MAGEC2 PRDX1 VTN CRHBP MAGEA11 PROZ CCL2 CSTB MAGEA8 PTTG1 CCL3 CTH FATE1 PUF60 ERBB2 CXCL12 MAGEA4 PYGB RARA CYP1A2 GABRE RBP4 P11388-3 CYP2A6 MAGEA10 RCAN1 KRT19 CYP2A7 MAGEA2B RHOA ACLY CYR61 MAGEA2 RHOB ETV4 DDR1 MAGEA3 RND3 GRN DLGAP5 MAGEA1 RPLP0 CBX1 ENO1 BCAP31 RPS5 NGFR FCGRT CTAG1A S100A6 NME1 FCN3 TSPY1_HUMAN SAA2 DYNLL2 GLUD1 RBMY1B SERPINC1 AXIN2 GRHPR TERT SERPINF2 SSTR2 GYS2 CCT5 SGK1 SLC9A3R1 HAMP NP_001030022.1 SLC16A2 GALK1 HAO1 GHR SLC7A2 PRPSAP1 HGFAC CRHBP SOD2 BIRC5 HMGA1 BHMT SPARCL1 SOCS3 HNRNPC APC SRGN NOTUM HPX AP3S1 STAT1 CD99 HSD17B6 SLC27A6 TGM2 SRPX IFI27 IRF1 THBS1 DDX3X IFIT1 HSPA4 TIMP1 RGN IGF2R FBXL21 TMED2 SSX5 ILF2 EGR1 TPM2 SSX1 ITIH2 HSPA9 UGT2B7 SSX4_HUMAN ITPR2 NRG2 ABAT RBM3 KIF23 HBEGF ACADM GAGE8 LPGAT1 FGF1 ACADS GAGD2_HUMAN LYZ SPARC ACLY SSX2_HUMAN MAD2L1 PTTG2 ACO1 AR MCM6 HMMR ACOX1 EFNB1 MDK NPM1 AKR1C3 GJB1 MT1F DUSP1 AKR1C4 PSMD10 NAMPT STC2 ANXA1 LUZP4 NFKBIA MUTED ANXA4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) EDN1 APOC1 SERPINE1 GMNN CAP2 APOC4 NP_114111.2 GOT2 DEK APOH SYPL1 GPX2 GMNN ARHGDIB DOCK4 GSN SLC17A3 ARNT MET GSTA2 HFE ASGR1 LEP H1F0 UBD_HUMAN ASGR2 SMO H2AFZ CLIC1_HUMAN BLVRB AKR1B10 HAGH HSPA1B C5 ZYX HIST1H4C HMGA1 C8B EZH2 HLA-DRA DEF6 CANX SHH HMGCL CDKN1A CCNB1 KBTBD11 HP PGC CCT4 ANGPT2 HRG GNMT CD74 CTSB HSPA4 VEGFA CDKN3 DLC1 HSPA9 MUT CEP55 VPS37A HSPD1 PNRC1 CETP MTUS1 ICAM1 ARG1 CFB FGL1 IFITM1 CTGF CRYL1 NAT2 IGF1 ALDH8A1 CSE1L STC1 IGFALS ESR1 CTSC NRG1 KCNJ8 ACAT2 CYP3A5 PRKDC KIAA0101 IGF2R CYP4A11 SNAI2 KIAA0196 SLC22A1 DAB2 ASPH LBR PLG DAO COPS5 LCN2 PARK2 DBI STMN2 LGALS3 ACTB DCN FABP5 LGALS3BP HOXA13 DDX5 CA1 LGALS8 PPIA_HUMAN DUSP1 CA3 MCM3 ADCY1 DUSP9 CA2 MME IGFBP1 ECH1 CDH17 MMP14 IGFBP3 EHHADH LAPTM4B MPST EGFR EHMT2 PABPC1 MT1E CLDN4 EIF6 ANGPT1 NAP1L1 HSPB1 ENPP1 EIF3S6 NAT2 GNAI1 F11 EBAG9 NEK2 HGF FAS EIF3S3 NME2 ABCB1 FBP1 ENPP2 OTC SGCE FLNB HAS2 PEBP1 PEG10 FOS ZHX2 PLIN2 AZGP1 GAMT ATAD2 PON1 MCM7 GBP1 MTSS1 POR Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PPAP2B MT1B AEBP1 PTK2 PPIA MT1F AGL LY6E PPP1CC MT1G AGRN GPAA1 PRDX3 MT1X AHCY RLN1 PSMC5 CETP AK3 MTAP RGS2 CDH1 AKR1D1 CDKN2A RGS5 HP ALDH9A1 CDKN2B RPL6 WWOX ALDOC TEK SEPP1 COMT AMACR AQP7 SERPINE1 UBE2L3 AMBP AQP3 SF3B4 MAPK1 ANG ALDH1A1 SHBG IGLV4-3 ANXA5 HNRPK SHC1 IGLL1 APOC2 GADD45G SHMT1 MIF AQP3 FBP1 SLC10A1 MMP11 AR PTCH1 SLC29A1 UPB1 ARHGDIA BAAT SLC38A3 TST ASAP1 ALDOB SLC39A14 SSTR3 ATP1A1 NEK6 SMC4 FAM10A6 ATP6AP1 HSPA5 SNRPB MLC1 AZGP1 ENG SORL1 ECGF1 BAAT LCN2 SPP1 SNRPB BCAP31 ASS1 SQLE CDC25B BCHE AXIN1 SYPL1 PCNA BLOC1S1 SSTR5 TPX2 ID1 C1orf9 NME3 TRIP13 DNMT3B C1S GFER TSPAN8 MAPRE1 C6orf97 SOCS1 TUBA1B C7 SMG1_HUMAN TUBA4A SRC CALR NP_060358.2 UBAP2L MYBL2 CAPZA1 ACSM3 WARS UBE2C CCL14 PLK1 XPO1 MMP9 CCL2 TAOK2 YWHAZ CD40 CCL20 MAPK3 ACOX2 SNAI1 CCL3 ZNF689 ACSL5 AURKA CCND1 PRSS8 ACSL6 PCK1 CCT6A PYDC1 ACSS3 GNAS CD302 SIAH1 ADAMTS1 TPTE CD46 RBL2 ADAR BAGE5 CD81 MMP2 ADH1A TIAM1 CDC14B MT3 ADH5 SOD1 CDC20 MT1JP ADM ETS2 CDC25B Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TFF3 CDH1 CYP2E1 GCKR CBS CDK1 IFITM1 GCLM FTCD CENPF H19 GCN1L1 USP14 CKLF IGF2 GGH TNFSF5IP1 CLDN1 Q8N2L8_HUMAN GJB1 AQP4 CMBL CD81 GLA TTR COL4A2 CDKN1C GLYAT ATP5A1 COL6A3 SLC22A18 GNPAT SMAD2 COLEC10 RRM1 GOT1 SMAD4 CPD XLKD1 GPAA1 DCC CRP BBOX1 GPD1 SERPINB2 CTSA CAT GPNMB CYB5A CTSS CD44 GRN KLF6 CXCR4 CD82 GSTM1 AKR1C3 CYBA MDK GSTO1 TRDMT1 CYP8B1 SERPING1 GSTP1 VIM DCI GLYAT GSTZ1 SVIL DECR1 FEN1 GUSB ITGB1 DEK FADS2 H3F3A RET DPP4 BAD HABP2 CXCL12 DPYSL2 PYGM HADH DKK1 DUSP5 CDCA5 HADHB MAWBP_HUMAN DUSP6 GSTP1 HBA1 SUPV3L1 EDNRB CCND1 HDAC2 PLAU EGFR FADD HIPK2 MAT1A EIF2S1 FUT4 HK2 NRG3 EIF3E MMP7 HLA-A SNCG EIF4A1 MMP3 HLA-B C10orf116 EIF4EBP2 MMP12 HLA-DQA1 PTENP1 EPCAM CASP1 HLF FAS EPHA1 NNMT HLTF RBP4 EPHX2 APOA1 HNRNPU CYP2C9 ETFA HSPA8 HSDL2 CYP2C8 FBN1 NP_689935.1 HSP90AA1 SCD FDPS NP_001032647.1 ID2 TCF7L2 FETUB FKBP4 IDH1 HABP2 FGFR2 CD9 IFI16 ACADSB FMO3 727728 IGHA1 OAT FYN CD163 IL6R MKI67 GATA6 A2M IL8 MGMT GATM CLEC1B INSIG1 ECHS1 GCH1 CSDA IQGAP1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) CDKN1B IRAK1 EML1 PEA15 ARHGDIB ITGB1 C14orf68 PHLDA1 SLCO1B1 KRT7 HSP90AA1 PIK3R1 GYS2 LAMA3 MTA1 PKLR KRAS LAMA4 IGHG3 PLA2G2A TMEM106C LAP3 GJB2 PLAUR LETMD1 LAPTM4B CRYL1 PLOD3 NR4A1 LARP1 HSPH1 PLP2 ERBB3 LCAT TNFSF11 PODXL SPRYD4 LDHA RB1 POSTN GLI1 LEAP2 CKAP2 PPARG LYZ LECT2 EDNRB PRCC TSPAN8 LGALS1 SPRY2 PRKDC LGR5 LGR5 DCT PROS1 DCN LIPC COL4A1 PRPSAP1 TMPO LMNA PROZ PSMB4 IGF1 LOX SPRED1 PSMD8 PAH LPA THBS1 PTK2 HSP90B1 MAP4K4 SPINT1 PTPLAD1 RPL6 MARCKS AQP9 RAD21 DTX1 MCM4 KIAA0101 SDS MKI67 MAP2K1 RBM3 TBX3 MSH2 CYP1A1 RFC3 PEBP1 MT1X ETFA RHOC RPLP0 MT3 CIB2 RPS2 ACADS MTHFD2 FAH RPS20 HPD MTTP AKAP13 RPS24 PARP2 MYBL2 PLIN RRAGD DAD1 MYO1B ARRDC4 RRBP1 MMP14 NCL CDC34 RRM1 SSTR1 NR0B2 KISS1R SAA1 RPL36AL NUCKS1 GADD45B SAT1 CDKN3 NUP37 MAP2K2 SEC23A LGALS3 OASL CREB3L3 SERPINA3 DLG7 OGDHL SAFB SERPINA6 DACT1 P4HB PIN1 SLC25A5 SGPP1 PAFAH1B3 DNMT1 SLC27A2 MTHFD1 PAH ICAM1 SLC2A1 GPX2 PAK1 ACP5 SLC38A1 SLC10A1 PBLD JUNB SLC38A4 FOS PCMT1 PRDX2 SLC6A12 GSTZ1 PDGFRA RAD23A SOCS2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PLVAP SOCS3 AFM CCNE1 SPINK1 AGT PDCD5 SPTAN1 AHNAK FXYD1 SRD5A1 AHSG HAMP SRP14 AK1 SPINT2 SSR1 AKAP12 LGALS4 STAT3 AKR1A1 ECH1 TACC3 ALDH18A1 AKT2 TAGLN2 ALDH6A1 BLVRB TAT ALDH8A1 CYP2A7 TFRC ALPL GSK3A THBD AMDHD1 PAFAH1B3 TMEM45A ANGPTL3 ETHE1 TMPO ANLN APOE TPR AP3S1 APOC1 TRIM28 APCS APOC4 TTK API5 ZNF342 TYMS APOA2 ERCC1 UBE2C APOA5 FOSB UCK2 APOB SULT2A1 UGT2B4 APOF BAX UQCRB AQP1 FTL USP1 AQP9 VCP ARF4 VNN1 ARID4B VWF ARL4A ZNF238 ATAD2 AADAC ATF2 ABCB10 ATF3 ABCB4 ATF5 ABCC6 ATIC ABCG2 ATP5D ABHD2 AURKA ABHD3 AURKB ABL2 B4GALT3 ACACA BAX ACADL BGN ACP5 BHLHE40 ACSL4 BIRC5 ACSM5 BMI1 ADI1 BMP4 ADSL BRP44 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) BUB1B COX5B C14orf68 CPA3 C1orf43 CPN1 C20orf3 CPNE1 C3 CRYZ CTNNB1 C4BPA CTSD C4BPB CUTA CA5A CXADR CALD1 CXCL1 CALM1 CXCL10 CAPN1 CXCL2 CASP4 CYB5R3 CBR1 CYP2B7P1 CBS CYP3A7 CCNA2 CYP4F11 CCNB2 CYP4F3 CCND2 DAD1 CCT2 DAK CD44 DCK CD58 DDOST CD70 DDX1 CD9 DDX3Y CD99 DES CDC42SE1 DKK1 CDK7 DPT CELF2 DSP CETN2 DSTN CFHR2 DYNC1H1 CFLAR E2F1 CHAF1A EBPL CHD9 ECT2 CKAP4 EEF1A1 CKB EEF1G CKS2 EGR1 CLDN4 EIF3B CLK2 ELL2 CLNS1A EMP2 COL18A1 ENO2 COL4A1 ENPP2 COL6A1 EPHA3 COTL1 EPHB4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) EPO HIST1H2AC ERBB3 HJURP ESD HKDC1 EZH2 HLA-C F12 HLA-DRB1 F2 HMGN2 F8 HMOX2 FAM169A HN1 FAM36A HNF4A FASTK HNRNPA0 FGFR1 HNRNPA1 FLNA HNRNPF FMO4 HSD11B1 FNBP1 HSP90AB1 FOXO1 HSPA1A GABRE HSPE1 GALE HTATIP2 GALK1 ID1 GBAP1 IDH3A GCDH IDI1 GCHFR IGFBP1 GCLC IGFBP2 GLDC IGHG1 GLRX3 IGL@ GLS2 IL12A GMFG IL1RN GNAI1 INTS8 GNB1 IPO7 GNB2L1 IPO9 GOLM1 ITGB2 GPLD1 KDM5B GPR88 KIF20A GPT KIF4A GSTA1 KLF13 GSTM2 KLF6 GTF2I KLF9 H19 KPNA2 HAL KRAS HBB KRT17 HCFC1 KRT18 HIBADH LAMB1 HINT1 LAPTM5 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) LCP1 PARP1 LDHB PARP12 LDLR PCCB LIFR PCTP LITAF PDIA4 LMNB1 PDIA6 LOXL2 PDK4 LRP6 PELI1 MAL2 PEPD MAP1B PHB MARCO PHYH MASP2 PIGC MGP PIPOX MGST2 PLOD1 MMP11 PLXNC1 MMP15 PNRC1 MMP7 POFUT1 MPDZ PPP2R1A MPV17 PRDX2 MPZL1 PRDX4 MRPL42 PRKAR1A MSN PRKCSH MST1 PRPS1 MX1 PSMB3 MYC PSMB9 N4BP2L1 PSMD4 NARS PTP4A1 NDRG2 PTPRC NDUFS8 PTPRF NEDD4 QSOX1 NEK3 RARRES2 NEU1 RBL2 NFYA RBP5 NONO RCL1 NR1I2 RCN1 NUF2 RDH16 NUP205 REG1A NUSAP1 REL OIT3 RFX5 ONECUT2 RGS1 ORM1 RHBG PABPC1 RPL29 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) RPL30 SNRPD2 RPL38 SOCS1 RPLP1 SORBS2 RPS13 SOX9 RPS16 SPCS2 RPS19 SPHK1 RPS27 SPRY2 RTN3 SRD5A2 S100A4 SREBF2 S100P SSB SAA4 ST6GAL1 SAR1B STIP1 SARDH STOML2 SART1 SUZ12 SCARB1 SYBU SDC1 TAF1 SDS TAGLN SEC61A1 TARBP1 SEMA3F TBCA SEMA5A TBCB SERPINA10 TBCE SERPINA5 TBL1XR1 SERPINA7 TCEA1 SERPINE2 TCF4 SFN TFF3 SFPQ TGFB1 SGCE THY1 SHB TIMM17A SIAH1 TIMP2 SLA TIMP3 SLC12A2 TKT SLC12A8 TMBIM6 SLC22A18 TMEM9 SLC25A13 TNF SLC25A15 TNFSF10 SLC28A1 TNFSF13B SLC38A2 TP53BP2 SLC4A4 TPD52 SLCO3A1 TPD52L1 SMARCA2 TPT1 SMG7 TRIB1 SNRPA1 TRIB2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TSN APEX1 TTPA APRT TUBA1A AQP7 TWF1 ARHGAP18 TXN ARHGAP4 UBAP2 ARMC1 UBE2T ARPC1A UBR5 ARSA UBXN2B ASL UQCRFS1 ASPH VCAN ASPSCR1 VDAC2 ATP2A2 VPS72 ATP5A1 YBX1 ATP5F1 YWHAH ATP5J ZC3H11A ATP6V0B ZWILCH ATP6V1B2 ZWINT ATRN A1BG BAK1 ABCB1 BAMBI ABCB11 BARD1 ABCD3 BASP1 ABCF1 BAT1 