Supplementary Table S7: Functional annotation enrichment analysis for genes down-regulated in patients with nonalcoholic steatohepatitis versus healthy controls

Terms with a false discovery rate (FDR) <0.05 are included.

Term / Count / % / List Total / Pop Hits / Pop Total / Fold Enrichment / FDR / Genes
KEGG_PATHWAY
hsa04630:Jak-STAT signaling pathway / 15 / 4.93 / 96 / 155 / 5085 / 5.126 / 8.92E-04 / CSF3, IL6, SOCS2, SOCS3, SOCS1, PIM1, IL24, IL10, SPRY4, CISH, LIF, OSM, CLCF1, IL4R, MYC
hsa04060:Cytokine-cytokine receptor interaction / 19 / 6.25 / 96 / 262 / 5085 / 3.841 / 0.0013 / CSF3, IL6, CCL3, IL18RAP, CCL2, IL8, TNFRSF12A, TGFB3, TNFSF14, IL24, IL10, LIF, OSM, TNFRSF1A, CCL20, TNFRSF10D, CLCF1, IL4R, IL1B
GOTERM_BP_FAT
GO:0009611~response to wounding / 36 / 11.84 / 237 / 530 / 13528 / 3.877 / 1.63E-08 / CCL3, CCL2, S100A8, ELF3, TGFB3, FPR2, MMP25, IL10, TNFRSF1A, FOS, SLC11A1, CCL20, SAA1, RAC1, SERPINE1, IL1B, SERPINA1, PTX3, THBS1, NRG1, RAB27A, NFKBIZ, KLF6, IL6, IL18RAP, IL8, IL1RN, S100A12, PLAUR, TNFAIP6, PROK2, THBD, SERPINB2, HBEGF, VCAN, IGFBP1
GO:0043066~negative regulation of apoptosis / 28 / 9.21 / 237 / 354 / 13528 / 4.515 / 1.97E-07 / IER3, CCL2, TGFB3, FOXO1, IL10, CLCF1, TGM2, IL1B, BCL3, BCL6, THBS1, NRG1, MYC, ANGPTL4, IL6, SOCS2, SOCS3, BCL2A1, PIM1, NR4A2, PIM3, BIRC3, PROK2, SERPINB9, CDKN1A, TNFRSF10D, SERPINB2, FOXC1
GO:0043069~negative regulation of programmed cell death / 28 / 9.21 / 237 / 359 / 13528 / 4.452 / 2.69E-07 / IER3, CCL2, TGFB3, FOXO1, IL10, CLCF1, TGM2, IL1B, BCL3, BCL6, THBS1, NRG1, MYC, ANGPTL4, IL6, SOCS2, SOCS3, BCL2A1, PIM1, NR4A2, PIM3, BIRC3, PROK2, SERPINB9, CDKN1A, TNFRSF10D, SERPINB2, FOXC1
GO:0060548~negative regulation of cell death / 28 / 9.21 / 237 / 360 / 13528 / 4.440 / 2.89E-07 / IER3, CCL2, TGFB3, FOXO1, IL10, CLCF1, TGM2, IL1B, BCL3, BCL6, THBS1, NRG1, MYC, ANGPTL4, IL6, SOCS2, SOCS3, BCL2A1, PIM1, NR4A2, PIM3, BIRC3, PROK2, SERPINB9, CDKN1A, TNFRSF10D, SERPINB2, FOXC1
GO:0006954~inflammatory response / 25 / 8.22 / 237 / 325 / 13528 / 4.391 / 4.33E-06 / CCL3, CCL2, S100A8, ELF3, FPR2, IL10, MMP25, FOS, SLC11A1, TNFRSF1A, CCL20, SAA1, RAC1, IL1B, SERPINA1, THBS1, PTX3, NFKBIZ, IL6, IL18RAP, IL8, IL1RN, S100A12, PROK2, TNFAIP6
GO:0042330~taxis / 18 / 5.92 / 237 / 160 / 13528 / 6.422 / 4.70E-06 / IL6, CCL3, CMTM2, CCL2, C5AR1, IL8, FPR1, FPR2, IL10, PLAUR, PROK2, CCL20, SAA1, LYST, RAC1, IL1B, FOSL1, CYR61
