Table 2.

 Candidate upstream and downstream genes of CDKN3 networks in human non‐malignancy associated hepatitis/cirrhosis and HCC transformation by GRNInfer respectively. control: human non‐malignancy associated hepatitis/cirrhosis, experiment: HCC patients

Control	Experiment
Upstream
NUSAP1, DLG7, LCN2, SFRP4, RRM2, TROAP, HIST1H3H, TAGLN2, MYBL2, TK1, PRCC, E2F1, BRCA1, CENPF, SCML2, BIRC5, TOP2A, SPINK1, MDK, GNG10, FOXM1, TRAF2, SPON2, RAB3B, ECT2, KIAA0859, PIGC, TTK, CDC20, GPSM2, PLK4, TSTA3, VDR, MCM2, CIAO1, XRCC2, MELK, MAP4K4, CCNE2, AMELY, CDC6, SEMA3B, TUBG1, KIAA0513, CSTF2, TNFRSF9, IGF2BP3, NCAPH, YWHAE, SBF1, PVRL2, ORC1L, EIF1AX, ZWINT, GDPD5, GRM1, ARHGDIG, MCM4, BUB1B, ACTN2, RBCK1, DDX10, C9orf127, PTTG1, ACTG2, CLIC1, RNF185, CCNA2, RBM34, LTBP2, SORT1, ZIC2, CDH13, GPC3, ST6GALNAC, CYP21A2, CEBPA, PRKCG, HIST1H2AG, UBE2C, CCNB2, CST6, NAT9, MYH6, HOXD4, CAMK1, CNTNAP2, MUTYH, PSMC3IP, SFTPA2, ALK, CDC2, CD34, TP53I11, CHST1, NOTCH3, HMGB2, BLVRA, LGALS3, MKRN3, CHAF1A, KPNA2, ITGA2, CELSR2, SLC16A3, GNAZ, KCTD2, MAPK3, GJA5, RRP1B, BAP1, CAD, HIST1H2BJ, REG3A, ESM1, WDR1, TRIP13, GML, CKS1B, ROBO1, ORC6L, FGF9, SYN2, MYCN, AFP, CCL20, LEF1, SERPINB2, IRF5, BCAT1, PRKG2, REG1A, TPST2, S100P, NR5A1, HIST1H2AD, MMP9, PTHLH, SQLE, PHLDA2, CSPG4, CCNB1, CRYGA, STX1A, UNG, SULT1C2, MYOM1, MAOA, ZNF43, FKBP1B, HOXA5, GAS7, CYP51A1, EYA1, PRSS1, CHRNA4, KATNB1, MAN2A1, OCRL, ALDH3A1, F13A1, VCAN, STMN1, FLJ33790, EFNA1, PLA2G1B, KCNQ3, PAGE4, TCAP, CDKN2C, NQO1, CYP17A1, KIAA0101, TSHB, KLRC3, ESPL1, MRPL49, RIMS3, NKX2‐5, PTHR2, NTN1, CTHRC1, TBL3, MMP11, PROK1, TSR1, ADAMDEC1, MS4A2, SCGB1D2, PCOLCE2, NUP62 NINJ2 LAPTM4B DMN RABGGTA SOX2 SSTR5 NRXN3 CDKN3	NEK2, NUSAP1, DLG7, LCN2, SFRP4, RRM2, TROAP, HIST1H3H, TAGLN2, MYBL2, TK1, PRCC, E2F1, BRCA1, CENPF, SCML2, TOP2A, SPINK1, MDK, GNG10, FOXM1, TRAF2, SPON2, RAB3B, ECT2, ENAH, SLC4A3, TTK, CDC20, GPSM2, PLK4, TSTA3, MAPT, VDR, MCM2, MELK, MAP4K4, CCNE2, MAP2, AMELY, SEMA3B, TUBG1, CSTF2, CPD, TNFRSF9, IGF2BP3, NCAPH, YWHAE, SBF1, PVRL2, EIF1AX, ZWINT, GDPD5, GRM1, ARHGDIG, BUB1B, GALK1, ACTN2, RBCK1, DDX10, C9orf127, PTTG1, ACTG2, CLIC1, RNF185, CCNA2, RBM34, LTBP2, SORT1, ZIC2, CDH13, GPC3, CYP21A2, CEBPA, PRKCG, HIST1H2AG, UBE2C, CCNB2, CST6, NAT9, MYH6, SFTPA2, ALK, CDC2, CD34, NFKBIB, TP53I11, NOTCH3, HMGB2, FOLR1, BLVRA, LGALS3, RFC4, MKRN3, CHAF1A, ITGA2, EPHA4, CELSR2, SLC16A3, GNAZ, MAPK3, TPSD1, GJA5, BAP1, CAD, HIST1H2BJ, PPP1R12B, REG3A, ESM1, WDR1, LYPD3, GML, CKS1B, ROBO1, FGF9, MYCN, ELAVL3, AFP, CCL20, CBX5, LEF1, IRF5, PRKG2, REG1A, C4orf8, TPST2, S100P, NR5A1, MAP2K6, CHL1, HIST1H2AD, MMP9, PTHLH, SQLE, PHLDA2, CSPG4, CCNB1, CRYGA, STX1A, SULT1C2, MYOM1, MAOA, ZNF43, GAS7, EYA1, PRSS1, CHRNA4, KATNB1, MAN2A1, OCRL, ALDH3A1, F13A1, STMN1, EFNA1, PLA2G1B, KCNQ3, PAGE4, TCAP, CDKN2C, NQO1, CYP17A1, KIAA0101, TSHB, KLRC3, DKK1, RIMS3, NKX2‐5, PTHR2, NTN1, TBL3, MMP11, PROK1, TSR1, ADAMDEC1, PCOLCE2, NUP62, NINJ2, LAPTM4B, RABGGTA, SOX2, SSTR5, NRXN3, CDKN3
Downstream
NEK2, NUSAP1, DLG7, LCN2, SFRP4, RRM2, TROAP, TAGLN2, MYBL2, TK1, PRCC, E2F1, BRCA1, CENPF, SCML2, BIRC5, TOP2A, SPINK1, MDK, GNG10, FOXM1, TRAF2, SPON2, RAB3B, ECT2, KIAA0859, ENAH, SLC4A3, TTK, CDC20, GPSM2, PLK4, TSTA3, MAPT, VDR, MCM2, CIAO1, XRCC2, MELK, MAP4K4, CCNE2, MAP2, AMELY, CDC6, SEMA3B, TUBG1, KIAA0513, CSTF2, CPD, TNFRSF9, IGF2BP3, NCAPH, YWHAE, SBF1, PVRL2, ORC1L, EIF1AX, ZWINT, GDPD5, GRM1, ARHGDIG, MCM4, LLGL2, BUB1B, GALK1, ACTN2, RBCK1, DDX10, C9orf127, PTTG1, ACTG2, CLIC1, RNF185, CCNA2, RBM34, LTBP2, SORT1, ZIC2, CDH13, GPC3, ST6GALNAC, CYP21A2, AKR1B10, CEBPA, PRKCG, HIST1H2AG, UBE2C, CCNB2, CST6, NAT9, MYH6, HOXD4, CAMK1, CNTNAP2, MUTYH, SFTPA2, ALK, CDC2, CD34, NFKBIB, TP53I11, CHST1, NOTCH3, HMGB2, FOLR1, BLVRA, LGALS3, RFC4, MKRN3, CHAF1A, KPNA2, ITGA2, EPHA4, CELSR2, SLC16A3, GNAZ, KCTD2, MAPK3, TPSD1, GJA5, RRP1B, BAP1, CAD, HIST1H2BJ, PPP1R12B, REG3A, ESM1, LYPD3, TRIP13, GML, CKS1B, ROBO1, ORC6L, FGF9, SYN2, MYCN, ELAVL3, AFP, CCL20, CBX5, LEF1, SERPINB2, IRF5, ISG20, BCAT1, SLC6A12, REG1A, C4orf8, TPST2, S100P, NR5A1, MAP2K6, CHL1, HIST1H2AD, MMP9, CORO2A, SQLE, PHLDA2, CSPG4, CCNB1, CRYGA, STX1A, UNG, SULT1C2, MYOM1, MAOA, ZNF43, FKBP1B, HOXA5, GAS7, CYP51A1, EYA1, PRSS1, CHRNA4, MAN2A1, OCRL, ALDH3A1, F13A1, VCAN, STMN1, FLJ33790, EFNA1, PLA2G1B, KCNQ3, PAGE4, TCAP, CDKN2C, NQO1, CYP17A1, KIAA0101, TSHB, KLRC3, DKK1, ESPL1, MRPL49, NKX2‐5, PTHR2, NTN1, CTHRC1, TBL3, MMP11, PROK1, TSR1, ADAMDEC1, MS4A2, SCGB1D2, PCOLCE2, NUP62, NINJ2, LAPTM4B, DMN, RABGGTA, LOX, SOX2, SSTR5, NRXN3, CDKN3	NEK2, NUSAP1, DLG7, LCN2, SFRP4, RRM2, HIST1H3H, TAGLN2, MYBL2, TK1, PRCC, E2F1, BRCA1, CENPF, SCML2, BIRC5, TOP2A, SPINK1, MDK, GNG10, FOXM1, RAB3B, ECT2, KIAA0859, PIGC, SLC4A3, TTK, CDC20, GPSM2, PLK4, TSTA3, MAPT, VDR, MCM2, CIAO1, XRCC2, MELK, MAP4K4, CCNE2, MAP2, AMELY, CDC6, SEMA3B, TUBG1, KIAA0513, CSTF2, CPD, TNFRSF9, IGF2BP3, NCAPH, YWHAE, SBF1, PVRL2, ORC1L, EIF1AX, GDPD5, GRM1, ARHGDIG, MCM4, LLGL2, BUB1B, GALK1, ACTN2, RBCK1, DDX10, C9orf127, PTTG1, ACTG2, CLIC1, RNF185, CCNA2, RBM34, LTBP2, SORT1, CDH13, GPC3, ST6GALNAC, CYP21A2, AKR1B10, PRKCG, HIST1H2AG, UBE2C, CCNB2, CST6, NAT9, MYH6, HOXD4, CAMK1, CNTNAP2, MUTYH, PSMC3IP, ALK, CDC2, CD34, NFKBIB, TP53I11, NOTCH3, HMGB2, FOLR1, BLVRA, LGALS3, RFC4, MKRN3, CHAF1A, KPNA2, ITGA2, EPHA4, CELSR2, SLC16A3, GNAZ, KCTD2, MAPK3, TPSD1, GJA5, RRP1B, CAD, HIST1H2BJ, PPP1R12B, REG3A, ESM1, WDR1, LYPD3, TRIP13, GML, CKS1B, ROBO1, ORC6L, SYN2, MYCN, ELAVL3, AFP, CCL20, CBX5, LEF1, SERPINB2, IRF5, ISG20, BCAT1, PRKG2, REG1A, C4orf8, TPST2, S100P, NR5A1, MAP2K6, CHL1, HIST1H2AD, MMP9, CORO2A, PTHLH, SQLE, PHLDA2, CSPG4, CCNB1, CRYGA, STX1A, UNG, SULT1C2, MYOM1, MAOA, FKBP1B, HOXA5, GAS7, CYP51A1, EYA1, PRSS1, CHRNA4, KATNB1, MAN2A1, OCRL, ALDH3A1, F13A1, VCAN, STMN1, FLJ33790, EFNA1, PLA2G1B, KCNQ3, PAGE4, TCAP, CDKN2C, NQO1, CYP17A1, KIAA0101, TSHB, KLRC3, DKK1, ESPL1, MRPL49, RIMS3, NKX2‐ 5, PTHR2, NTN1, CTHRC1, TBL3, MMP11, PROK1, TSR1, ADAMDEC1, MS4A2, SCGB1D2, PCOLCE2, NUP62, NINJ2, LAPTM4B, DMN, RABGGTA, LOX, SOX2, SSTR5, NRXN3, CDKN3