ABHD6 BAT2L2 ACO2 BCL2 ACP1 BCL2L1 ACSM2A BCLAF1 ACSM3 BCOR ACTG1 BDH1 ACTR6 BDH2 ADAM15 BIN1 ADAM9 BLMH ADK BMP2 ADRB2 BPTF AGXT2L1 BRCA2 AHCYL1 BTG2 AKR1C1 BZW1 AMT C13orf37 ANAPC13 C14orf1 ANGPTL4 C14orf109 ANXA10 C19orf43 ANXA7 C1orf112 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) C1QB CDO1 C21orf33 CDSN C6orf108 CENPE C9orf103 CENPI C9orf150 CENPM CA1 CFL1 CALM2 CFL2 CAMSAP1L1 CFP CAPN2 CGREF1 CAPZA2 CHKA CASP10 CHML CASP2 CIDEB CASP3 CIITA CASP8 CIT CBR4 CITED2 CBX3 CITED4 CCDC109B CLEC1B CCDC21 CLEC3B CCDC93 CLEC4M CCL16 CLGN CCL19 CLSTN1 CCNE1 CLTA CCNG1 CNBP CCT7 CNDP2 CD163 CNGA1 CD19 CNIH4 CD34 CNN3 CD36 COL15A1 CD37 COL3A1 CD4 COL5A1 CD47 COL6A2 CD48 COMMD1 CD53 COPA CD8A COPS5 CDC6 CORO1A CDCA5 COX6C CDCA7 COX7A2L CDCA8 CPE CDK3 CRAT CDKN1C CRIP1 CDKN2A CSDA CDKN2C CSNK2B Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) CSRP2 DNAJC6 CTBS DOCK5 CTNNA1 DOCK9 CTNNA2 DPM1 CTNNAL1 DPM2 CTPS2 DRG2 CTSO DTYMK CTTN DUSP12 CUL4A DUSP3 CUX2 DUT CXCL16 DVL1 CYC1 DVL3 CYFIP2 DYRK2 CYP1A1 ECHDC2 CYP1B1 ECM2 CYP2C19 EEF1D CYP39A1 EEF2 CYP3A43 EFNB1 CYP4F2 EIF3H DAB1 EIF4A2 DAPK1 EIF4B DAZAP2 EIF4G1 DBN1 ELOVL5 DCAF7 ENAH DDT EPAS1 DDX11 ERP44 DDX3X ESRP2 DEF6 ETFB DEPDC1B ETFDH DGCR2 ETHE1 DHFR ETNK2 DHODH ETS1 DHRS1 ETV4 DHX9 EXPH5 DIO1 F5 DIRAS3 FADD DLD FADS1 DMGDH FAM13A DNAJA1 FAM49B DNAJB4 FAM83H DNAJB9 FAM8A1 DNAJC10 FANCI Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) FBXO2 HAT1 FCER1G HBA2 FCGR2B HCLS1 FCGR3A HDAC1 FDX1 HDLBP FERMT2 HELLS FGFR4 HELZ FHIT HEXB FHL1 HGF FHOD3 HGS FKBP11 HIC2 FKBP5 HIF1A FOXF1 HIF1AN FOXM1 HIST1H2BK FOXN3 HIST2H2BE FTL HLA-DQB1 G3BP2 HMGCR G6PD HMOX1 GABARAPL1 HNRNPH1 GADD45A HNRNPM GALNT10 HNRNPR GATA4 HPGD GCGR HYAL1 GDF15 HYOU1 GEM IDUA GINS1 IER3 GJA1 IFI44 GLG1 IFI6 GLRX IGHG3 GLYATL1 IGHM GMFB IGLL1 GNAI2 IGSF1 GNE IL10 GOLGA4 IL10RA GPX3 IL15RA GSTA4 IL7R GSTM3 ILF3 GTF3C2 IMPA1 GZMB IMPA2 H2AFV INHBE H2AFX INPP5D HADHA IQGAP2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) IQGAP3 MATN2 IRF9 MATR3 ITGA5 MAZ ITGA6 MBNL2 ITGB1BP1 MBNL3 ITIH1 MCC IVD MCF2L JUNB MCL1 KAL1 MCM5 KIAA0100 MCM7 KIAA1211 MCRS1 KIAA1310 MED1 KIF11 MEF2C KLB MEIS2 KLHL23 MERTK KLK3 MFAP3 KNTC1 MFAP4 KPNB1 MGLL LAMP1 MGMT LANCL1 MIF LDHD MLF1IP LGALS4 MLLT11 LIF MMAB LPCAT1 MMD LRRC42 MMP12 LRRC59 MRPL55 LTB4R2 MRPS23 LUM MT1G LY6E MT1L MAD1L1 MTDH MAF1 MTFR1 MAFB MTSS1 MAFG MUC2 MAOA MUT MAOB MYH9 MAP2 MYLK MAP3K5 MYO10 MAPK1 MYO1E MAPK13 MYO5C MAPK3 MYPN MAPK6 MYRIP MAPRE1 NARF Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) NAT1 PDGFA NAV2 PDK1 NCALD PFKFB1 NCAPD2 PFN1 NCBP1 PFN2 NCK2 PGD NCOA2 PHGDH NCOA3 PHKA2 NCRNA00081 PHLDA2 NCSTN PIGF NDUFB8 PIR NF2 PKMYT1 NFIC PLAU NHP2 PLCG2 NID1 PLEKHF2 NOTCH3 PLK1 NPAS2 PLOD2 NPC1 PML NQO1 PNN NQO2 PNP NR4A1 PNPO NR5A2 POLD1 NRG1 POLR2K NTS PON2 NUCB1 PPA2 NUDT6 PPOX NUP133 PPP1R1A NUP155 PPP2R3C OAS2 PPP2R5A OCRL PPT1 OGT PRDX5 OLIG2 PRIC285 ONECUT1 PRKAB2 OPCML PRKAR2A ORC3L PRKCA OSTC PRKCI P2RX5 PROC PADI2 PRPF38B PAG1 PRPF6 PAM PRPF8 PBK PRUNE PCCA PSD3 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PSMB10 RPL35 PSMD10 RPL5 PSMD11 RPL8 PSMD14 RPN1 PSMD6 RPN2 PSME1 RPP21 PSME2 RPS11 PSPH RPS4X PTEN RREB1 PTGFRN RUNDC3B PTGR1 S100A11 PTP4A3 S100A13 PVRL2 SAC3D1 PWP1 SCD PYCR1 SDPR PYCR2 SEC14L2 PYGL SEL1L3 PYGO2 SEPT4 QPRT SERPINA4 RAB10 SERPINB9 RAB14 SERPINF1 RAB1A SFRS1 RAB27A SH3BGRL3 RAB4A SKP2 RAB7L1 SLC11A2 RAD51AP1 SLC13A3 RAP2A SLC16A1 RARRES3 SLC16A10 RBBP7 SLC1A2 RBM25 SLC1A4 RBPMS SLC1A5 RCN2 SLC22A15 REG3A SLC22A4 RER1 SLC23A2 RFTN1 SLC27A5 RHOBTB1 SLC2A3 RIT1 SLC37A4 RMI1 SLC38A6 RNASE1 SLC39A10 RNF43 SLC39A6 RNPEP SLC3A2 RPIA SLC44A1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) SLC5A6 TLN1 SLC7A1 TM9SF2 SLC7A5 TMED5 SLC9A3R1 TMEM106C SLCO1B1 TMEM194A SLPI TMEM27 SMAD2 TMEM48 SMAD4 TMEM49 SMARCA1 TMEM65 SMARCC1 TMEM97 SMG5 TMEM98 SMYD3 TMSB10 SORD TMSB4X SPAG7 TMX1 SPINT1 TNFAIP3 SPINT2 TNFSF4 SRI TOB1 SRPX TP53I3 SSR2 TP53TG1 SSRP1 TPM3 ST13 TPM4 ST3GAL6 TRDMT1 STT3A TREX2 STXBP6 TRIM22 SUCLG2 TRIM24 SULT1A1 TRIM55 SULT1B1 TRIO SUMO3 TRIOBP SUPV3L1 TRMT112 SYNCRIP TROAP TAF9 TRPC1 TALDO1 TSKU TAP1 TTYH3 TAX1BP3 TUBE1 TBC1D9B TUBG1 TBCK TUFM TCEB2 UBA2 TENC1 UBE2L6 TFPI2 UBE2V2 TFR2 UCP2 THOC5 UGCG TIA1 UGDH Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) UGP2 ACBD3 UGT1A1 ACMSD UGT1A10 ACTA2 UQCRC1 ACTL6A USP14 ACTN1 USP30 ACTN2 USP37 ACTR2 UXS1 ACVR1 VARS ACYP2 VAT1 ADAM8 VCL ADCY5 VEGFA ADCYAP1 VEGFB ADD3 VPS35 ADNP WNK1 ADRA1A WNK3 ADSSL1 WWC1 AGPAT2 XPOT AGPAT3 XPR1 AGR2 YKT6 AIFM1 YWHAQ AIG1 ZEB2 AIM1 ZFP36L1 AIP ZNF184 AK4 ZNF185 AKAP1 ZNF652 AKR1B1 ZNF706 AKR7A2 ZNHIT3 AKR7A3 ZXDA AKT1S1 ZYG11B AKT3 A2BP1 ALAD AARS ALCAM AASS ALDH3A1 ABCA1 ALDH5A1 ABCC1 ALKBH1 ABCC5 ALOX5AP ABCF2 AMFR ABCG1 AMIGO2 ABI3 ANAPC7 ABP1 ANGEL1 ACAN ANGPT2 ACAT2 ANGPTL6 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) ANKRD27 ASNS ANKRD42 ASPA ANKRD46 ASRGL1 ANPEP ATF1 ANXA6 ATM AOC3 ATOX1 AP2A2 ATP12A AP2B1 ATP1B3 AP3B1 ATP2B1 AP3M2 ATP2B2 APH1A ATP2C1 APLNR ATP4B APOE ATP5G2 APOL3 ATP5H APOL6 ATP5J2 APOM ATP5O AQP11 ATP6V0C AQP6 ATP6V0E2 AQP7P1 ATP6V1A ARAP3 ATP6V1D AREG ATP6V1E1 ARF1 ATP6V1F ARF3 ATP6V1H ARF6 ATP7A ARFGEF1 ATP8B1 ARFGEF2 ATXN10 ARHGAP1 ATXN1L ARHGAP8 AUP1 ARHGEF1 AVPR1B ARHGEF12 AVPR2 ARHGEF6 AXIN2 ARL1 AZI1 ARL2 B3GNT5 ARL4C B4GALT1 ARL5A BACE2 ARNTL2 BAD ARPC1B BAG2 ARRDC4 BAI2 AS3MT BAIAP2 ASAP2 BAIAP2L1 ASCC3 BAIAP2L2 ASF1B BANF1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) BBX C1orf77 BCAM C1RL BCAT2 C2 BCL2A1 C20orf24 BCL6 C21orf2 BCORL1 C2orf27A BDKRB1 C2orf54 BEND5 C2orf88 BEST1 C4orf34 BEX2 C5orf22 BHMT2 C5orf24 BIRC3 C5orf32 BMP1 C5orf33 BMS1 C6orf192 BOK C7orf25 BOLA1 C7orf27 BPHL C7orf30 BRD3 C7orf58 BSG C8orf4 BTD C9orf100 BTG3 C9orf16 BTN2A1 C9orf3 BTN2A2 C9orf5 BTN3A3 CA14 BUB3 CABLES2 C10orf35 CACYBP C10orf82 CALCR C12orf32 CALCRL C12orf57 CAMK2G C13orf33 CAMLG C14orf159 CAPRIN1 C14orf182 CAPZA3 C14orf93 CASC3 C15orf23 CASP6 C15orf41 CASP9 C16orf75 CAV1 C19orf2 CAV2 C19orf6 CBFA2T3 C1orf100 CCDC132 C1orf106 CCDC53 C1orf128 CCDC88A C1orf151 CCHCR1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) CCL13 CEACAM5 CCL21 CEBPA CCL4 CEBPD CCL5 CENPA CCND3 CENPW CCNF CEP192 CCNH CEP97 CCNI CFHR1 CCT8 CFHR3 CD109 CFHR4 CD151 CFTR CD164 CG012 CD2 CHCHD2 CD3D CHD4 CD40 CHEK1 CD59 CHERP CD5L CHI3L1 CD63 CHN1 CD83 CHST11 CDA CHUK CDC123 CIAO1 CDC23 CISH CDC25A CKS1B CDC25C CLDN10 CDC42 CLDN14 CDC42EP1 CLDN15 CDC7 CLDN7 CDCA4 CLEC10A CDCA7L CLEC2B CDH13 CLEC4G CDH17 CLIC4 CDHR2 CLN3 CDK13 CLOCK CDK2 CLPTM1 CDK2AP1 CLPTM1L CDK5 CMTM3 CDK5RAP2 CNOT6 CDK5RAP3 CNPY2 CDK6 COBLL1 CDK9 COCH CDKN2B COG5 CDRT1 COL11A1 CDV3 COL14A1 CEACAM1 COL5A2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) COL7A1 CYP26A1 COLEC11 CYP2C18 COPB1 CYP2D7P1 COX4I1 CYP4B1 CPA4 CYP4F12 CPN2 CYP4V2 CPNE3 CYP51A1 CPPED1 CYP7A1 CPSF2 CYP7B1 CPT2 CYTH3 CRABP1 DACT1 CRABP2 DAG1 CREM DAP CRH DAXX CRISPLD2 DCAF6 CRLS1 DCPS CROT DCTN4 CRYAA DCUN1D5 CRYAB DDX12 CRYM DDX17 CS DDX18 CSAD DDX53 CSF1 DEFA1 CSNK1A1 DEFB1 CSNK1G3 DEGS1 CSNK2A1 DENND5B CSRP2BP DEPDC1 CTBP2 DEPDC7 CTNNBL1 DFNA5 CTNND1 DHTKD1 CTNND2 DHX15 CTPS DIABLO CTRB1 DIAPH2 CTSL1 DICER1 CXCL14 DKC1 CXCL6 DLAT CXCL9 DMD CXorf40A DNAH1 CYB5B DNAJC12 CYCS DNAJC25- CYP17A1 GNG10 CYP21A2 DNAJC9 DNMBP Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) DNMT3A ELMO1 DONSON EML1 DPAGT1 EML2 DPM3 EMR1 DPP3 ENO3 DPYS ENPEP DPYSL3 EPB41L2 DR1 EPB41L3 DSE EPB41L4B DSG1 EPHA2 DSTYK EPRS DTL ERAL1 DUSP23 ERBB2 DUSP4 ERI3 DUXAP10 ERMP1 DVL2 ERP29 DYNC1I1 ESR1 DYNLL1 ETF1 ETV1 EVI2A EBAG9 EVL ECE1 EXT1 ECEL1 EXTL3 ECM1 EZR EDEM1 F13A1 EFEMP1 F2R EFHC1 F2RL1 EFR3A F3 EFR3B F7 EFTUD2 F9 EGF FAAH EGLN3 FABP12 EHD2 FADS2 EIF2B3 FAM120A EIF2C2 FAM129B EIF3I FAM134B EIF4A3 FAM136A EIF4G2 FAM189B EIF5A FAM20B ELAVL1 FAM21A ELF3 FAM38A ELF4 FAM48A Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) FAM63A FXN FAM72B FXYD1 FARSB G6PC FASLG GAA FASN GAB1 FAT4 GABARAP FBL GADD45B FBXW2 GALNT1 FCN2 GALNT4 FDXR GALNT7 FES GBA FGF22 GDAP1 FGFR3 GDF11 FGFRL1 GDI2 FGL2 GEMIN4 FGR GFI1 FIBP GGPS1 FILIP1L GGT5 FKBP1A GIMAP5 FKBP2 GLO1 FKBP4 GLUD2 FLAD1 GMPPA FLJ22763 GMPR2 FLJ39653 GMPS FLJ39739 GNA12 FLNC GNAO1 FLOT2 GNAS FLT1 GNB2 FLT4 GNB4 FMR1 GORASP2 FNIP2 GPATCH4 FOLH1 GPBP1 FOSB GPC6 FOXA3 GPI FRAT2 GPM6A FTH1 GPS1 FUBP1 GPX1 FUCA2 GRAMD1A FUNDC1 GRB10 GRB14 FUS GRB2 FUT6 