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Table SI. Targets of Berberine. Gene Symbol Gene Name ABL1 ABO

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Table SI. Targets of Berberine. Gene Symbol Gene Name ABL1 ABO Table SI. Targets of berberine. Table SI. Continued. Gene 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 LCK 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. Genes differentially expressed in liver cancer. 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 RND3 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) MYC 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 E2F1 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.
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