Table S1 List of / shared between NAFLD, fibrosis, and inflammation symbol Description Gene ID

ANGPTL2 ANGPTL2 (angiopoietin like 2) 23452

ESM1 ESM1 (endothelial cell specific molecule 1) 11082

CXCL16 CXCL16 (C-X-C motif chemokine ligand 16) 58191

DUSP1 DUSP1 (dual specificity phosphatase 1) 1843

CD163 CD163 (CD163 molecule) 9332

TNFRSF6B TNFRSF6B (TNF receptor superfamily member 6b) 8771

NR1H2 NR1H2 (nuclear receptor subfamily 1 group H member 2) 7376

PLA2G2A PLA2G2A (phospholipase A2 group IIA) 5320

NOX4 NOX4 (NADPH oxidase 4) 50507

DDIT3 DDIT3 (DNA damage inducible transcript 3) 1649

CXCR3 CXCR3 (C-X-C motif chemokine receptor 3) 2833

IL6ST IL6ST ( 6 signal transducer) 3572

OLR1 OLR1 (oxidized low-density lipoprotein receptor 1) 4973

CNR2 CNR2 (cannabinoid receptor 2) 1269

TFPI TFPI (tissue factor pathway inhibitor) 7035

P2RX7 P2RX7 (purinergic receptor P2X 7) 5027

WNT5A WNT5A (Wnt family member 5A) 7474

THBD THBD (thrombomodulin) 7056

HAMP HAMP (hepcidin antimicrobial peptide) 57817

CHI3L1 CHI3L1 (chitinase 3 like 1) 1116

SMAD7 SMAD7 (SMAD family member 7) 4092

PPARD PPARD (peroxisome proliferator activated receptor delta) 5467

CD36 CD36 (CD36 molecule) 948

TIMP1 TIMP1 (TIMP metallopeptidase inhibitor 1) 7076

PDCD1 PDCD1 (programmed cell death 1) 5133

MMP3 MMP3 (matrix metallopeptidase 3) 4314

TNF TNF () 7124

IL6 IL6 () 3569

CXCL8 CXCL8 (C-X-C motif chemokine ligand 8) 3576

IL1B IL1B (interleukin 1 beta) 3553

IL17A IL17A (interleukin 17A) 3605

NFKB1 NFKB1 (nuclear factor kappa B subunit 1) 4790

HMGB1 HMGB1 (high mobility group box 1) 3146

TLR4 TLR4 (toll like receptor 4) 7099

IL10 IL10 () 3586

TLR2 TLR2 (toll like receptor 2) 7097

MIF MIF ( migration inhibitory factor) 4282

CCL2 CCL2 (C-C motif chemokine ligand 2) 6347

IL33 IL33 () 90865

NLRP3 NLRP3 (NLR family pyrin domain containing 3) 114548

STAT3 STAT3 (signal transducer and activator of transcription 3) 6774

IFNG IFNG (interferon gamma) 3458

TGFB1 TGFB1 (transforming growth factor beta 1) 7040

IL18 IL18 () 3606

NFE2L2 NFE2L2 (nuclear factor, erythroid 2 like 2) 4780

TNFSF12 TNFSF12 (TNF superfamily member 12) 8742

IL22 IL22 () 50616

MAPK14 MAPK14 (mitogen-activated kinase 14) 1432

SOCS3 SOCS3 (suppressor of signaling 3) 9021

IL32 IL32 () 9235

HMOX1 HMOX1 (heme oxygenase 1) 3162

PTGS2 PTGS2 (prostaglandin-endoperoxide synthase 2) 5743

IL4 IL4 () 3565

CXCL10 CXCL10 (C-X-C motif chemokine ligand 10) 3627

IL23A IL23A ( subunit alpha) 51561

MAPK1 MAPK1 (mitogen-activated protein kinase 1) 5594

IL13 IL13 () 3596

SOCS1 SOCS1 (suppressor of cytokine signaling 1) 8651

AGER AGER (advanced glycosylation end-product specific receptor) 177

CCL5 CCL5 (C-C motif chemokine ligand 5) 6352

TNFSF10 TNFSF10 (TNF superfamily member 10) 8743

IL1RN IL1RN (interleukin 1 receptor antagonist) 3557

MMP9 MMP9 (matrix metallopeptidase 9) 4318

VCAM1 VCAM1 (vascular cell adhesion molecule 1) 7412

VEGFA VEGFA (vascular endothelial growth factor A) 7422

ICAM1 ICAM1 (intercellular adhesion molecule 1) 3383

F3 F3 (coagulation factor III, tissue factor) 2152

TLR3 TLR3 (toll like receptor 3) 7098

PPARG PPARG (peroxisome proliferator activated receptor gamma) 5468

MAPK8 MAPK8 (mitogen-activated protein kinase 8) 5599

STAT1 STAT1 (signal transducer and activator of transcription 1) 6772

TNFRSF1A TNFRSF1A (TNF receptor superfamily member 1A) 7132

IL27 IL27 () 246778

IL1RL1 IL1RL1 (interleukin 1 receptor like 1) 9173

NAMPT NAMPT (nicotinamide phosphoribosyltransferase) 10135

IL21 IL21 () 59067

CRP CRP (C-reactive protein) 1401

LEP LEP (leptin) 3952

AKT1 AKT1 (AKT serine/threonine kinase 1) 207

NOS2 NOS2 (nitric oxide synthase 2) 4843

CTGF CTGF (connective tissue growth factor) 1490

TREM1 TREM1 (triggering receptor expressed on myeloid cells 1) 54210

CCL20 CCL20 (C-C motif chemokine ligand 20) 6364

CD40 CD40 (CD40 molecule) 958