GREM2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) GRHL1 HLA-F GRIN2A HMGB1 GRIN2C HMGB2 GRLF1 HMGCS1 GSPT1 HMGN1 GSR HMGN3 GSTA3 HNF1A GSTK1 HNRNPA3 GSTT1 HNRNPD GTF2A2 HNRNPH3 GTF2B HNRNPK GTF2E1 HOMER1 GTF2E2 HPS5 GTF3C3 HRCT1 GTPBP4 HRK GUK1 HS2ST1 GZMK HSD3B1 HAO2 HSPA4L HAX1 HSPG2 HBD HSPH1 HBXIP IARS HCG9 IARS2 HDAC11 ICAM3 HDAC6 ID3 HDAC9 IDH2 HDC IER2 HEATR6 IER3IP1 HERC2P2 IFI30 HERC3 IFIT3 HERC4 IFITM3 HES1 IFNG HEXA IFRD1 HFE IFT88 HHAT IGF2BP1 HIST1H2AE IGF2BP2 HIST1H2BC IGF2BP3 HIST1H2BH IGFBP4 HIST1H3J IKBKAP HIST2H4B IKBKB HK1 IKZF1 HLA-DPA1 IL10RB HLA-DPB1 IL18 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) IL18R1 KCMF1 IL1A KCNJ3 IL1R1 KCNJ4 IL1RAP KCNK1 IL1RL1 KCNN3 IL2 KCNQ2 IL2RB KCNT2 IL2RG KCTD11 IL3 KCTD12 IL32 KDELR2 IL4R KDELR3 IL5 KDM3A ILK KIAA0317 IMMT KIAA0427 IMPAD1 KIAA1147 INPP5E KIAA1267 INSL3 KIAA1522 INSR KIAA1967 IP6K1 KIF14 IPO5 KIF18B IRF1 KIF2C IRF2BP2 KIFC3 IRF7 KLC1 IRS1 KLF15 IRX3 KLF5 ISL2 KLRB1 ITGA2 KLRK1 ITGA3 KMO ITGA7 KPNA4 ITGA9 KRT10 ITGAV KRT19 ITGAX KRT20 ITGB5 KRT23 ITIH3 L1CAM ITLN1 LACTB2 ITM2B LAGE3 ITPA LAMA5 ITPR1 LAMB3 IVNS1ABP LAMC1 JUND LARP4B KANK1 LASP1 KARS LBH Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) LCMT1 LOC541471 LENG8 LOC55908 LEPR LOC642852 LEPRE1 LOC642943 LGALS9 LOC645561 LGMN LOC654342 LHFPL2 LOC727941 LHX3 LOC728743 LIG1 LOC729083 LILRA2 LONP1 LLGL2 LONP2 LMAN1 LPIN1 LMAN2 LPL LMO7 LPP LMTK2 LQK1 LOC100128164 LRP1 LOC100128988 LRP11 LOC100129250 LRP12 LOC100129272 LRP8 LOC100129931 LRPAP1 LOC100130744 LRRC17 LOC100131706 LRRC32 LOC100131811 LRRCC1 LOC100132649 LSM2 LOC100132790 LSP1 LOC100133990 LSR LOC100287064 LTBP2 LOC100287530 LTBP4 LOC100287913 LTF LOC100287927 LUZP2 LOC100287938 LYAR LOC100288068 MAD2L2 LOC100288412 MAFF LOC100288937 MAML1 LOC100288985 MAN1A1 LOC100289405 MANF LOC100289469 MAP2K1 LOC100289866 MAP2K3 LOC255167 MAP3K13 LOC283761 MAP3K9 LOC284939 MAP4 LOC339803 MAP6 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) MAPK12 MLEC MAPK8IP1 MLH1 MAPK8IP2 MLXIPL MARCH3 MLYCD MARCKSL1 MMP1 MARK4 MNDA MARS MOGAT1 MARVELD2 MOGS MAT2A MOSPD1 MBD4 MOXD1 MBL2 MPHOSPH10 MBOAT7 MPHOSPH9 MCAM MPZL2 MCEE MRC1 MCM8 MRPL12 MCPH1 MRPL46 MDH1 MRPL9 MDH2 MRPS21 MRPS28 MECOM MSH5 MED21 MSH6 MED23 MSTO1 MEF2B MT1A MEF2D MT1B MELK MT1H MEMO1 MTA3 MEN1 MTAP MEP1A MTCH1 MESDC2 MTHFD2L MET MTHFS METTL7A MTMR4 MFAP3L MVD MFGE8 MXD4 MFSD2A MYADM MGAT4A MYCBP2 MIB1 MYCN MICA MYH11 MICAL3 MYH4 MICB MYL6 MID1 MYL9 MIR155HG MYPOP MKL1 N4BP2L2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) NAAA NOLC1 NAGA NOP10 NAGLU NOS2 NAGS NOV NAPRT1 NPNT NAPSA NPR1 NARS2 NPTX2 NAT15 NR1D2 NAT8 NR1H4 NAT9 NR2C1 NAV3 NRG2 NCAPG NRM NCAPG2 NRP1 NCF1C NRSN1 NCKAP5 NSF NCKIPSD NSMCE1 NCRNA00201 NSUN2 NDC80 NT5DC2 NDFIP2 NT5E NDUFA5 NTRK2 NDUFAF4 NUAK1 NDUFB2 NUDT1 NDUFB7 NUDT21 NDUFS1 NUDT3 NDUFS2 NUDT5 NDUFV1 NUFIP2 NDUFV2 NUP62 NECAB2 NUPR1 NEDD4L OAT NEFL OAZ2 NEK7 OAZ3 NENF ODAM NET1 ODZ2 NFIB OIP5 NHLRC4 OLA1 NHP2L1 OPLAH NKD1 OSMR NKX2-1 OSTM1 NLRP2 OTX2OS1 NME1-NME2 OXA1L NME5 PAAF1 NMI PABPC4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PAFAH1B2 PIK3C3 PAGE4 PIK3R2 PANX1 PIM1 PAPLN PIM2 PAPOLA PIM3 PAPSS1 PITPNB PARD6G PIWIL2 PARP2 PJA2 PAX8 PKD2 PCBD1 PKDCC PCBP1 PKP2 PCGF3 PLA2G15 PCOLCE PLA2G16 PCSK1 PLAC8 PCSK2 PLAGL1 PCYT2 PLBD1 PDCD4 PLCB1 PDCD5 PLCG1 PDCD6 PLEKHA8 PDCD6IP PLGLB1 PDGFB PLGLB2 PDK2 PLK4 PDPK1 PLSCR1 PDXK PLTP PDZK1 PLVAP PECR PLXNB1 PEG3 PMM2 PER1 PMP22 PER2 PMS1 PERP PNMA1 PFDN4 PNMT PFKFB4 POGZ PFKM POLD3 PGCP POLR3G PGP POM121L8P PHB2 POMC PHC2 POP7 PHF3 POT1 PHIP POU2AF1 PHYHIPL PPAP2A PIAS3 PPARA PIF1 PPM1A Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PPM1D PTGIR PPM1F PTGS2 PPP1CB PTMA PPP2R1B PTP4A2 PPP2R2A PTPN1 PPP4R1 PTPN11 PRAP1 PTPN3 PRC1 PTPRD PRDM2 PTPRN2 PRDM5 PTPRO PREB PTS PRELP PUM2 PRG4 PURA PRIM1 PVRL3 PRKACA PXMP2 PRKACB PXMP4 PRKCD PZP PRKD2 RAB11A PRLR RAB11FIP1 PRMT5 RAB11FIP2 PROM1 RAB24 PRPF40A RAB25 PSAT1 RAB28 PSENEN RAB2A PSMA1 RAB31 PSMA2 RAB3A PSMA4 RAB3IP PSMA5 RAB7A PSMB8 RAB8A PSMC2 RABEPK PSMC3 RAC1 PSMC4 RACGAP1 PSMD1 RAD23B PSMD2 RAD51C PSPC1 RALGAPA2 PTAFR RALGDS PTCHD2 RAMP1 PTDSS1 RAPGEF2 PTGDS RASSF1 PTGES RB1 PTGES2 RB1CC1 PTGES3 RBBP4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) RBCK1 RPL7 RBKS RPLP2 RBM10 RPRD2 RBM15B RPS10 RBM34 RPS17 RBM39 RPS18 RBM9 RPS27A RCC2 RPS3 RDH10 RPS6KA1 RDH14 RPS7 RDX RPS8 RECQL4 RRAS REEP5 RRM2 REEP6 RRP1B RELB RSF1 RFC5 RSL24D1 RGS10 RSPRY1 RHBDD3 RSRC1 RHOBTB3 RTCD1 RHOU RTN2 RNASE4 RTP3 RNASE6 RUFY1 RNF103 RUFY3 RNF13 RUSC1 RNF157 S100A12 RNF213 S100A16 RNF4 S1PR1 ROBO1 SAFB ROD1 SBDS RPA1 SCARB2 RPA3 SCOC RPGR SCUBE2 RPL10A SCYL1 RPL13A SDC2 RPL17 SDF2L1 RPL23 SDHA RPL27 SDHB RPL27A SDHC RPL3 SDHD RPL37 SEC11A RPL37A SEC31A RPL39L SEC62 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) SELM SLC20A2 SEMA3C SLC22A11 SEMA6A SLC22A3 SEPHS1 SLC22A5 SEPHS2 SLC22A7 SEPN1 SLC23A1 SEPT2 SLC25A18 SEPT9 SLC25A3 SERINC1 SLC26A2 SERPINB1 SLC26A6 SERPINB12 SLC2A5 SERPINB3 SLC2A9 SERPINB8 SLC31A2 SERPINH1 SLC34A1 SESTD1 SLC35B1 SF1 SLC36A1 SF3A3 SLC39A1 SF3B1 SLC39A4 SFRS17A SLC39A5 SFRS2B SLC46A3 SFRS2IP SLC47A1 SFRS3 SLC5A5 SFRS4 SLC6A13 SFXN1 SLC6A2 SGK223 SLC6A5 SH3GLB2 SLC6A6 SHARPIN SLC6A8 SHISA4 SLC9A3R2 SIRPA SLCO1A2 SIRT5 SLCO1B3 SKAP1 SLCO2A1 SKP1 SLIT2 SLBP SLIT3 SLC12A7 SMAD6 SLC15A2 SMARCA4 SLC16A11 SMARCC2 SLC16A3 SMARCD1 SLC16A4 SMARCE1 SLC16A5 SMC1A SLC19A2 SMC2 SLC19A3 SMPDL3A SLC20A1 SMYD2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) SNAI1 STX16 SNAI2 STX6 SNAR-C1 SUB1 SND1 SULT1A4 SNORA43 SUMO1 SNRNP200 SUN2 SNRNP27 SUPT16H SNRPC SWAP70 SNRPD1 SYK SNRPF SYNJ2 SNRPG SYTL4 SNX27 TACO1 SNX7 TADA1 SOCS6 TAF2 SOD3 TAF6 SORBS1 TAGAP SORBS3 TAP2 SOS1 TAPBP SOX12 TATDN2 SP3 TAX1BP1 SPEN TBC1D13 SPN TBX3 SPR TCF21 SPRR2G TCL1A SPRYD4 TCOF1 SREBF1 TDP2 SRP72 TEAD4 SRXN1 TERF1 SS18L1 TESC SST TFDP1 ST7 TFIP11 STAG2 TFPI STARD13 TGFA STARD5 TGFB1I1 STARD7 TGFB2 STAT4 TGFB3 STAT6 TGFBI STEAP3 TH1L STK24 THBS2 STK35 TIAL1 STK39 TIE1 STOM TIMD4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TINF2 TPRKB TK1 TPST1 TLR3 TRA@ TM4SF1 TRAM1 TM4SF4 TRIM15 TM4SF5 TRIM23 TM9SF3 TRIM26 TMC6 TRIM35 TMCO1 TRNP1 TMED1 TROVE2 TMEM109 TSC22D1 TMEM150C TSC22D2 TMEM183A TSC22D3 TMEM194B TSEN54 TMEM205 TSPAN13 TMEM45B TSPAN5 TMEM50B TSPAN7 TMEM66 TSPY1 TMOD1 TTC13 TNC TTC3 TNFAIP1 TTC38 TNFRSF10A TTC5 TNFRSF10B TTC9 TNFRSF10C TUBA1C TNFRSF12A TUBA3D TNFRSF19 TUBB2C TNFRSF1B TUBB4 TNFRSF25 TUBG2 TNFSF14 TUG1 TNS1 TXN2 TNXB TXNDC5 TOMM20 TXNIP TOR1B TXNL4A TP53 TXNRD1 TP53BP1 TYMP TP63 TYROBP TP73 TYSND1 TPD52L2 U2AF2 TPM1 UAP1 TPRA1 UBA1 TPRG1 UBA52 TPRG1L UBC Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) UBE2A WNT11 UBE2D1 WRB UBE2L3 WRNIP1 UBE2M XAGE1A UBE2Q1 XK UBE3B XPO5 UBE4A XPO7 UBN2 XRCC5 UBXN4 XRCC6 UGT1A4 YAP1 UGT1A9 YPEL1 UGT2B15 YWHAB UPB1 YWHAE UPF1 YY1AP1 UQCRH ZBTB20 URM1 ZC3H13 UROC1 ZC3H15 USO1 ZDHHC5 USP10 ZFAND5 USP15 ZFHX3 USP21 ZGPAT USP5 ZHX1 UTP3 ZIC2 UTRN ZKSCAN1 UXT ZNF165 VAMP3 ZNF202 VAMP8 ZNF24 VANGL1 ZNF266 VIL1 ZNF32 VIPR1 ZNF323 VPS41 ZNF354A VSNL1 ZNF384 WAC ZNF385B WAS ZNF431 WASF1 ZNF451 WBP2NL ZNF551 WDR1 ZNF595 WDR20 ZNF702P WEE1 ZNF83 WFDC1 ZNRF3 WIPF1 ZRANB2 WIZ ZSCAN21 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) A1CF ACSL3 AACS ACTC1 AADAT ACTL8 AAMP ACTN4 AAVS1 ACTR10 ABCA2 ACTR1A ABCA4 ACTR3 ABCA6 ACVR1C ABCA8 ACVRL1 ABCA9 ADAM10 ABCB6 ADAM17 ABCC10 ADAM29 ABCC2 ADAMTS17 ABCC3 ADAMTS2 ABCC4 ADAMTS4 ABCC9 ADAMTS7 ABCD2 ADAMTS9 ABCG5 ADAMTSL4 ABCG8 ADARB1 ABHD12 ADCY1 ABHD13 ADCY7 ABHD14B ADCYAP1R1 ABI2 ADD2 ABL1 ADIPOR1 ABLIM1 ADORA1 ABLIM3 ADORA2A ABO ADORA3 ABR ADRA2B ACACB ADRB3 ACAD11 ADRBK2 ACBD4 ADSS ACBD5 AEBP2 ACCN3 AFF2 ACCS AFF4 ACE AFG3L1 ACE2 AFG3L2 ACIN1 AG2 ACOT12 AGA ACOT2 AGER ACOX3 AGMAT ACPL2 AGPAT1 ACPP AGPAT4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) AGPAT9 AMZ1 AGPS ANAPC11 AGTR1 ANGEL2 AGTR2 ANGPT1 AGXT2 ANK1 AGXT2L2 ANKFN1 AHCTF1 ANKIB1 AHDC1 ANKMY2 AHR ANKRD1 AHSA2 ANKRD10 AIF1 ANKRD12 AIM2 ANKRD36 AIMP1 ANKRD36B AK2 ANKRD37 AKAP10 ANKS1A AKAP13 ANO1 AKAP2 ANO3 AKAP8 ANP32B AKAP8L ANP32E AKAP9 ANTXR2 AKIRIN1 ANXA2P1 AKT1 ANXA2P3 AKT2 ANXA3 AKTIP ANXA9 ALDH3B1 AP1AR ALDH3B2 AP1B1 ALDH7A1 AP1M2 ALG13 AP1S1 ALG14 AP1S2 ALG9 AP2M1 ALK AP2S1 ALMS1 APAF1 ALPI APBB1IP ALPK3 APC ALS2CL APCDD1 ALS2CR4 APIP AMD1 APOA1BP AMICA1 APOA4 AMN APOL2 AMPD1 APOO AMPD2 