GO:0006935~chemotaxis / 18 / 5.92 / 237 / 160 / 13528 / 6.422 / 4.70E-06 / IL6, CCL3, CMTM2, CCL2, C5AR1, IL8, FPR1, FPR2, IL10, PLAUR, PROK2, CCL20, SAA1, LYST, RAC1, IL1B, FOSL1, CYR61
GO:0002237~response to molecule of bacterial origin / 14 / 4.61 / 237 / 86 / 13528 / 9.292 / 4.87E-06 / IL6, CCL2, PTGS2, SOCS3, SOCS1, IL10, IRAK3, SLC11A1, FOS, TNFRSF1A, THBD, JUN, IL1B, SERPINA1
GO:0042981~regulation of apoptosis / 40 / 13.16 / 237 / 804 / 13528 / 2.840 / 8.96E-06 / IER3, CCL2, PTGS2, TGFB3, TNFSF14, FOXO1, IL10, CASP4, CLCF1, ALDH1A3, RAC1, TGM2, BCL3, IL1B, BCL6, NRG1, THBS1, FOSL1, MYC, RAB27A, ANGPTL4, PHLDA1, IL6, SOCS2, SOCS3, BCL2A1, PIM1, NR4A2, NR4A1, PIM3, BIRC3, PROK2, SERPINB9, CDKN1A, TNFRSF10D, JUN, LYST, ERN1, SERPINB2, FOXC1
GO:0019220~regulation of phosphate metabolic process / 30 / 9.87 / 237 / 485 / 13528 / 3.531 / 1.14E-05 / C13ORF15, TGFB3, FPR1, LPAR1, SDC4, SPRY4, CALCA, LIF, SLC11A1, IRAK3, CLCF1, RAC1, IL1B, NRG1, THBS1, SERTAD1, IL6, C5AR1, SOCS3, SOCS1, PIM1, RCAN1, CISH, OSM, PROK2, CDKN1A, JUN, GADD45G, ERN1, GADD45B
GO:0051174~regulation of phosphorus metabolic process / 30 / 9.87 / 237 / 485 / 13528 / 3.531 / 1.14E-05 / C13ORF15, TGFB3, FPR1, LPAR1, SDC4, SPRY4, CALCA, LIF, SLC11A1, IRAK3, CLCF1, RAC1, IL1B, NRG1, THBS1, SERTAD1, IL6, C5AR1, SOCS3, SOCS1, PIM1, RCAN1, CISH, OSM, PROK2, CDKN1A, JUN, GADD45G, ERN1, GADD45B
GO:0043067~regulation of programmed cell death / 40 / 13.16 / 237 / 812 / 13528 / 2.812 / 1.18E-05 / IER3, CCL2, PTGS2, TGFB3, TNFSF14, FOXO1, IL10, CASP4, CLCF1, ALDH1A3, RAC1, TGM2, BCL3, IL1B, BCL6, NRG1, THBS1, FOSL1, MYC, RAB27A, ANGPTL4, PHLDA1, IL6, SOCS2, SOCS3, BCL2A1, PIM1, NR4A2, NR4A1, PIM3, BIRC3, PROK2, SERPINB9, CDKN1A, TNFRSF10D, JUN, LYST, ERN1, SERPINB2, FOXC1
GO:0048545~response to steroid hormone stimulus / 19 / 6.25 / 237 / 192 / 13528 / 5.649 / 1.19E-05 / IL6, CCL2, PTGS2, SOCS2, SOCS3, IL1RN, SOCS1, TGFB3, RCAN1, JUNB, IL10, FOS, CDKN1A, AVPR1A, IL1B, SERPINA1, IGFBP2, THBS1, FOSL1
GO:0009617~response to bacterium / 19 / 6.25 / 237 / 193 / 13528 / 5.619 / 1.29E-05 / IL6, CCL2, PTGS2, SOCS3, SOCS1, IL10, S100A12, IRAK3, SLC11A1, FOS, TNFRSF1A, THBD, CCL20, JUN, LYST, DEFB118, BCL3, IL1B, SERPINA1
