Gene symbol Gene name GO CCL21B chemokine (C-C motif) ligand 21b (serine) 1–2 CD276 CD276 antigen 1–2 SPP1 secreted phosphoprotein 1 1–2 CD24 CD24 antigen 1 C1QG complement component 1, q subcomponent, gamma polypeptide 1 CD74 CD74 antigen 1 HLA-DMA major histocompatibility complex, class II, DM alpha 1 HLA-DMB major histocompatibility complex, class II, DM beta 1 DEFB1 defensin beta 1 1 FCGR3 Fc receptor, IgG, low affinity III 1 PLSCR1 phospholipid scramblase 1 1 PRNP prion protein 1 RT1-BA RT1 class II, locus Ba 1 RT1-CE5 RT1 class I, CE5 1

RT1-DA RT1 class II, locus Da 1 RT1-DB1 RT1 class II, locus Db1 1 RT1-BB RT1 class II, locus Bb 1 ANXA1 annexin A1 2 FABP4 fatty acid binding protein 4, adipocyte 2 S100A8 S100 calcium binding protein A8 2 S100A9 S100 calcium PF-6463922 binding protein A9 2 CDC2A cell division cycle 2 homolog A 3 EGR1 early growth response 1 3 CRYAB crystallin, alpha B 3 CCND1 Wortmannin cyclin D1 3 CD36 cd36 antigen 3 GCLC glutamate-cysteine MS-275 molecular weight ligase, catalytic subunit 3 GGT1 gamma-glutamyltransferase 1 3 GPX2 glutathione peroxidase 2 3 GPX3 glutathione peroxidase 3 3 GSR glutathione reductase 3 GSS glutathione synthetase 3 HSPCB heat shock 90 kDa protein 1, beta 3 LAMC1 laminin, gamma 1 3 MTAP2 microtubule-associated

protein 2 3 NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) 3 NQO1 NAD(P)H dehydrogenase, quinone 1 3 PDLIM1 PDZ and LIM domain 1 (elfin) 3 SLC25A4 solute carrier family 25 3 TXNRD1 thioredoxin reductase 1 3 NOTE: The numbers from 1–3 indicate immune response, inflammatory response and oxidative stress, respectively. Table 5 The down-regulated DEGs sharing from cirrhosis to metastasis stage relating to the following GO process. Gene Symbol Gene Title Tyrosine-protein kinase BLK GO C5 complement component 5 1–2 IL4RA interleukin 4 receptor, alpha 1–2 MBL2 mannose binding lectin 2 (protein C) 1–3 NOX4 NADPH oxidase 4 2–3 ATRN Attractin 2–3 C1S complement component 1, s subcomponent 1 C4BPB complement component 4 binding protein, beta 1 AZGP1 alpha-2-glycoprotein 1, zinc 1 C6 complement component 6 1 CXCL12 chemokine (C-X-C motif) ligand 12

1 MX2 myxovirus (influenza virus) resistance 2 1 OAS1 2′,5′-oligoadenylate synthetase 1, 40/46 kDa 1 RT1-S3 RT1 class Ib, locus S3 1 VIPR1 vasoactive intestinal peptide receptor 1 1 APOA2 apolipoprotein A-II 2 BCL6_predicted B-cell leukemia/lymphoma 6 (predicted) 2 KLKB1 kallikrein B, plasma 1 2 PROC protein C 2 PTGER3 Prostaglandin E receptor 3 (subtype EP3) 2 MEOX2 mesenchyme homeobox 2 3 CA3 carbonic anhydrase 3 3 ABCB11 ATP-binding cassette, sub-family B (MDR/TAP), member 11 3 ALAD aminolevulinate, delta-, dehydratase 3 CYP2E1 cytochrome P450, family 2, subfamily e, polypeptide 1 3 EGFR epidermal growth factor receptor 3 HAO1 hydroxyacid oxidase 1 3 HNF4A Hepatocyte nuclear factor 4, alpha 3 NOTE: The numbers from 1–3 indicate immune reponse, inflammatory response and oxidative stress, respectively.