APPBP2 AMPH AQP4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) ARCN1 ASH1L ARF5 ASNA1 ARFGAP1 ASNSD1 ARFRP1 ASPM ARHGAP24 ASPN ARHGAP29 ASXL1 ARHGAP32 ATAD3A ARHGAP39 ATAD3B ARHGAP5 ATCAY ARHGAP9 ATE1 ARHGEF10L ATF4 ARHGEF2 ATF6 ARHGEF3 ATF7 ARHGEF7 ATG10 ARHGEF9 ATG12 ARID2 ATG2A ARIH2 ATG3 ARL2BP ATG4B ARL4D ATG5 ARL6IP5 ATG9B ARMC4 ATL3 ARMC6 ATP10B ARMC8 ATP13A2 ARMCX2 ATP13A3 ARMCX3 ATP1A3 ARNT2 ATP1B1 ARNTL ATP1B4 ARPC2 ATP2A3 ARPC3 ATP2B4 ARPC4 ATP2C2 ARPP19 ATP4A ARPP21 ATP5B ART1 ATP5C1 ART4 ATP5E ASAH1 ATP5G3 ASAP3 ATP5L ASB12 ATP6AP2 ASB15 ATP6V0D1 ASB4 ATP6V0E1 ASCC1 ATP6V1B1 ASCL1 ATP6V1C1 ASF1A ATP7B Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) ATP8B2 BLZF1 ATP8B5P BMP8A ATXN1 BMPR1B ATXN2L BNIP3L AVIL BNIPL AVPR1A BOD1 AXIN1 BOLA2 AZGP1P2 BOLA2B AZIN1 BOP1 AZU1 BPNT1 B3GAT1 BRAF B3GAT3 BRCA1 B3GNTL1 BRD4 B4GALNT2 BRD7 B4GALT5 BRMS1 B4GALT6 BRP44L BACH2 BRPF1 BAGE BSDC1 BAI3 BSND BAP1 BST2 BARX1 BTBD1 BAT3 BTBD6 BAZ2A BTF3 BAZ2B BTG1 BBS2 BTN3A2 BCAS1 BTNL9 BCAT1 C10orf10 BCKDHA C10orf116 BCKDHB C10orf119 BCL10 C10orf26 BCL2L11 C10orf46 BCL3 C10orf53 BCR C10orf72 BDNF C11orf10 BEND6 C11orf54 BHLHE41 C11orf71 BID C11orf73 BIK C11orf9 BIRC8 C12orf4 BLCAP C12orf49 BLM C12orf53 BLVRA C12orf60 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) C12orf73 C1orf203 C12orf75 C1orf212 C13orf1 C1orf216 C14orf101 C1orf25 C14orf102 C1orf38 C14orf105 C1orf53 C14orf119 C1orf57 C14orf128 C1orf91 C14orf129 C1QBP C14orf142 C1QTNF3 C14orf166 C20orf166 C14orf4 C20orf199 C14orf43 C20orf30 C14orf45 C20orf4 C15orf17 C20orf79 C15orf48 C20orf94 C15orf5 C21orf45 C15orf63 C21orf59 C16orf13 C21orf63 C16orf3 C22orf28 C16orf45 C2orf24 C16orf5 C2orf29 C16orf54 C2orf55 C16orf58 C2orf72 C16orf62 C3AR1 C16orf72 C3orf34 C17orf107 C3P1 C17orf108 C4B C17orf53 C4orf3 C17orf71 C4orf41 C18orf32 C4orf43 C18orf55 C4orf44 C19orf12 C4orf7 C19orf22 C5AR1 C19orf25 C5orf27 C19orf42 C5orf30 C19orf56 C5orf44 C19orf66 C5orf58 C1GALT1C1 C6orf106 C1orf131 C6orf129 C1orf135 C6orf136 C1orf194 C6orf145 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) C6orf165 CAPNS1 C6orf203 CAPS C6orf211 CARD18 C6orf48 CARD6 C6orf62 CARM1 C6orf64 CARS C6orf81 CASK C7orf13 CASP1 C7orf28A CASP7 C7orf28B CAST C8G CBFB C8orf47 CBLB C8orf59 CBWD1 C8orf76 CBX2 C9orf11 CBX4 C9orf125 CBX8 C9orf156 CCDC102B C9orf44 CCDC104 C9orf69 CCDC109A C9orf91 CCDC117 CA12 CCDC124 CA6 CCDC126 CAB39 CCDC14 CABC1 CCDC146 CACHD1 CCDC3 CACNA1D CCDC39 CACNA2D1 CCDC47 CACNB1 CCDC55 CACNB2 CCDC6 CACNB3 CCDC62 CAD CCDC68 CADM1 CCDC71 CALB1 CCDC8 CALB2 CCDC80 CALCOCO2 CCDC85A CALHM2 CCDC86 CALU CCDC88C CAMK1D CCDC94 CAND1 CCDC97 CANT1 CCK CAP1 CCL1 CAPN7 CCL11 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) CCL17 CDC42EP4 CCL3L3 CDC45 CCL8 CDC5L CCNC CDCP2 CCNDBP1 CDH10 CCNE2 CDH11 CCNG2 CDH15 CCNO CDH4 CCNT1 CDH5 CCNT2 CDH8 CCR1 CDHR3 CCR2 CDHR5 CCR5 CDK11B CCR6 CDK19 CCR7 CDK2AP2 CCRN4L CDKN1B CD1C CDKN2AIPNL CD200 CDKN2D CD22 CDT1 CD244 CDX1 CD247 CDX2 CD28 CEACAM6 CD300A CEBPG CD3E CECR1 CD3EAP CEL CD40LG CELSR2 CD5 CENPBD1 CD52 CENPC1 CD55 CENPH CD68 CENPJ CD69 CENPK CD7 CENPN CD80 CENPQ CD82 CEP135 CD86 CEP164 CD97 CEP170 CDAN1 CEP57 CDC16 CES8 CDC27 CFC1 CDC34 CFHR5 CDC37 CGB5 CDC40 CGGBP1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) CHAC1 CLTB CHAT CLTC CHCHD10 CLYBL CHCHD8 CMAS CHD3 CMPK1 CHEK2 CMTM6 CHFR CMTM8 CHGB CNDP1 CHIC1 CNOT4 CHMP2A CNP CHMP5 CNTD1 CHN2 CNTF CHORDC1 CNTN2 CHPT1 CNTN3 CHRM4 CNTNAP1 CHRNA5 COASY CHRNB4 COBL CHST13 COIL CHST5 COL12A1 CHSY1 COL16A1 CIC COL22A1 CIR1 COL2A1 CIRBP COL5A3 CITED1 COL9A1 CIZ1 COL9A2 CKAP2 COLEC12 CKAP2L COMMD6 CKAP5 COPE CKMT1B COPS2 CLASP2 COPS3 CLC COPS6 CLCC1 COPS8 CLCN5 COQ3 CLCN7 COQ6 CLDN2 COQ9 CLDN3 CORIN CLEC18C CORO1C CLIC3 CORO2A CLN5 COX11 CLPB COX4NB CLPP COX6A1 CLRN1 COX6B1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) COX7A1 CTAG2 COX8A CTCF CPA1 CTCFL CPEB4 CTDSPL CPLX2 CTDSPL2 CPOX CTF1 CPSF6 CTHRC1 CPVL CTLA4 CR1 CTNS CR2 CTR9 CRADD CTSZ CRBN CTTNBP2NL CRCP CUL1 CREB1 CUL2 CREB3L1 CUL3 CREB3L2 CUL4B CREB3L3 CUL5 CRELD2 CUL7 CRHR2 CUX1 CRIP2 CUZD1 CRISP3 CWC27 CRK CX3CL1 CRLF2 CX3CR1 CRNKL1 CXCL11 CRTAP CXCR3 CRY2 CXCR7 CSDE1 CXorf36 CSF1R CYBB CSF2 CYBRD1 CSF3 CYFIP1 CSF3R CYLD CSGALNACT1 CYP21A1P CSNK1D CYP24A1 CSNK1G2 CYP2A CSNK2A2 CYP2A13 CSRP1 CYP2D6 CSRP3 CYP2F1 CST1 CYP3A CST6 CYP46A1 CSTF1 CYP4A22 CTAG1A CYP4F22 CTAG1B CYTH1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) CYTH4 DEF8 CYTIP DEFA6 D4S234E DENND3 DAAM1 DENND4A DAB2IP DENND4C DAND5 DERA DAP3 DERL1 DAPP1 DERL2 DARC DERL3 DARS2 DEXI DAZL DGAT1 DBC1 DGCR5 DBF4 DGKA DBH DGKD DBNDD1 DGKE DBP DGKG DCAF11 DGKI DCAF13 DGKZ DCAF17 DHCR24 DCAF8 DHDPSL DCBLD2 DHRS13 DCDC2 DHRS2 DCLRE1A DHRS4 DCT DHRS7 DCTN2 DHRS9 DCTN3 DHX34 DDAH1 DHX35 DDB1 DHX36 DDHD2 DIDO1 DDIT3 DIP2A DDIT4 DIP2B DDR2 DISC1 DDX10 DIXDC1 DDX18P3 DKK2 DDX25 DKK3 DDX28 DLC1 DDX31 DLEC1 DDX42 DLEU2 DDX43 DLEU2L DDX58 DLG4 DDX6 DLG5 DEDD DLGAP4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) DLK1 DUSP8 DLX4 DYM DMWD DYNLL2 DMXL1 DYNLRB2 DNAJB1 DYNLT3 DNAJB2 DYRK1A DNAJC13 DYRK1B DNAJC7 DYRK3 DNALI1 DZIP3 DNM1 DNM2 DNMT1 E2F8 DNPEP DNTTIP2 EAF1 DOCK4 EBNA1BP2 DOCK6 EBP DOK1 ECHDC1 DOK4 ECHDC3 DPCD EDC3 DPF2 EDC4 DPH1 EDEM3 DPH2 EDF1 DPH3 EDN1 DPP7 EDN2 DPP9 EDN3 DPPA5 EDNRA DPY19L1 EED DPYD EEF1A2 DRAM1 EEPD1 DSC2 EFCAB2 DSC3 EFCAB4B DSCC1 EFNA3 DSG2 EFNB3 DST EGLN1 DTD1 EGLN2 DTNA EGR2 DTNB EGR3 DTX1 EHD1 DUS4L EHD3 DUSP14 EHD4 DUSP16 EID1 DUSP18 EIF1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) EIF1AY EP400NL EIF2AK2 EPB42 EIF2AK4 EPDR1 EIF2B1 EPHA4 EIF2B2 EPHB2 EIF2C1 EPHB6 EIF2S2 EPM2A EIF2S3 EPM2AIP1 EIF3CL EPOR EIF3G EPPK1 EIF3K EPS8L1 EIF3M EPS8L3 EIF4E EPT1 EIF4E2 EPYC EIF4E3 ERBB4 EIF4EBP1 ERC1 EIF4H ERCC2 EIF5A2 ERCC5 EIF5AL1 ERGIC3 EIF5B ERLIN1 ELAC2 ERO1L ELK3 ESCO2 ELL ESM1 ELOVL2 ESPL1 ELOVL7 ESPN ELP3 ESR2 EMD ESRRG EMILIN1 ESYT1 EMILIN2 ESYT2 EML4 EVC2 EMP1 EVI2B EMP3 EVI5L ENAM ENC1 EWSR1 ENDOD1 EXO1 ENG EXOC2 ENGASE EXOC4 ENOPH1 EXOC5 ENPP5 EXOSC9 ENTPD1 EXTL1 ENTPD5 EYA2 EP300 EZH1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) F10 FAM96A F11R FAM96B F13B FANCA FABP4 FANCC FAM104A FANCG FAM107B FARSA FAM10A4 FATE1 FAM110B FAU FAM115A FBLN1 FAM118A FBLN2 FAM118B FBLN5 FAM122B FBN2 FAM129A FBRS FAM131C FBRSL1 FAM149A FBXL5 FBXO10 FAM162A FBXO21 FAM164A FBXO22 FAM171A1 FBXO3 FAM175B FBXO31 FAM176A FBXO45 FAM193A FBXO46 FAM195A FBXO5 FAM198B FBXW11 FAM200B FCER1A FAM20C FCGBP FAM21C FCGR1A FAM32A FCGR2A FAM35A FCGR3B FAM38B FCHO1 FAM3B FCN1 FAM41AY1 FER FAM46A FERMT3 FAM50A FGD6 FAM53C FGF12 FAM65A FGF13 FAM65C FGF19 FAM76B FGF2 FAM78A FGF3 FAM83D FGF8 FAM91A2 FGF9 FAM92A1 FGFR1OP Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) FGFR1OP2 FRA16D FHAD1 FRA5C FHL3 FRA7G FHOD1 FRAT1 FIGF FRG1 FIGN FRK FITM2 FRMD3 FKBP10 FSCN3 FKBP3 FSD1L FKBP7 FSHB FKBP8 FST FKTN FSTL1 FLJ10357 FTSJ2 FLJ11235 FUT1 FLJ30679 FUT3 FLJ34208 FUT4 FLJ42627 FUT8 FLJ46321 FXR1 FLOT1 FXR2 FLT3LG FXYD3 FLVCR1 FXYD5 FMN2 FXYD6 FMNL2 FYB FMO1 FZD1 FMO5 FZD2 FN3KRP FZD4 FNBP1L FZD5 FNBP4 FZD7 FNDC3B FZR1 FNDC5 G0S2 FNDC8 G2E3 FNIP1 G6PC2 FNTA GABPB2 FNTB GABRA3 FOLR1 GABRA5 FOSL2 GAK FOXA2 GAL FOXD1 GALM FOXG1 GALR2 FOXO4 GALT FOXQ1 GANAB FPR1 GAR1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) GARNL3 GLDN GARS GLI1 GAS1 GLI2 GAS2 GLIPR1 GAS5 GLIS2 GAS6 GLIS3 GAS7 GLOD4 GATA3 GLP1R GATA5 GLRA2 GATAD2A GLRB GBA3 GLS GBE1 GLT1D1 GBF1 GLTSCR2 GBP2 GLYCTK GBP3 GLYR1 GCA GM2A GCK GMCL1 GCY GMPR GDA GNAZ GDAP1L1 GNG10 GDF5 GNG11 GDI1 GNG2 GET4 GNG4 GFAP GNG5 GFER GNL1 GFI1B GNL2 GFM1 GNL3 GFM2 GNPNAT1 GFPT1 GNRH1 GFRA1 GNRHR GGCX GNS GGT1 GOLGA5 GGT2 GOLT1B GH1 GON4L GIF GPA33 GIMAP4 GPAM GIMAP6 GPC4 GIN1 GPCPD1 GINS3 GPD1L GJB2 GPHN GK4P GPIHBP1 GLCCI1 GPN1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) GPN3 GSTM4 GPR108 GTF2A1 GPR109B GTF2F1 GPR110 GTF2H1 GPR125 GTF2H3 GPR128 GTF2IP1 GPR137B GTF3A GPR146 GTSF1L GPR160 GUCA2B GPR172A GUCY1A3 GPR183 GUCY2C GPR56 GULOP GPR65 GULP1 GPR68 GUSBL2 GPR89A GYG1 GPRC5B GYPA GPRIN3 GYPC GPSM1 GYPE GPSM2 GYS1 GPT2 GZMA GPX4 H1FX GPX7 H2AFVP1 GRAMD1C H2AFY GRAMD4 H2AFY2 GREB1 H3F3B GRHL2 H6PD GRHL3 HABP4 GRIN2D HAP1 GRINA HAPLN1 GRK1 HAUS1 GRK4 HAUS3 GRK5 HAUS4 GRK6 HBD GRM1 HBEGF GRM5 HBG1 GRM7 HBP1 GRP HCG11 GRPEL1 HCG2P7 GSDMB HCN3 GSDMC HCRTR2 GSG1L HDAC5 GSS HDDC2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) HDGFL1 