GO:0010941~regulation of cell death / 40 / 13.16 / 237 / 815 / 13528 / 2.801 / 1.31E-05 / IER3, CCL2, PTGS2, TGFB3, TNFSF14, FOXO1, IL10, CASP4, CLCF1, ALDH1A3, RAC1, TGM2, BCL3, IL1B, BCL6, NRG1, THBS1, FOSL1, MYC, RAB27A, ANGPTL4, PHLDA1, IL6, SOCS2, SOCS3, BCL2A1, PIM1, NR4A2, NR4A1, PIM3, BIRC3, PROK2, SERPINB9, CDKN1A, TNFRSF10D, JUN, LYST, ERN1, SERPINB2, FOXC1
GO:0032496~response to lipopolysaccharide / 13 / 4.28 / 237 / 77 / 13528 / 9.637 / 1.41E-05 / CCL2, PTGS2, SOCS3, SOCS1, IL10, IRAK3, SLC11A1, FOS, TNFRSF1A, THBD, JUN, IL1B, SERPINA1
GO:0042325~regulation of phosphorylation / 29 / 9.54 / 237 / 466 / 13528 / 3.552 / 1.91E-05 / C13ORF15, TGFB3, FPR1, LPAR1, SDC4, SPRY4, CALCA, LIF, SLC11A1, IRAK3, CLCF1, RAC1, IL1B, NRG1, THBS1, SERTAD1, IL6, C5AR1, SOCS3, SOCS1, PIM1, CISH, OSM, PROK2, CDKN1A, JUN, GADD45G, ERN1, GADD45B
GO:0007610~behavior / 29 / 9.54 / 237 / 469 / 13528 / 3.529 / 2.20E-05 / CCL3, CCL2, PTGS2, FPR1, FPR2, IL10, FOS, CCL20, SAA1, RAC1, IL1B, FOSL1, CDH23, CYR61, EGR1, IL6, S100P, CMTM2, C5AR1, IL8, NR4A2, FOSB, NR4A3, PLAUR, OSM, PROK2, JUN, LYST, AVPR1A
GO:0032570~response to progesterone stimulus / 8 / 2.63 / 237 / 20 / 13528 / 22.832 / 4.98E-05 / FOS, CCL2, SOCS3, SOCS1, TGFB3, THBS1, FOSL1, JUNB
GO:0006952~defense response / 33 / 10.86 / 237 / 615 / 13528 / 3.063 / 4.99E-05 / CCL3, CCL2, S100A8, ELF3, FPR2, MMP25, IL10, TNFRSF1A, FOS, SLC11A1, CCL20, SAA1, RAC1, DEFB118, IL1B, BCL3, SERPINA1, PTX3, THBS1, FOSL1, RAB27A, NFKBIZ, IL6, C5AR1, IL18RAP, IL8, IL1RL1, IL1RN, GAGE2B, GAGE12C, S100A12, TNFAIP6, PROK2, GAGE5, GAGE4, LYST
GO:0001944~vasculature development / 20 / 6.58 / 237 / 251 / 13528 / 4.548 / 1.46E-04 / KLF5, IL8, TNFRSF12A, TIPARP, MMP19, PRRX1, APOLD1, FOXO1, JUNB, CALCA, PROK2, JUN, TGM2, ZC3H12A, IL1B, FOXC1, SOX17, THBS1, CYR61, ANGPTL4
GO:0042127~regulation of cell proliferation / 37 / 12.17 / 237 / 787 / 13528 / 2.684 / 1.67E-04 / CSF3, NAMPT, FOSL2, CCL2, PTGS2, TGFB3, PRRX1, GJA1, FOXO1, IL10, LIF, SERPINE1, TGM2, IL1B, BCL6, THBS1, NRG1, FOSL1, MYC, SERTAD1, KLF5, PTGER2, IRS2, IL6, IL8, KLF11, OSM, CDKN1A, ATF3, JUN, CD274, AVPR1A, HBEGF, ADAMTS1, PMP22, NR5A2, KLF4
GO:0051384~response to glucocorticoid stimulus / 12 / 3.95 / 237 / 78 / 13528 / 8.782 / 1.74E-04 / FOS, CDKN1A, IL6, CCL2, PTGS2, IL1RN, AVPR1A, IL1B, IGFBP2, FOSL1, JUNB, IL10
GO:0031328~positive regulation of cellular biosynthetic process / 34 / 11.18 / 237 / 685 / 13528 / 2.833 / 1.86E-04 / TGFB3, FOXO1, IL10, LIF, TNFRSF1A, FOS, SLC11A1, TEAD4, IL1B, BCL3, PTX3, THBS1, MYC, FOSL1, SERTAD1, EGR1, KLF5, KLF6, IL6, IRS2, NFE2, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, AVPR1A, IRF1, FOXC1, NR5A2, KLF4
GO:0006916~anti-apoptosis / 18 / 5.92 / 237 / 206 / 13528 / 4.988 / 2.08E-04 / IER3, CCL2, SOCS2, SOCS3, BCL2A1, FOXO1, BIRC3, IL10, SERPINB9, PROK2, TNFRSF10D, SERPINB2, TGM2, IL1B, FOXC1, NRG1, THBS1, MYC
GO:0009891~positive regulation of biosynthetic process / 34 / 11.18 / 237 / 695 / 13528 / 2.792 / 2.60E-04 / TGFB3, FOXO1, IL10, LIF, TNFRSF1A, FOS, SLC11A1, TEAD4, IL1B, BCL3, PTX3, THBS1, MYC, FOSL1, SERTAD1, EGR1, KLF5, KLF6, IL6, IRS2, NFE2, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, AVPR1A, IRF1, FOXC1, NR5A2, KLF4
GO:0048514~blood vessel morphogenesis / 18 / 5.92 / 237 / 211 / 13528 / 4.869 / 2.94E-04 / KLF5, IL8, TNFRSF12A, TIPARP, MMP19, PRRX1, APOLD1, JUNB, PROK2, JUN, TGM2, ZC3H12A, IL1B, FOXC1, SOX17, THBS1, CYR61, ANGPTL4
GO:0031960~response to corticosteroid stimulus / 12 / 3.95 / 237 / 85 / 13528 / 8.058 / 4.28E-04 / FOS, CDKN1A, IL6, CCL2, PTGS2, IL1RN, AVPR1A, IL1B, IGFBP2, FOSL1, JUNB, IL10
GO:0001568~blood vessel development / 19 / 6.25 / 237 / 245 / 13528 / 4.427 / 5.04E-04 / KLF5, IL8, TNFRSF12A, TIPARP, MMP19, PRRX1, APOLD1, FOXO1, JUNB, PROK2, JUN, TGM2, ZC3H12A, IL1B, FOXC1, SOX17, THBS1, CYR61, ANGPTL4
GO:0007626~locomotory behavior / 20 / 6.58 / 237 / 274 / 13528 / 4.166 / 5.74E-04 / IL6, CCL3, CMTM2, CCL2, C5AR1, IL8, NR4A2, FPR1, FPR2, IL10, PLAUR, PROK2, CCL20, SAA1, LYST, RAC1, IL1B, FOSL1, CYR61, CDH23
GO:0010033~response to organic substance / 34 / 11.18 / 237 / 721 / 13528 / 2.692 / 6.03E-04 / CCL2, PTGS2, TGFB3, FOXO1, IL10, TNFRSF1A, FOS, SLC11A1, IRAK3, IL1B, SERPINA1, THBS1, MYC, FOSL1, CYR61, EGR1, IRS2, IL6, SOCS2, SOCS3, IL1RN, SOCS1, NR4A2, RCAN1, NR4A3, JUNB, CDKN1A, THBD, JUN, AVPR1A, ERN1, IGFBP1, IGFBP2, PPP1R15A
GO:0010557~positive regulation of macromolecule biosynthetic process / 32 / 10.53 / 237 / 654 / 13528 / 2.793 / 6.71E-04 / TGFB3, FOXO1, IL10, LIF, TNFRSF1A, FOS, SLC11A1, TEAD4, IL1B, BCL3, THBS1, MYC, FOSL1, SERTAD1, EGR1, KLF5, KLF6, IL6, IRS2, NFE2, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, IRF1, FOXC1, NR5A2, KLF4