HMI HEATR7A HNF1B HEPACAM HNF4G HERC1 HNMT HERC2 HNRNPA3P1 HERC5 HNRNPL HERPUD2 HNRPDL HES4 HOMER2 HES6 HOMER3 HFE2 HOOK2 HHCM HOOK3 HHEX HORMAD1 HHLA3 HOXA10 HINT2 HOXB13 HIP1 HOXD9 HIRA HPCAL1 HIRIP3 HPN HIST1H1E HPR HIST1H2BD HPRT1 HIST1H2BL HPS3 HIST1H2BM HPS4 HIST1H2BO HPSE HIST1H4A HPSE2 HIST1H4J HPT HIST2H2AA3 HRASLS2 HIST2H2AC HS3ST3B1 HIST2H3C HSBP1 HIVEP1 HSD17B1 HLA-DMA HSD17B11 HLA-DOA HSD17B2 HLA-DOB HSD17B3 HLA-DQA2 HSD3B2 HLA-DRB4 HSF1 HLA-H HSF4 HM13 HSP90AA2 HMBOX1 HSPA13 HMBS HSPA14 HMG20B HSPB6 HMGA1L3 HSPB7 HMGB1L6 HSPBAP1 HMGB4 HTC2 HMGN4 HTR2B Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) HTRA1 IL15 HTT IL17F HULC IL17RA HUNK IL19 IAPP IL1B IBSP IL21 ICA1 IL22 ICAM2 IL23A ICK IL24 ID2B IL28RA ID4 IL33 IDO1 IL4 IDO2 IL6 IDS IL9 IER5L ILKAP IFNAR1 ILVBL IFNAR2 INA IFNB1 ING1 IFNGR2 INHA IFNR INHBA IFT80 INHBB IFT81 INPP1 IGBP1 INPP5A IGF1R INPP5B IGFBP5 INS IGFBP6 INSIG2 IGFBP7 INSM1 IGH@ INTS2 IGHD INTS4 IGJ INTS7 IGK@ IPO11 IGKV1-5 IPP IGLJ4 IPW IGLL3 IQSEC1 IGLV3-25 IRAK2 IHH IRF2 IK IRF8 IKBKE IRS2 IL11 ISG20L2 IL11RA ISLR IL13 ISOC1 IL13RA1 ISYNA1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) ITGA1 KCNJ5 ITGA10 KCNK15 ITGA11 KCNK4 ITGA8 KCNK9 ITGB3 KCNMA1 ITGB4 KCNMB2 ITGB8 KCNN2 ITM2A KCNQ1OT1 ITM2C KCTD1 ITPKA KCTD18 ITPKB KCTD3 ITPR3 KDELC1 ITPRIP KDM3B IWS1 KDR IYD KEAP1 JAG1 KERA JAG2 KHDRBS1 JAGN1 KHSRP JAK1 KIAA0040 JAK2 KIAA0090 JMJD4 KIAA0146 JMJD6 KIAA0195 JOSD1 KIAA0232 JPH3 KIAA0355 JRKL KIAA0406 JTB KIAA0494 KANK2 KIAA0528 KANK3 KIAA0562 KAT2B KIAA0564 KATNB1 KIAA0652 KAZALD1 KIAA0895 KBTBD11 KIAA0907 KCNA3 KIAA0913 KCNAB2 KIAA1409 KCNAB3 KIAA1429 KCND3 KIAA1671 KCNF1 KIAA1919 KCNH7 KIDINS220 KCNIP1 KIF1A KCNIP4 KIF1B KCNJ16 KIF20B KCNJ2 KIF25 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) KIF2A LASS2 KIF3B LASS6 KIF3C LBP KIF5A LCK KIFC1 LCLAT1 KIFC2 LCN8 KIR2DL4 LDB2 KIRREL2 LDLRAD3 KIT LEF1 KL LEMD2 KLC2 LEP KLF10 LETMD1 KLF3 LHPP KLHDC2 LHX6 KLHDC5 LIG3 KLHL12 LILRA3 KLHL18 LILRB2 KLHL26 LIMA1 KLHL7 LIMCH1 KLK12 LIMK1 KLK5 LIMS1 KLKB1 LIPA KLRA1 LIPE KLRAQ1 LIPF KRT4 LMBRD2 KRT6C LMLN KRT76 LMO4 KRTAP5-4 LOC100128025 KTN1 LOC100128416 KYNU LOC100128751 L2HGDH LOC100128770 L3MBTL4 LOC100128868 LAD1 LOC100129112 LAIR2 LOC100129260 LAMA2 LOC100129292 LAMB2 LOC100130288 LAMC2 LOC100130325 LAMP3 LOC100130452 LAPTM4A LOC100131512 LARP4 LOC100131774 LARP6 LOC100132015 LASS1 LOC100132043 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) LOC100132101 LOC220594 LOC100132288 LOC221442 LOC100132469 LOC257396 LOC100132814 LOC283267 LOC100133078 LOC284408 LOC100133153 LOC284749 LOC100133790 LOC285540 LOC100189589 LOC285766 LOC100190986 LOC338799 LOC100287170 LOC388789 LOC100287357 LOC388796 LOC100287415 LOC399491 LOC100287522 LOC401022 LOC100287951 LOC440264 LOC100288047 LOC441528 LOC100288052 LOC494150 LOC100288273 LOC642236 LOC100288432 LOC642620 LOC100288534 LOC643733 LOC100288679 LOC644714 LOC100288737 LOC645086 LOC100288756 LOC645158 LOC100288779 LOC646216 LOC100288888 LOC649294 LOC100288954 LOC652276 LOC100289232 LOC728190 LOC100289319 LOC728431 LOC100289362 LOC728673 LOC100289453 LOC729566 LOC100289612 LOC730101 LOC100289615 LONRF1 LOC100289632 LOXL1 LOC100293748 LPAR2 LOC115110 LPAR6 LOC145837 LPIN2 LOC149832 LPPR1 LOC150519 LPPR3 LOC1518 LRAT LOC1720 LRBA LOC200030 LRCH1 LOC201651 LRG1 LOC203274 LRMP Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) LRP2BP MAGEA2B LRP3 MAGEA3 LRRC1 MAGEA5 LRRC23 MAGEB2 LRRC31 MAGEC1 LRRC47 MAGEC2 LRRC8C MAGED1 LRRFIP2 MAGED4 LRRN3 MAGIX LRRTM2 MALL LRRTM4 MAN1A2 LSM14B MAN2A1 LSM4 MAN2B1 LSM5 MAP1A LST1 MAP1LC3A LTA MAP2K2 LTBP3 MAP2K4 LTBR MAP2K5 LUC7L2 MAP2K6 LUZP4 MAP2K7 LXN MAP3K10 LY6D MAP3K11 LY6G6C MAP3K12 LY75 MAP3K8 LYN MAP4K1 LYRM1 MAP4K3 LYST MAP4K5 LYVE1 MAP7 LYZL6 MAPK14 LZTR1 MAPK7 LZTS1 MAPK8 M6PR MAPK8IP3 MAA MAPK9 MAB21L2 MAPRE2 MACROD1 MAPRE3 MAEL MARCH5 MAF MARCH6 MAFK MARK2 MAG MARK3 MAGEA1 MARVELD1 MAGEA10 MASP1 MAGEA2 MATK Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) MATN1 MGAT4B MAVS MGC10997 MBD2 MGC12982 MBD3L5 MGC16121 MBL1P MGC29506 MBNL1 MGST3 MBP MIA3 MBTPS1 MIB2 MC3R MICAL1 MCHR2 MICALL2 MCS MID1IP1 MCTP1 MID2 MCTS1 MINK1 MDFI MIPOL1 MDFIC MIR1259 MDGA1 MIR21 MDM4 MIR345 ME1 MITF ME2 MKKS MEA1 MKLN1 MECP2 MKNK1 MED22 MKRN2 MED24 MLC1 MED27 MLF2 MED28 MLL5 MED7 MLLT6 MED8 MLXIP MED9 MMGT1 MEFV MMP13 MEP1B MMP2 MEST MMP23B METAP1 MMP3 METTL13 MMRN2 METTL5 MNAT1 MEX3D MNS1 MFAP1 MOAP1 MFF MOBKL1A MFN2 MOGAT3 MFSD1 MON1B MFSD11 MORC3 MFSD7 MORF4L1 MGA MORF4L2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) MORN1 MSI1 MORN2 MSMB MOS MSRA MOSC1 MSRB2 MOSC2 MST1P9 MPDU1 MSX2 MPHOSPH6 MT1M MPI MT2P1 MPND MTA1 MPP1 MTERFD2 MPP6 MTF2 MPPED1 MTHFD1L MPRIP MTHFR MRAS MTIF2 MREG MTMR2 MRM1 MTR MRPL13 MTRR MRPL2 MTX1 MRPL27 MTX3 MRPL39 MUC1 MRPL40 MUC12 MRPL43 MUC13 MRPL44 MUC16 MRPL45 MUC17 MRPL49 MUC20 MRPL50 MUC3A MRPS10 MUC3B MRPS11 MUC6 MRPS12 MUC7 MRPS14 MUDENG MRPS18B MVK MRPS22 MXD3 MRPS35 MXI1 MRPS36 MXRA5 MRPS6 MXRA8 MRPS7 MYB MRTO4 MYBPC2 MRVI1 MYCBP MS4A1 MYCL1 MS4A14 MYCT1 MS4A4A MYD88 MSH3 MYEF2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) MYH10 NCR3 MYH8 NCRNA00152 MYL12A NCRNA00176 MYL12B NCRNA00188 MYL6B NCRNA00242 MYLK4 NCS1 MYLPF NDEL1 MYNN NDRG3 MYO16 NDST1 MYO1A NDST2 MYO1C NDUFA1 MYO1D NDUFA10 MYO6 NDUFA12 MYO9B NDUFA13 MYOD1 NDUFA2 MYOF NDUFA3 MYOG NDUFA4 MYOM1 NDUFA9 MYOZ2 NDUFB1 MYSM1 NDUFB10 MYST1 NDUFB4 N4BP1 NDUFB6 NAA10 NDUFB9 NACA NDUFC1 NACC2 NDUFS3 NANS NDUFS6 NAP1L3 NEAT1 NAP1L5 NEBL NAPA NEIL3 NARG2 NEK4 NAT10 NELL2 NBL1 NETO2 NBPF12 NEURL NCAM1 NEURL1B NCAN NEURL4 NCAPH NF1 NCEH1 NFAT5 NCF4 NFE2L2 NCKAP1 NFIL3 NCOA1 NFKB1 NCOA4 NFKB2 NCOR2 NFKBIB Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) NFKBIZ NOTCH4 NFRKB NPAT NFS1 NPC1 NFX1 NPC1L1 NFYC NPC2 NGF NPEPPS NGFR NPIP NGLY1 NPL NHCP1 NPPA NHEJ1 NPR2 NHSL1 NPR3 NID2 NPY NINJ2 NPY2R NIPA1 NPY6R NIPSNAP1 NP_079555 NKD2 NR1I3 NKG7 NR2C2 NKTR NR2F1 NKX1-1 NR2F6 NKX3-1 NR3C1 NLE1 NRAS NLGN2 NRBP1 NLRC5 NRCAM NLRP11 NRGN NME3 NRIP1 NME4 NRN1 NMNAT1 NRP2 NMNAT2 NRXN1 NMNAT3 NRXN2 NMT1 NRXN3 NNT NSDHL NOC3L NSFL1C NOD1 NSMAF NOG NSMCE2 NOL11 NSUN3 NOL3 NSUN6 NOL7 NT5C NOL8 NTAN1 NOP56 NTM NOS1 NTN3 NOTCH2 NTN4 NOTCH2NL NTRK3 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) NUBPL OSBPL3 NUCB2 OSBPL9 NUDC OSM NUDCD2 OTUB1 NUDCD3 OTUB2 NUDT7 OTUD5 NUDT8 OXCT1 NUDT9 OXTR NUMA1 P2RX7 NUP107 P2RY4 NUP153 P4HA2 NUP35 P4HTM NUP54 PABPC1L NUP88 PABPN1 NUP93 PACS1 NUP98 PACSIN2 NXF1 PAEP OAS1 PAFAH1B1 OAZ1 PAIP1 OBFC2B PAK1IP1 OBSL1 PAK2 OCIAD2 PAK7 OCLN PALLD OGDH PALM3 OGFR PAOX OGG1 PAPD7 OLFM4 PAQR8 OMD PARD3 OPA1 PARD3B OPHN1 PARK7 OPN3 PARM1 OPN4 PARN OPRL1 PARP10 OR2AG1 PARP14 OR4F7P PARP4 OR51B4 PARP6 OR51B5 PARVA OR52D1 PARVB ORC6L PASD1 ORM2 PAWR OSBP2 PAXIP1 OSBPL10 PBX1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PCDH17 PFDN6 PCDH19 PFKFB3 PCDH7 PFKL PCDHB15 PFKP PCDHB4 PGAM1 PCM1 PGF PCNP PGGT1B PCNXL2 PGLYRP2 PCOLCE2 PGM2L1 PCSK7 PGM3 PCSK9 PGM5 PCYOX1 PGPEP1 PCYT1A PGRMC2 PDCD11 PHACTR2 PDCD2 PHF15 PDCL PHF17 PDCL3 PHF20 PDE2A PHF21A PDE4A PHKB PDE6B PHLDB2 PDE7B PHLDB3 PDE9A PHLPP1 PDF PHOSPHO2 PDGFRB PIAS1 PDGFRL PIAS4 PDHB PIBF1 PDHX PID1 PDLIM3 PIGAP1 PDLIM5 PIGG PDP1 PIGH PDS5A PIGK PDXDC1 PIGR PDZK1IP1 PIGS PELI2 PIK3C2G PER3 PIK3CA PES1 PIK3CB PET112L PIK3R4 PEX11A PILRA PEX2 PILRB PEX5 PIN1 PEX7 PINX1 PFDN2 PION Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PIP4K2A PNO1 PITX2 PNPLA4 PKD2L2 PNPLA8 PKN1 POC1A PKP1 POGK PKP3 POLA2 PLA2G12B POLD2 PLA2G1B POLD4 PLA2G4B POLDIP2 PLA2G6 POLE2 PLA2G7 POLE3 PLCB2 POLQ PLCB3 POLR2B PLCB4 POLR2C PLCD1 POLR2H PLCE1 POLR2J PLCH1 POLR2L PLCL2 POLR3F PLD1 POLR3H PLD2 POLRMT PLD3 POMT1 PLEC POMT2 PLEKHA2 POU1F1 PLEKHB2 POU2F2 PLEKHM2 POU3F1 PLEKHO1 POU5F1 PLIN1 PPA1 PLIN3 PPAP2C PLIN4 PPAPDC1B PLK3 PPARD PLS3 PPARGC1A PLSCR4 PPBP PLXDC1 PPDPF PLXNA2 PPIC PM20D2 PPIF PMAIP1 PPIL1 PMEPA1 PPIL6 PMM1 PPIP5K1 PMPCA PPL PMS2L1 PPM1G PMS2L11 PPME1 PNKP PPP1CA Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PPP1R11 PROK2 PPP1R12A ProSAPiP1 PPP1R15A PROX1 PPP1R16A PRPF4B PPP1R2 PRPH2 PPP1R3C PRR11 PPP1R7 PRR15L PPP1R8 PRR3 PPP2R5C PRR5 PPP2R5D PRR5L PPP3CA PRRG1 PPP3R1 PRRG2 PPP4C PRRX2 PPP6C PRSS1 PQLC1 PRSS23 PQLC3 PRSS50 PRAMEF10 PRSS8 PRB1 PRTFDC1 PRCP PSAP PRDM10 PSEN1 PRDM16 PSEN2 PRG2 PSG10 PRG4 PSG7 PRH1 PSIP1 PRICKLE4 psiTPTE22 PRIM2 PSKH1 