GO:0009725~response to hormone stimulus / 23 / 7.57 / 237 / 367 / 13528 / 3.577 / 8.19E-04 / IL6, IRS2, CCL2, SOCS2, PTGS2, SOCS3, IL1RN, SOCS1, TGFB3, FOXO1, RCAN1, NR4A3, JUNB, IL10, FOS, CDKN1A, AVPR1A, IL1B, SERPINA1, IGFBP1, IGFBP2, THBS1, FOSL1
GO:0045944~positive regulation of transcription from RNA polymerase II promoter / 23 / 7.57 / 237 / 371 / 13528 / 3.539 / 9.80E-04 / EGR1, KLF6, IL6, NR4A2, TGFB3, FOXO1, NR4A1, NR4A3, JUNB, LIF, OSM, SLC11A1, FOS, TNFRSF1A, JUN, TEAD4, IRF1, BCL3, FOXC1, NR5A2, FOSL1, MYC, KLF4
GO:0045941~positive regulation of transcription / 29 / 9.54 / 237 / 564 / 13528 / 2.935 / 0.0010 / TGFB3, FOXO1, IL10, LIF, FOS, SLC11A1, TNFRSF1A, TEAD4, BCL3, MYC, FOSL1, SERTAD1, EGR1, KLF5, KLF6, IL6, NFE2, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, IRF1, FOXC1, NR5A2, KLF4
GO:0009719~response to endogenous stimulus / 24 / 7.90 / 237 / 405 / 13528 / 3.383 / 0.0012 / IL6, IRS2, CCL2, SOCS2, PTGS2, SOCS3, IL1RN, SOCS1, NR4A2, TGFB3, FOXO1, RCAN1, NR4A3, JUNB, IL10, FOS, CDKN1A, AVPR1A, IL1B, SERPINA1, IGFBP1, IGFBP2, THBS1, FOSL1
GO:0051173~positive regulation of nitrogen compound metabolic process / 31 / 10.20 / 237 / 644 / 13528 / 2.748 / 0.0015 / TGFB3, FOXO1, IL10, LIF, FOS, SLC11A1, TNFRSF1A, TEAD4, IL1B, BCL3, PTX3, MYC, FOSL1, SERTAD1, EGR1, KLF5, KLF6, IL6, NFE2, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, IRF1, FOXC1, NR5A2, KLF4
GO:0045893~positive regulation of transcription, DNA-dependent / 26 / 8.55 / 237 / 477 / 13528 / 3.111 / 0.0016 / TGFB3, FOXO1, IL10, LIF, FOS, SLC11A1, TNFRSF1A, TEAD4, BCL3, MYC, FOSL1, EGR1, KLF6, IL6, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, IRF1, FOXC1, NR5A2, KLF4
GO:0010628~positive regulation of gene expression / 29 / 9.54 / 237 / 581 / 13528 / 2.849 / 0.0019 / TGFB3, FOXO1, IL10, LIF, FOS, SLC11A1, TNFRSF1A, TEAD4, BCL3, MYC, FOSL1, SERTAD1, EGR1, KLF5, KLF6, IL6, NFE2, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, IRF1, FOXC1, NR5A2, KLF4
GO:0051254~positive regulation of RNA metabolic process / 26 / 8.55 / 237 / 481 / 13528 / 3.085 / 0.0019 / TGFB3, FOXO1, IL10, LIF, FOS, SLC11A1, TNFRSF1A, TEAD4, BCL3, MYC, FOSL1, EGR1, KLF6, IL6, NR4A2, NR4A1, CREB5, NR4A3, JUNB, OSM, JUN, ETS2, IRF1, FOXC1, NR5A2, KLF4
GO:0043549~regulation of kinase activity / 22 / 7.24 / 237 / 357 / 13528 / 3.518 / 0.0021 / C5AR1, C13ORF15, PIM1, FPR1, TGFB3, LPAR1, SDC4, CISH, SPRY4, CALCA, PROK2, IRAK3, SLC11A1, CDKN1A, GADD45G, RAC1, ERN1, IL1B, THBS1, GADD45B, NRG1, SERTAD1
GO:0016477~cell migration / 19 / 6.25 / 237 / 276 / 13528 / 3.929 / 0.0029 / PVR, IL6, CCL2, S100P, IL8, TNFRSF12A, ARID5B, NR4A2, IL10, CALCA, SAA1, LYST, RAC1, HBEGF, IL1B, VCAN, FOXC1, THBS1, GFRA3
GO:0051338~regulation of transferase activity / 22 / 7.24 / 237 / 372 / 13528 / 3.376 / 0.0040 / C5AR1, C13ORF15, PIM1, FPR1, TGFB3, LPAR1, SDC4, CISH, SPRY4, CALCA, PROK2, IRAK3, SLC11A1, CDKN1A, GADD45G, RAC1, ERN1, IL1B, THBS1, GADD45B, NRG1, SERTAD1
GO:0045859~regulation of protein kinase activity / 21 / 6.91 / 237 / 345 / 13528 / 3.474 / 0.0047 / C5AR1, C13ORF15, PIM1, FPR1, TGFB3, LPAR1, SDC4, CISH, SPRY4, CALCA, PROK2, IRAK3, SLC11A1, CDKN1A, GADD45G, ERN1, IL1B, THBS1, GADD45B, NRG1, SERTAD1
GO:0033674~positive regulation of kinase activity / 17 / 5.59 / 237 / 231 / 13528 / 4.201 / 0.0051 / C5AR1, PIM1, FPR1, TGFB3, LPAR1, SDC4, CISH, CALCA, SLC11A1, PROK2, GADD45G, RAC1, ERN1, IL1B, GADD45B, NRG1, THBS1
GO:0031099~regeneration / 10 / 3.29 / 237 / 69 / 13528 / 8.272 / 0.0051 / LIF, CDKN1A, CCL2, SOCS3, SOCS1, SERPINE1, VCAN, NR4A3, IGFBP1, PLAUR
GO:0006928~cell motion / 25 / 8.22 / 237 / 475 / 13528 / 3.004 / 0.0051 / PVR, CCL3, CCL2, PTGS2, TNFRSF12A, FPR1, FPR2, IL10, CALCA, SAA1, RAC1, IL1B, THBS1, VNN2, IL6, S100P, IL8, ARID5B, NR4A2, PLAUR, LYST, HBEGF, VCAN, FOXC1, GFRA3
GO:0019221~cytokine-mediated signaling pathway / 10 / 3.29 / 237 / 70 / 13528 / 8.154 / 0.0057 / CSF3, TNFRSF1A, KLF6, IRAK3, IL6, CCL2, CLCF1, SOCS1, TGM2, IL1B
GO:0007565~female pregnancy / 12 / 3.95 / 237 / 110 / 13528 / 6.227 / 0.0058 / LIF, CALCA, FOS, THBD, PTGS2, PAPPA, TEAD4, TGFB3, IL1B, IGFBP2, FOSL1, JUNB
GO:0008284~positive regulation of cell proliferation / 23 / 7.57 / 237 / 414 / 13528 / 3.171 / 0.0060 / KLF5, CSF3, NAMPT, IL6, IRS2, FOSL2, CCL2, PTGS2, PRRX1, OSM, LIF, CDKN1A, ATF3, JUN, TGM2, AVPR1A, HBEGF, IL1B, BCL6, NRG1, MYC, FOSL1, SERTAD1
GO:0006955~immune response / 31 / 10.20 / 237 / 690 / 13528 / 2.564 / 0.0062 / CSF3, CCL3, SBNO2, CCL2, TNFSF14, NFKB2, IL10, LIF, TNFRSF1A, SLC11A1, CCL20, IL4R, DEFB118, IL1B, BCL3, PTX3, NFIL3, THBS1, RAB27A, IL6, IL18RAP, C5AR1, IL8, IL1RL1, IL1RN, GEM, OSM, RGS1, FCAR, LYST, CD274