PRKAB1 PSMA6 PRKAG1 PSMA7 PRKAG2 PSMC6 PRKAR1B PSMD12 PRKAR2B PSMD13 PRKCB PSME3 PRKCE PSME4 PRKG2 PSMG1 PRKRIP1 PSMG2 PRKX PSORS1C1 PRL PSPHL PRMT1 PSPN PRMT3 PSTPIP2 PRMT6 PTBP2 PROCR PTCD3 PRODH2 PTCH1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) PTENP1 RAB38 PTGER4 RAB3GAP2 PTH RAB3IL1 PTH1R RAB4B PTH2R RAB6A PTK6 RABGAP1 PTK7 RABGAP1L PTMS RABGEF1 PTN RABIF PTOV1 RABL5 PTPN14 RAC2 PTPN18 PTPN2 RAD1 PTPN21 RAD17 PTPRG RAD23A PTPRH RAD51 PTPRK RAD52 PTPRN RAD54L2 PTPRU RAD9A PTRF RAE1 PTRH2 RAF1 PTTG1IP RAGE PUS3 RALA PUS7 RALB PVRIG RALGPS1 PXT1 RALGPS2 PYCARD RALY PYGM RAMP3 QARS RANBP1 QPCTL RANBP10 QTRT1 RANBP9 QTRTD1 RAP1A R3HDM1 RAP1B RAB13 RAP2B RAB17 RAPGEF4 RAB1B RAPGEF5 RAB22A RARB RAB26 RARRES1 RAB27B RARS RAB32 RASA1 RAB34 RASA3 RAB37 RASAL2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) RASAL3 RFC2 RASD1 RFWD2 RASGRF1 RFWD3 RASGRP1 RFX7 RASGRP2 RFXAP RASGRP3 RGL1 RASL10A RGPD1 RASSF2 RGS13 RASSF5 RGS16 RASSF7 RGS20 RAX RGS22 RBBP6 RHAG RBM12B RHCE RBM14 RHD RBM17 RHOD RBM28 RHOF RBM41 RHOT2 RBM42 RHPN2 RBM6 RIN2 RBM8A RING1 RBMS1 RIOK3 RBMS2 RIPK2 RBMS3 RLBP1 RBMX RLF RBPJ RLTPR RCAN2 RN7SL1 RCC1 RNASE3 RCN3 RNASEH2A RCOR1 RCOR3 RNF10 RCVRN RNF112 RDH12 RNF115 RDH13 RNF125 RECK RNF130 RECQL RNF133 RELN RNF138 REN RNF141 RENBP RNF146 RET RNF160 RETSAT RNF185 REV3L RNF19A RFC1 RNF2 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) RNF216L RPP38 RNF24 RPP40 RNF26 RPRD1A RNF34 RPRD1B RNF40 RPS10P5 RNFT2 RPS10P7 RNH1 RPS14 RNMTL1 RPS15 RNU1-1 RPS23 RNU2-3P RPS25 RNU2-5P RPS27L RNU3P1 RPS29 RNU3P4 RPS2P28 RNU4-6P RPS3A RNU6-50P RPS4Y1 ROBLD3 RPS6 ROCK1 RPS6KA3 ROMO1 RPS6KA4 ROPN1L RPS6KA5 RORA RPS6KC1 RORC RPS9 RP1L1 RPSAP15 RPA2 RPTOR RPF2P RPUSD3 RPL18 RRAGC RPL19 RRAS2 RPL21 RRM2B RPL24 RRN3P1 RPL26 RRP8 RPL28 RSBN1 RPL31 RSBN1L RPL31P52 RSL1D1 RPL35A RSPO3 RPL36A RSS RPL36AP27 RSU1 RPL39 RTEL1 RPL4 RTF1 RPL41 RTKN RPL41P4 RTN1 RPL7A RTN4 RPL7P32 RUFY2 RPLP0P2 RUNX1T1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) RUNX3 SCML1 RUSC2 SCML2 RUVBL1 SCN1B RUVBL2 SCN2A RWDD1 SCN7A RWDD3 SCN8A RXRA SCNM1 RXRB SCNN1B RXRG SCO1 RYBP SCRG1 S100A1 SCRIB S100A14 SCRT1 S100A2 SCT S100A8 SCYL2 SAA3P SDC3 SAE1 SDC4 SAFB2 SDCCAG3 SALL1 SDCCAG8 SALL2 SDF2 SALL4 SDHAP1 SAMD4A SDSL SAMHD1 SEC11B SAMM50 SEC13 SAP130 SEC22A SAP18 SEC23B SAP30 SEC61B SAP30BP SEC61G SAR1A SELE SARS SELO SASS6 SELP SAT2 SELS SATB1 SELT SATB2 SEMA6C SBF1 SEMG2 SC4MOL SENP5 SC5DL SEPT11 SC65 SEPT6 SCAMPER SEPT7 SCFD1 SEPT8 SCFD2 SEPX1 SCG5 SERHL2 SCGB3A1 SERP1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) SERPINA2 SHD SERPINB2 SHFM1 SERPINB6 SHH SERPIND1 SHISA7 SERPINI1 SHKBP1 SERTAD4 SHOC2 SETD8 SI SETDB1 SIAE SETX SIAH2 SEZ6L2 SIGLEC7 SF3A1 SIGMAR1 SF3A2 SIK3 SF3B14 SILV SFI1 SIN3A SFRP1 SIN3B SFRP2 SIPA1 SFRS11 SIPA1L1 SFRS12IP1 SIRPB1 SFRS13A SIVA1 SFRS14 SKA1 SFRS16 SKA2 SFRS2 SKAP2 SFRS7 SKI SFT2D1 SLAIN2 SFTA3 SLAMF8 SFTPD SLC13A5 SGCB SLC14A2 SGCD SLC15A1 SGK3 SLC15A3 SGOL2 SLC16A14 SGPP1 SLC16A7 SH2B3 SLC16A9 SH3BGR SLC17A1 SH3BGRL SLC17A2 SH3BGRL2 SLC17A3 SH3BP2 SLC17A4 SH3GL2 SLC17A5 SH3GLB1 SLC17A9 SH3PXD2B SLC18A2 SH3YL1 SLC1A1 SHC4 SLC22A2 SHCBP1 SLC22A25 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) SLC25A1 SMAD1 SLC25A14 SMAD5 SLC25A19 SMAP1 SLC25A20 SMARCA5 SLC25A24 SMARCAD1 SLC25A30 SMARCD2 SLC25A33 SMC3 SLC25A37 SMCR7L SLC25A6 SMCR8 SLC28A2 SMO SLC29A4 SMOX SLC2A10 SMPD1 SLC2A12 SMPX SLC2A14 SMTN SLC2A6 SMURF1 SLC30A1 SMURF2 SLC30A10 SMYD5 SLC30A9 SNAI3 SLC35A2 SNAP47 SLC35B2 SNCB SLC35C2 SNF8 SLC35D1 SNHG11 SLC35E1 SNHG3 SLC35F4 SNHG6 SLC38A10 SNORD35A SLC38A5 SNRK SLC39A7 SNRNP40 SLC39A8 SNRNP48 SLC40A1 SNRPA SLC41A2 SNRPN SLC44A3 SNTB1 SLC48A1 SNX10 SLC5A3 SNX18 SLC6A1 SNX19 SLC6A18 SNX2 SLC7A7 SNX25 SLC7A9 SNX8 SLC9A8 SNX9 SLC9A9 SOAT1 SLFN12 SOAT2 SLK SOBP SLTM SOCS4 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) SOCS5 SR140 SOX13 SRC SOX30 SRCAP SOX4 SRF SOX6 SRGAP1 SP1 SRM SP100 SRP54 SP110 SRP9 SP4 SRP9L1 SP6 SRPK3 SPACA3 SRRM2 SPAG11B SRRT SPAG8 SSBP1 SPAM1 SSFA2 SPANXC SSNA1 SPATA17 SSPN SPATA21 SSR4 SPATS1 SSTR1 SPATS2 SSTR2 SPATS2L SSTR3 SPC25 SSTR4 SPCS1 SSTR5 SPDYE2 SSU72 SPDYE5 SSX1 SPEG SSX2IP SPG11 SSX3 SPG20 SSX4B SPG21 ST14 SPIN1 ST3GAL4 SPINK2 ST5 SPNS1 ST7OT1 SPOCK2 ST8SIA1 SPON2 STAB1 SPOPL STAB2 SPP2 STAC SPPL2B STAM SPRR1A STAM2 SPRY4 STARD10 SPSB3 STARD3 SPTBN1 STARD9 SPTBN2 STAT2 SQRDL STAT5A Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) STAU1 TAC1 STC1 TACR2 STK11 TACR3 STK25 TACSTD2 STK3 TAF1C STK38 TAF3 STK40 TAF5 STOML1 TAF9B STOML3 tAKR STOX2 TAOK1 STRA13 TARDBP STRADA TARS2 STRAP TAS1R1 STRN TAS2R9 STUB1 TATDN1 STX10 TBC1D22A STX3 TBC1D2B STX5 TBC1D30 STXBP1 TBC1D3C SUCLG1 TBCC SUDS3 TBL2 SULF1 TBX15 SULT1E1 TBX18 SULT4A1 TCEA2 SUMO2 TCEAL1 SUN1 TCEB1 SUOX TCF7L2 SUPT7L TCFL5 SUV420H1 TCN1 SUV420H2 TCP1 SUZ12P TCP10 SV2A TCTN2 SV2C TDG SVEP1 TEAD1 SVIP TEAD2 SYF2 TEAD3 SYNE1 TEF SYNGR2 TEKT3 SYT17 TEP1 SYT6 TERC TAB1 TERF2 TAB2 TERT Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TEX10 TLE1 TEX13B TLE2 TFAP2A TLK2 TFB2M TLR2 TFCP2 TLR5 TFDP3 TM2D1 TFEB TM4SF20 TFG TM7SF2 TFPT TM9SF4 TGDS TMBIM4 TGFBR3 TMC7 TGIF1 TMED10 TGM5 TMED3 TH TMED7 THAP11 TMED8 THAP4 TMED9 THAP6 TMEM100 THBS4 TMEM101 THG1L TMEM102 THNSL2 TMEM104 THOC2 TMEM106B THOC4 TMEM111 THOP1 TMEM120A THPO TMEM131 THRA TMEM136 THRAP3 TMEM139 THRB TMEM141 THRSP TMEM147 THSD1P1 TMEM14A THUMPD3 TMEM14B TIAF1 TMEM14C TIGD2 TMEM150A TIGD5 TMEM168 TIMM50 TMEM176B TIMM8A TMEM178 TINAGL1 TMEM185B TIPIN TMEM2 TIPRL TMEM204 TJAP1 TMEM206 TJP1 TMEM30A TJP2 TMEM38B TJP3 TMEM41B Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TMEM47 TP53RK TMEM50A TPBG TMEM51 TPCN1 TMEM55A TPCN2 TMEM59 TPI1 TMEM63A TPMT TMEM64 TPTE TMEM85 TRA2A TMEM8A TRA2B TMEM90A TRADD TMPRSS2 TRAF2 TMPRSS3 TRAF3 TMPRSS4 TRAF5 TMPRSS6 TRAF6 TMSB4Y TRAFD1 TNFAIP8 TRAIP TNFAIP8L3 TRAM2 TNFRSF11B TREM2 TNFRSF1A TRH TNFRSF21 TRHR TNFRSF6B TRIL TNFSF11 TRIM10 TNFSF12 TRIM17 TNK1 TRIM2 TNK2 TRIM25 TNKS TRIM27 TNKS1BP1 TRIM31 TNNC2 TRIM32 TNPO1 TRIP10 TNPO2 TRMT11 TNRC18 TRMT2B TNRC6A TRMT5 TNRC6C TRMT6 TNXA TRMT61A TOB2 TRPM1 TOM1 TRPM7 TOMM40 TRPS1 TOP1 TRRAP TOP2B TSC1 TOPBP1 TSG101 TOR3A TSGA10 TP53I11 TSHR Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) TSHZ1 UBE2N TSPAN3 UBE2S TSPAN31 UBE3A TSPAN33 UBE4B TSPAN6 UBFD1 TSPYL1 UBL3 TSTA3 UBN1 TTC30A UBP1 TTC36 UBQLN1 TTC39A UBQLN2 TTC39B UBQLN4 TTF2 UBR7 TTL UBXN10 TTLL4 UBXN7 TTTY12 UBXN8 TUBB2A UCHL1 TUBB2B UCHL3 TUBB6 UCHL5 TUFT1 UCP1 TULP4 UFC1 TUSC3 UFM1 TWF2 UGGT1 TWIST1 UGGT2 TWISTNB UGT1A TXNDC12 UGT1A3 TXNDC3 UGT1A6 TXNDC9 UGT1A7 TXNRD2 UGT1A8 TYRO3 UGT2B10 TYW1 UHRF1BP1 UACA ULK4 UBA3 UNC119B UBAP1 UNC13A UBB UNC13D UBE2B UNC45A UBE2D2 UNC5B UBE2D3 UPF3A UBE2E3 UPF3B UBE2E4P UPK1A UBE2G2 UPP1 UBE2I UPP2 UBE2K UQCC Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) UQCR11 VPS33B UQCRC2 VPS37A URB1 VPS37B UROD VPS45 UROS VPS52 USF1 VPS8 USF2 VSIG2 USH1C VSIG4 USMG5 VTCN1 USP20 VTI1B USP24 VWA1 USP3 VWA3A USP39 VWA5A USP54 VWCE UST WASL UTP18 WDFY1 UTP20 WDFY3 UTP23 WDR11 VAMP2 WDR12 VAMP4 WDR13 VAMP5 WDR16 VAPA WDR26 VAPB WDR45L VAV3 WDR46 VBP1 WDR59 VDAC1 WDR61 VDAC1P5 WDR62 VDAC3 WDR75 VENTX WDR91 VEZF1 WDSUB1 VGLL1 WDYHV1 VGLL4 WFDC2 VHL WHSC2 VIP WIF1 VKORC1 WIPF2 VLDLR WISP1 VNN2 WISP3 VNN3 WNK2 VPREB1 WNT2 VPS16 WNT5A VPS25 WSB1 VPS29 WT1 Table SII. Continued. Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) HCC (n=611) liverome (n=6,927) (n=167) WWC3 ZFP36L2 WWP2 ZFP41 WWTR1 ZFR XBP1 ZFR2 XCL1 ZFYVE1 XDH ZFYVE26 XIAP ZG16 XPA ZMPSTE24 XPNPEP2 ZMYND8 XP_139814 ZNF14 XRCC1 ZNF143 XRCC3 ZNF146 XRCC4 ZNF148 XRN1 ZNF155 XRN2 ZNF160 YARS ZNF175 YES1 ZNF197 YME1L1 ZNF20 YTHDF1 ZNF205 YWHAG ZNF211 ZBP1 ZNF248 ZBTB17 ZNF254 ZBTB22 ZNF259 ZBTB38 ZNF271 ZBTB4 ZNF273 ZBTB43 ZNF274 ZBTB6 ZNF281 ZBTB7A ZNF282 ZBTB8OS ZNF286A ZC3H7B ZNF292 ZC3HAV1 ZNF3 ZC3HAV1L ZNF320 ZCCHC14 ZNF330 ZCCHC17 ZNF335 ZCCHC24 ZNF337 ZDHHC1 ZNF343 ZDHHC11B ZNF365 ZDHHC20 ZNF37B ZER1 ZNF410 ZFAND6 ZNF443 ZFHX4 ZNF446 ZFP36 ZNF474 Table SII. Continued. Gene-OncoDB. Gene symbol- Common targets HCC (n=611) liverome (n=6,927) (n=167) ZNF493 ZNF510 ZNF512B ZNF521 ZNF532 ZNF552 ZNF559 ZNF567 ZNF586 ZNF593 ZNF597 ZNF638 ZNF644 ZNF646 ZNF668 ZNF682 ZNF692 ZNF703 ZNF738 ZNF740 ZNF747 ZNF764 ZNF77 ZNF847P ZNF85 ZNF862 ZNF90 ZNF91 ZNF92 ZNRD1 ZPBP ZSCAN18 ZSWIM1 ZSWIM5 ZXDC Table SIII. GO terms and pathways.

A, Biological process List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_BP_ GO:0046777~ 19 11.37725 8.37E-14 FGFR2, EGFR, FGFR1, 166 172 16792 11.17428 1.68E-10 1.68E-10 1.44E-10 DIRECT autophosphorylation ERBB4, PIM1, AURKA, KIT, EPHB4, SRC, KDR, DAPK1, AKT1, IGF1R, PTK2, PDPK1, PRKACA, JAK2, ABL1, INSR GOTERM_BP_ GO:0043401~steroid 12 7.185629 7.36E-12 PPARA, PPARD, NR1I2, 166 57 16792 21.29613 1.48E-08 7.40E- 09 1.27E-08 DIRECT hormone mediated THRB, RXRB, RXRA, signaling pathway PPARG, ESRRG, ESR1, RORA, HNF4G, NR1H4 GOTERM_BP_ GO:0006367~ 16 9.580838 2.53E-11 PPARA, AR, PPARD, 166 152 16792 10.64807 5.09E-08 1.70E-08 4.35E-08 DIRECT initiation from RNA KAT2B, THRB, RXRB, II RXRA, PPARG, ESR1, ESRRG, NR3C1, RORA, ESR2, HNF4G, NR1I2, NR1H4 GOTERM_BP_ GO:0042493~response 20 11.97605 1.58E-10 SORD, HSP90AA1, 166 304 16792 6.655041 3.18E-07 7.95E- 08 2.72E-07 DIRECT to drug PTGS2, PGF, OTC, MAOB, PPARG, STAT1, SRC, TGFB2, TYMS, CASP3, APOA2, BCHE, LCK, DHODH, ADAM17, ABL1, HADH, DUSP6 GOTERM_BP_ GO:0018108~peptidyl- 15 8.982036 3.31E-10 EGFR, FGFR2, FGFR1, 166 153 16792 9.917316 6.64E-07 1.33E-07 5.69E-07 DIRECT PTK2, HSP90AA1, MAP2K1, ERBB4, MET, JAK2, KIT, ABL1, EPHB4, INSR, SRC, KDR GOTERM_BP_ GO:0014068~positive 11 6.586826 7.17E-10 FGFR1, PTK2, PPARD, 166 65 16792 17.11881 1.44E-06 2.40E-07 1.23E-06 DIRECT regulation of ERBB4, F2, IGF1, JAK2, phosphatidylinositol KIT, CCL5, KDR, TGFB2 3- signaling Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_BP_ GO:0070374~positive 15 8.982036 1.94E-09 EGFR, FGFR2, BMP2, 166 175 16792 8.670568 3.91E-06 5.58E-07 3.35E-06 DIRECT regulation of ERK1 and ERBB4, BRAF, MAP2K1, ERK2 cascade HMGCR, CCL5, SRC, KDR, PTPN11, FGG, PLA2G2A, ABL1, NQO2 GOTERM_BP_ GO:0043101~purine- 7 4.191617 2.31E-09 GMPR2, ADK, DCK, 166 14 16792 50.57831 4.65E-06 5.81E-07 3.98E-06 DIRECT containing compound salvage MTAP, GMPR, HPRT1, APRT GOTERM_BP_ GO:0030522~intracellular 9 5.389222 2.79E-09 PPARA, AR, PPARD, 166 38 16792 23.95815 5.61E-06 6.23E-07 4.80E-06 DIRECT signaling pathway NR1I2, NCOA2, THRB, RORA, HNF4G, NR1H4 GOTERM_BP_ GO:0032869~cellular 11 6.586826 3.97E-09 AKT1, PDPK1, KAT2B, 166 77 16792 14.45095 7.99E- 06 7.99E- 07 6.84E-06 DIRECT response to stimulus PKLR, PPARG, STAT1, INSR, SRC, GSTP1, PCK1, APRT GOTERM_BP_ GO:0043066~negative 22 13.17365 4.08E-09 EGFR, PPARD, XIAP, 166 455 16792 4.89109 8.20E-06 7.45E- 07 7.02E- 06 DIRECT regulation of apoptotic ERBB4, BRAF, MMP9, process PIM1, IGF1, AURKA, BCL2L1, ANXA5, SRC, KDR, AKT1, IGF1R, PTK2, CASP3, ALB, NQO1, NR1H4, GSTP1, IL2 GOTERM_BP_ GO:0038083~peptidyl- 9 5.389222 4.31E-09 IGF1R, PTK2, ERBB4, 166 40 16792 22.76024 8.67E-06 7.23E- 07 7.42E- 06 DIRECT tyrosine autophosphorylation LCK, JAK2, ABL1, INSR, SRC, KDR GOTERM_BP_ GO:0055114~oxidation- 24 14.37126 1.81E-08 BMP2, SORD, ACADM, 166 592 16792 4.100944 3.65E-05 2.80E-06 3.12E-05 DIRECT reduction process GMPR2, PTGS2, CYP2C9, HMGCR, HSD17B1, MAOB, PAH, GMPR, AKR1C3, MTHFD1, GSR, AKR1C2, DHFR, AKR1B1, DHODH, HSD11B1, SPR, NOS2, NQO1, AKR1C1, NQO2 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_BP_ GO:0008284~positive 21 12.57485 3.31E-08 FGFR2, EGFR, FGFR1, 166 466 16792 4.55856 6.64E-05 4.75E-06 5.69E-05 DIRECT regulation of AR, ERBB4, PGF, IGF1, proliferation BCL2L1, KIT, CDK2, KDR, TGFB2, AKR1C3, IGF1R, AKR1C2, PTK2, F2, ADAM17, INSR, DPP4, IL2 GOTERM_BP_ GO:0001934~positive 12 7.185629 4.91E-08 AKT1, EGFR, RAP2A, 166 127 16792 9.558106 9.88E-05 6.59E-06 8.45E-05 DIRECT regulation of protein PTK2, BMP2, ERBB4, phosphorylation MMP9, F2, ADAM17, ABL1, INSR, KDR

B, Molecular function List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_ GO:0003707~steroid hormone 15 8.982036 1.79E-16 PPARA, AR, PPARD, 167 56 16881 27.07603 1.22E-13 1.22E-13 3.22E-13 MF_DIRECT receptor activity THRB, RXRB, RXRA, PPARG, ESR1, ESRRG, NR3C1, RORA, ESR2, HNF4G, NR1I2, NR1H4 GOTERM_ GO:0004879~RNA 12 7.185629 2.89E-14 PPARA, AR, PPARD, 167 36 16881 33.69461 1.59E-11 7.95E-12 4.21E-11 MF_DIRECT polymerase II transcription NR1I2, RXRB, RXRA, factor activity, - PPARG, ESR1, RORA, activated sequence-specific HNF4G, ESR2, NR1H4 DNA binding GOTERM_ GO:0004713~protein tyrosine 16 9.580838 3.66E-12 FGFR2, EGFR, FGFR1, 167 133 16881 12.16046 2.01E-09 6.71E-10 5.34E-09 MF_DIRECT kinase activity HSP90AA1, ERBB4, MAP2K1, MET, KIT, SRC, KDR, IGF1R, PTK2, LCK, JAK2, ABL1, INSR GOTERM_ GO:0008144~drug binding 13 7.784431 9.86E-12 HSP90AB1, PPARA, 167 76 16881 17.29066 5.43E-09 1.36E-09 1.44E-08 MF_DIRECT PPARD, CYP2C9, PPARG, DCK, TYMS, DHFR, NR1I2, ALB, PYGL, DHODH, GSTP1 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_ GO:0042803~protein 29 17.36527 5.73E-10 FGFR2, FGFR1, ERBB4, 167 730 16881 4.015659 3.16E-07 6.31E-08 8.36E-07 MF_DIRECT homodimerization activity PTGS2, HMGCR, PGF, DCK, ADH5, FKBP1A, BCL2L1, KIT, HPRT1, CCL5, TGFB2, GSTM1, TYMS, GSTM2, APOA2, TAP1, NOS2, DPP4, PDK2, HSP90AA1, MAOB, EPHX2, STAT1, ADRB2, PYGL, SDS GOTERM_ GO:0004714~ 9 5.389222 2.81E-09 FGFR2, EGFR, IGF1R, 167 38 16881 23.94091 1.55E-06 2.58E-07 4.10E-06 MF_DIRECT transmembrane receptor ERBB4, MET, KIT, INSR, protein EPHB4, KDR activity GOTERM_ GO:0005524~ATP binding 41 24.5509 3.41E-09 HSP90AB1, FGFR2, 167 1495 16881 2.772199 1.88E-06 2.69E-07 4.98E-06 MF_DIRECT FGFR1, ERBB4, DTYMK, DCK, CHEK1, AURKA, KIT, EPHB4, SRC, AKT1, MTHFD1, IGF1R, PTK2, PDPK1, TAP1, PRKACA, PAPSS1, INSR, EGFR, PDK2, HSP90AA1, KIF11, BRAF, MAP2K1, MET, PIM1, CDK6, CDK2, KDR, DAPK1, PYGL, MAPK14, ADK, LCK, PKLR, JAK2, APAF1, ABL1, NMNAT1 GOTERM_ GO:0019899~ binding 18 10.77844 3.21E-08 EGFR, AR, THRB, PTGS2, 167 333 16881 5.463991 1.77E-05 2.21E-06 4.69E-05 MF_DIRECT RXRA, PPARG, ESR1, FKBP1A, ESR2, STAT1, SRC, GSTM1, AKT1, GSTM2, EIF4E, BCHE, MAPK14, PTPN1 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_ GO:0042802~identical protein 26 15.56886 8.22E-08 EGFR, FGFR1, HSP90AA1, 167 749 16881 3.508918 4.53E-05 5.03E-06 1.20E-04 MF_DIRECT binding SORD, ACADM, BRAF, XIAP, MMP9, PPARG, ESR1, BCL2L1, STAT1, HPRT1, DAPK1, AKT1, TTR, IGF1R, BCHE, ALB, LCK, SERPINA1, APAF1, NQO1, OAT, DPP4, NMNAT1 GOTERM_ GO:0005496~steroid binding 7 4.191617 2.06E-07 SHBG, AR, ESRRG, ESR1, 167 27 16881 26.20692 1.14E-04 1.14E-05 3.01E-04 MF_DIRECT NR3C1, SULT1E1, ESR2 GOTERM_ GO:0004672~ 17 10.17964 5.23E-07 EGFR, PDK2, BRAF, 167 359 16881 4.7867 2.88E-04 2.62E-05 7.64E- 04 MF_DIRECT activity MAP2K1, MET, AURKA, CHEK1, CCL5, CDK2, SRC, DAPK1, AKT1, PTK2, PDPK1, MAPK14, JAK2, ABL1 GOTERM_ GO:0030235~nitric-oxide 5 2.994012 6.12E-07 HSP90AB1, AKT1, EGFR, 167 8 16881 63.1774 3.37E-04 2.81E-05 8.94E-04 MF_DIRECT synthase regulator activity HSP90AA1, ESR1 GOTERM_ GO:0016491~ 13 7.784431 6.80E-07 AKR1C3, GSR, AKR1C2, 167 200 16881 6.570449 3.74E-04 2.88E-05 9.92E-04 MF_DIRECT activity SORD, GMPR2, CYP2C9, AKR1B1, MAOB, ADH1C, HSD11B1, ADH5, AKR1C1, NQO2 GOTERM_ GO:0004716~receptor 5 2.994012 1.81E-06 EGFR, ERBB4, KIT, INSR, 167 10 16881 50.54192 9.96E-04 7.12E- 05 0.00264 MF_DIRECT signaling protein tyrosine KDR kinase activity GOTERM_ GO:0008270~zinc ion binding 29 17.36527 9.83E-06 PPARA, PPARD, SORD, 167 1169 16881 2.50764 0.005399 3.61E-04 0.014341 MF_DIRECT THRB, XIAP, MMP9, PPARG, ADH1C, ADH5, MME, NR3C1, RORA, MMP3, MMP2, NR1H4, AR, RXRB, RXRA, ESR1, ESRRG, SIRT5, HNF4G, ESR2, MMP13, MMP12, NR1I2, BHMT, CA2, PTPN1 Table SIII. Continued. C, Cellular component List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_CC_ GO:0005829~cytosol 90 53.89222 5.14E-25 HSP90AB1, GMPR2, 167 3315 18224 2.96269 1.23E-22 1.23E-22 6.63E-22 DIRECT PNMT, DTYMK, PPARG, CRABP2, ADH1C, TTPA, AURKA, DCPS, AKR1C3, MTHFD1, GSTM1, AKT1, GSR, GSTM2, CASP3, PDPK1, APOA2, CASP7, SULT1A1, PRKACA, SPR, SULT1E1, NOS2, CASP1, NQO1, AKR1C1, RAP2A, AR, KIF11, HSP90AA1, BRAF, SULT2A1, CDK6, GMPR, CTNNA1, PPP1CC, CDK2, ADK, BHMT, PKLR, LCK, MTAP, CA2, GSTP1, GC, RBP4, FGFR1, SORD, XIAP, ERBB4, HSD17B1, ADH5, DCK, FKBP1A, PAH, CHEK1, BCL2L1, HPRT1, EPHB4, SRC, TYMS, PTK2, HNMT, PAPSS1, AMD1, GSTA1, GSTA3, CES1, MAP2K1, EPHX2, FDPS, SIRT5, STAT1, APRT, PCK1, PTPN11, GPI, DHFR, EIF4E, PPIA, PYGL, MAPK14, AKR1B1, JAK2, PTPN1, APAF1, ABL1, DUSP6 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_CC_ GO:0070062~extracellular 64 38.32335 1.11E-12 HSP90AB1, THRB, MMP9, 167 2811 18224 2.484542 2.67E-10 1.34E-10 1.44E-09 DIRECT exosome HINT1, CRABP2, MTHFD1, AKR1C3, TTR, GSTM2, GSR, APOA2, SERPINA1, SPR, PRKACA, NQO1, INSR, DPP4, AKR1C1, NQO2, SHBG, RAP2A, ACADM, HSP90AA1, F2, PKLR, LCK, BHMT, PLA2G2A, MTAP, CTSB, CA2, GSTP1, GC, RBP4, SORD, ADH5, PRSS1, MME, FKBP1A, PAH, HPRT1, SEC14L2, EPHB4, SRC, FGG, PROCR, HNMT, ALB, GSTA1, GSTA3, MAP2K1, MAOB, EPHX2, ANXA5, APRT, PCK1, GPI, EIF4E, PYGL, PPIA, MAPK14, AKR1B1, APAF1, DUT GOTERM_CC_ GO:0005739~ 36 21.55689 9.43E-09 HSP90AB1, BCAT2, 167 1331 18224 2.95156 2.26E-06 7.54E- 07 1.22E-05 DIRECT ERBB4, DTYMK, ADH5, BCL2L1, MMP2, SRC, AKT1, MTHFD1, DCPS, TYMS, GSR, TAP1, DHODH, PRKACA, HADH, CASP1, PDK2, ACADM, BRAF, MAP2K1, OTC, MAOB, FDPS, SIRT5, ESR2, PPP1CC, PTPN11, SDS, MAPK14, CTSB, ABL1, OAT, GSTP1, DUT Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_CC_ GO:0005654~nucleoplasm 55 32.93413 1.94E-08 HSP90AB1, PPARA, 167 2784 18224 2.155861 4.67E-06 1.17E-06 2.51E-05 DIRECT PPARD, THRB, CRABP2, PPARG, AURKA, RORA, AKT1, DCPS, CASP3, PDPK1, CASP7, SPR, PRKACA, HADH, CCNA2, NQO2, AR, HSP90AA1, RXRB, RXRA, ESR1, CDK6, HNF4G, ESR2, CDK2, NCOA2, ADK, NMNAT1, FGFR2, ERBB4, XIAP, HSD17B1, CHEK1, NR3C1, TYMS, HNMT, DHODH, NR1H4, PDK2, KAT2B, ESRRG, FDPS, STAT1, APRT, GPI, NR1I2, DHFR, MAPK14, AKR1B1, JAK2, ABL1, DUT, DUSP6 GOTERM_CC_ GO:0005576~extracellular 39 23.35329 3.52E-08 GC, FGFR2, FGFR1, RBP4, 167 1610 18224 2.643419 8.44E-06 1.69E-06 4.54E-05 DIRECT region ERBB4, PGF, MMP9, PRSS1, MMP3, CCL5, MMP2, EPHB4, TGFB2, TTR, APOA2, FGG, PROCR, BCHE, ALB, REN, SERPINA1, CASP1, SHBG, BMP2, F10, HSP90AA1, MET, IGF1, CTSS, ESR2, MMP13, MMP12, KDR, PPIA, F2, PLA2G2A, CTSB, ABO, IL2 GOTERM_CC_ GO:0005615~extracellular 31 18.56287 4.19E-06 GC, RBP4, SORD, PGF, 167 1347 18224 2.511431 0.001006 1.68E-04 0.005411 DIRECT space MMP9, CHEK1, KIT, MMP3, CCL5, MMP2, TGFB2, TTR, FGG, ALB, REN, SERPINA1, EGFR, BMP2, CES1, IGF1, CTSS, MMP13, GPI, PPIA, F2, AKR1B1, PLA2G2A, CTSB, CA2, GSTP1, IL2 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_CC_ GO:0005737~ 74 44.31138 1.72E-05 HSP90AB1, GMPR2, 167 5222 18224 1.546401 0.004126 5.91E-04 0.022235 DIRECT PTGS2, HINT1, CRABP2, DCPS, AKR1C3, GSTM1, AKT1, AKR1C2, TTR, GSTM2, CASP3, PDPK1, CASP7, SPR, NOS2, HADH, NQO1, CCNA2, NQO2, EGFR, AR, KIF11, HSP90AA1, BRAF, SULT2A1, ESR1, PIM1, CDK6, GMPR, PPP1CC, CDK2, DAPK1, NCOA2, SDS, ADK, BHMT, MTAP, ADAM17, CA2, GSTP1, FGFR2, XIAP, HSD17B1, MME, FKBP1A, NR3C1, BCL2L1, CCL5, HPRT1, SEC14L2, SRC, TYMS, PTK2, HNMT, DHODH, PDK2, MAP2K1, FDPS, EPHX2, STAT1, ANXA5, APRT, PCK1, PTPN11, GPI, EIF4E, PYGL, MAPK14, AKR1B1, JAK2, ABL1, DUSP6 GOTERM_CC_ GO:0005759~mitochondrial 13 7.784431 4.70E-05 PDK2, ACADM, BCAT2, 167 327 18224 4.338333 0.01122 0.001409 0.060668 DIRECT matrix ERBB4, OTC, DTYMK, SIRT5, NR3C1, BCL2L1, TYMS, GSR, HADH, OAT GOTERM_CC_ GO:0005925~focal adhesion 12 7.185629 9.34E-04 EGFR, PTK2, PDPK1, 167 391 18224 3.349128 0.200964 0.02462 1.199325 DIRECT PROCR, MAP2K1, PPIA, ADAM17, MME, ANXA5, PPP1CC, CTNNA1, DPP4 GOTERM_CC_ GO:0043235~receptor 7 4.191617 0.001088 EGFR, IGF1R, FGFR1, 167 127 18224 6.014805 0.229955 0.025792 1.395509 DIRECT complex ADRB2, ERBB4, RXRA, INSR Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

GOTERM_CC_ GO:0031093~ alpha 5 2.994012 0.001577 FGG, ALB, IGF1, 167 55 18224 9.920523 0.315369 0.033857 2.017022 DIRECT granule lumen SERPINA1, TGFB2 GOTERM_CC_ GO:0005634~nucleus 68 40.71856 0.002114 HSP90AB1, PPARA, 167 5415 18224 1.37037 0.398308 0.041451 2.695155 DIRECT PPARD, PTGS2, THRB, HINT1, PPARG, CRABP2, DTYMK, AURKA, RORA, MMP2, DCPS, AKR1C3, AKT1, CASP3, CASP7, PRKACA, NOS2, CCNA2, EGFR, AR, ACADM, HSP90AA1, BRAF, RXRB, RXRA, ESR1, PIM1, CDK6, ESR2, HNF4G, PPP1CC, CDK2, ADRB2, NCOA2, ADK, MTAP, GSTP1, NMNAT1, FGFR2, FGFR1, XIAP, ERBB4, FKBP3, DCK, CHEK1, NR3C1, SEC14L2, SRC, TYMS, PTK2, ALB, NR1H4, KAT2B, MAP2K1, ESRRG, SIRT5, STAT1, PTPN11, KDR, NR1I2, PPIA, MAPK14, JAK2, APAF1, ABL1, DUT GOTERM_CC_ GO:0072562~ 7 4.191617 0.002718 GC, APOA2, FGG, BCHE, 167 152 18224 5.025528 0.479641 0.049007 3.452189 DIRECT microparticle ALB, F2, PRSS1 GOTERM_CC_ GO:0031234~extrinsic 5 2.994012 0.003438 PTK2, LCK, JAK2, ABL1, 167 68 18224 8.023952 0.562405 0.057324 4.347473 DIRECT component of cytoplasmic SRC side of plasma membrane GOTERM_CC_ GO:0005788~endoplasmic 7 4.191617 0.008365 APOA2, F10, CES1, PTGS2, 167 192 18224 3.978543 0.866819 0.125762 10.27542 DIRECT reticulum lumen BCHE, F2, SERPINA1 D, Pathway List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

KEGG_ hsa05200:Pathways in cancer 35 20.95808 2.81E-13 HSP90AB1, FGFR2, 143 393 6910 4.303457 6.58E-11 6.58E-11 3.61E-10 PATHWAY FGFR1, PPARD, XIAP, PTGS2, PGF, MMP9, PPARG, BCL2L1, KIT, MMP2, TGFB2, AKT1, IGF1R, PTK2, CASP3, PRKACA, NOS2, EGFR, AR, BMP2, HSP90AA1, BRAF, MAP2K1, RXRB, RXRA, MET, IGF1, CDK6, STAT1, CTNNA1, CDK2, DAPK1, ABL1 KEGG_ hsa05205: in 22 13.17365 5.26E-10 EGFR, FGFR1, MAP2K1, 143 200 6910 5.315385 1.23E-07 6.16E-08 6.76E-07 PATHWAY cancer ERBB4, BRAF, MMP9, MET, ESR1, IGF1, PPP1CC, MMP2, SRC, KDR, TGFB2, PTPN11, AKT1, IGF1R, PTK2, PDPK1, CASP3, MAPK14, PRKACA KEGG_ hsa05215: 13 7.784431 1.92E-07 HSP90AB1, FGFR2, EGFR, 143 88 6910 7.13843 4.49E-05 1.50E-05 2.47E-04 PATHWAY FGFR1, AR, HSP90AA1, BRAF, MAP2K1, IGF1, CDK2, AKT1, IGF1R, PDPK1 KEGG_ hsa00980: of 12 7.185629 2.59E-07 GSTM1, GSTA1, GSTM2, 143 74 6910 7.835948 6.05E-05 1.51E-05 3.32E-04 PATHWAY xenobiotics by AKR1C2, GSTA3, SULT2A1, P450 CYP2C9, HSD11B1, ADH1C, ADH5, GSTP1, AKR1C1 KEGG_ hsa04151:PI3K-Akt signaling 24 14.37126 4.45E-07 EGFR, HSP90AB1, FGFR2, 143 345 6910 3.361508 1.04E-04 2.08E-05 5.73E-04 PATHWAY pathway FGFR1, HSP90AA1, MAP2K1, PGF, RXRA, MET, IGF1, CDK6, BCL2L1, KIT, CDK2, KDR, PCK1, AKT1, IGF1R, PTK2, PDPK1, EIF4E, JAK2, INSR, IL2 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR

KEGG_ hsa05204:Chemical 12 7.185629 5.83E-07 GSTM1, GSTA1, GSTM2, 143 80 6910 7.248252 1.36E-04 2.27E-05 7.50E- 04 PATHWAY GSTA3, SULT2A1, PTGS2, CYP2C9, SULT1A1, HSD11B1, ADH1C, ADH5, GSTP1 KEGG_ hsa05222:Small cell lung 11 6.586826 8.22E-06 AKT1, PTK2, XIAP, PTGS2, 143 85 6910 6.253394 0.001921 2.75E-04 0.010562 PATHWAY cancer RXRB, RXRA, CDK6, APAF1, BCL2L1, NOS2, CDK2 KEGG_ hsa04914:Progesterone- 11 6.586826 1.01E-05 HSP90AB1, AKT1, IGF1R, 143 87 6910 6.109637 0.002371 2.97E-04 0.013039 PATHWAY mediated oocyte maturation HSP90AA1, BRAF, MAP2K1, MAPK14, IGF1, PRKACA, CCNA2, CDK2 KEGG_ hsa04014:Ras signaling 17 10.17964 1.40E-05 FGFR2, EGFR, FGFR1, 143 226 6910 3.634817 0.003276 3.65E-04 0.018028 PATHWAY pathway MAP2K1, PGF, MET, IGF1, BCL2L1, KIT, KDR, PTPN11, AKT1, IGF1R, PLA2G2A, PRKACA, ABL1, INSR KEGG_ hsa04919:Thyroid hormone 12 7.185629 1.97E-05 AKT1, PDPK1, KAT2B, 143 114 6910 5.086492 0.004605 4.61E-04 0.025356 PATHWAY signaling pathway NCOA2, THRB, MAP2K1, RXRB, RXRA, ESR1, PRKACA, STAT1, SRC KEGG_ hsa04915:Estrogen signaling 11 6.586826 3.20E-05 HSP90AB1, AKT1, EGFR, 143 99 6910 5.369075 0.007465 6.81E-04 0.041155 PATHWAY pathway HSP90AA1, MAP2K1, MMP9, ESR1, PRKACA, ESR2, MMP2, SRC KEGG_ hsa03320:PPAR signaling 9 5.389222 6.12E-05 PPARA, PDPK1, APOA2, 143 67 6910 6.490972 0.01422 0.001193 0.078651 PATHWAY pathway PPARD, ACADM, RXRB, RXRA, PPARG, PCK1 KEGG_ hsa00982:Drug metabolism- 9 5.389222 6.82E-05 GSTM1, GSTA1, GSTM2, 143 68 6910 6.395516 0.015827 0.001226 0.087606 PATHWAY cytochrome P450 GSTA3, CYP2C9, MAOB, ADH1C, ADH5, GSTP1 Table SIII. Continued. List Pop Pop Fold Category Term Count % P-value Genes Total Hits Total Enrichment Bonferroni Benjamini FDR KEGG_ hsa01100:Metabolic pathways 45 26.94611 7.60E- 05 BCAT2, SORD, PTGS2, 143 1228 6910 1.770746 0.017633 0.00127 0.097691 PATHWAY PNMT, HMGCR, HSD17B1, DTYMK, ADH1C, DCK, ADH5, PAH, HPRT1, MTHFD1, AKR1C3, TYMS, DHODH, SPR, NOS2, HADH, AMD1, PAPSS1, CES1, ACADM, CYP2C9, OTC, MAOB, FDPS, EPHX2, APRT, PCK1, GPI, DHFR, PYGL, SDS, ADK, AKR1B1, PKLR, BHMT, PLA2G2A, HSD11B1, MTAP, OAT, ABO, NMNAT1, DUT KEGG_ hsa04068:FoxO signaling 12 7.185629 8.87E-05 AKT1, EGFR, IGF1R, 143 134 6910 4.327314 0.020551 0.001383 0.114016 PATHWAY pathway PDPK1, BRAF, MAP2K1, MAPK14, IGF1, INSR, CDK2, TGFB2, PCK1