RETN RETN (resistin) 56729

SIRT1 SIRT1 (sirtuin 1) 23411

SPP1 SPP1 (secreted phosphoprotein 1) 6696

NFKBIA NFKBIA (NFKB inhibitor alpha) 4792

IL2 IL2 () 3558

TLR7 TLR7 (toll like receptor 7) 51284

GDF15 GDF15 (growth differentiation factor 15) 9518

SAA1 SAA1 (serum amyloid A1) 6288

HIF1A HIF1A (hypoxia inducible factor 1 subunit alpha) 3091

TNFAIP3 TNFAIP3 (TNF alpha induced protein 3) 7128

ADIPOQ ADIPOQ (adiponectin, C1Q and collagen domain containing) 9370

CX3CL1 CX3CL1 (C-X3-C motif chemokine ligand 1) 6376

TLR9 TLR9 (toll like receptor 9) 54106

S100A9 S100A9 (S100 calcium binding protein A9) 6280

JUN JUN (Jun proto-oncogene, AP-1 transcription factor subunit) 3725

PTX3 PTX3 (pentraxin 3) 5806

MMP1 MMP1 (matrix metallopeptidase 1) 4312

TNFSF13B TNFSF13B (TNF superfamily member 13b) 10673

NR1H3 NR1H3 (nuclear receptor subfamily 1 group H member 3) 10062

MMP2 MMP2 (matrix metallopeptidase 2) 4313

CD40LG CD40LG (CD40 ligand) 959

S100A8 S100A8 (S100 calcium binding protein A8) 6279

EGFR EGFR (epidermal growth factor receptor) 1956

SERPINE1 SERPINE1 (serpin family E member 1) 5054

TNFRSF1B TNFRSF1B (TNF receptor superfamily member 1B) 7133

CD14 CD14 (CD14 molecule) 929

CD274 CD274 (CD274 molecule) 29126

HGF HGF (hepatocyte growth factor) 3082

LCN2 LCN2 (lipocalin 2) 3934

PPARA PPARA (peroxisome proliferator activated receptor alpha) 5465

MTOR MTOR (mechanistic target of rapamycin kinase) 2475

FOXO3 FOXO3 (forkhead box O3) 2309

TNFSF11 TNFSF11 (TNF superfamily member 11) 8600

TNFRSF11B TNFRSF11B (TNF receptor superfamily member 11b) 4982

PIK3CA PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) 5290

EDN1 EDN1 ( 1) 1906

GSK3B GSK3B (glycogen synthase kinase 3 beta) 2932

CXCL12 CXCL12 (C-X-C motif chemokine ligand 12) 6387

SMAD3 SMAD3 (SMAD family member 3) 4088

TP53 TP53 (tumor protein p53) 7157

CXCL9 CXCL9 (C-X-C motif chemokine ligand 9) 4283

FAS FAS (Fas cell surface death receptor) 355

LTA LTA (lymphotoxin alpha) 4049

CX3CR1 CX3CR1 (C-X3-C motif chemokine receptor 1) 1524

RARRES2 RARRES2 (retinoic acid receptor responder 2) 5919

FASLG FASLG () 356

ENPP2 ENPP2 (ectonucleotide pyrophosphatase/phosphodiesterase 2) 5168

THBS1 THBS1 (thrombospondin 1) 7057

NGF NGF (nerve growth factor) 4803

IGF1R IGF1R (insulin like growth factor 1 receptor) 3480

LGALS3 LGALS3 (galectin 3) 3958

PGF PGF (placental growth factor) 5228

FOXP3 FOXP3 (forkhead box P3) 50943

TNFSF13 TNFSF13 (TNF superfamily member 13) 8741

MAPK9 MAPK9 (mitogen-activated protein kinase 9) 5601

TNFAIP8L2 TNFAIP8L2 (TNF alpha induced protein 8 like 2) 79626

ANGPT2 ANGPT2 (angiopoietin 2) 285

CXCL11 CXCL11 (C-X-C motif chemokine ligand 11) 6373

SIRT6 SIRT6 (sirtuin 6) 51548

CFH CFH (complement factor H) 3075

FABP4 FABP4 (fatty acid binding protein 4) 2167

CXCL13 CXCL13 (C-X-C motif chemokine ligand 13) 10563

ITGAV ITGAV (integrin subunit alpha V) 3685

DPP4 DPP4 (dipeptidyl peptidase 4) 1803

PRKAA1 PRKAA1 (protein kinase AMP-activated catalytic subunit alpha 1) 5562

MET MET (MET proto-oncogene, receptor tyrosine kinase) 4233

ANGPT1 ANGPT1 (angiopoietin 1) 284

NR1H4 NR1H4 (nuclear receptor subfamily 1 group H member 4) 9971

BIRC5 BIRC5 (baculoviral IAP repeat containing 5) 332

GRN GRN (granulin precursor) 2896

ADM ADM (adrenomedullin) 133

PTEN PTEN (phosphatase and tensin homolog) 5728

NOS3 NOS3 (nitric oxide synthase 3) 4846

C3 C3 (complement C3) 718

EPO EPO (erythropoietin) 2056

BCL2 BCL2 (BCL2, regulator) 596

YAP1 YAP1 (Yes associated protein 1) 10413

NOTCH1 NOTCH1 (notch 1) 4851

POSTN POSTN (periostin) 10631

LEPR LEPR (leptin receptor) 3953

HSPD1 HSPD1 ( family D (Hsp60) member 1) 3329

BBC3 BBC3 (BCL2 binding component 3) 27113

APOA1 APOA1 (apolipoprotein A1) 335

CDKN1A CDKN1A (cyclin dependent kinase inhibitor 1A) 1026

HSPB1 HSPB1 (heat shock protein family B (small) member 1) 3315

MFGE8 MFGE8 (milk fat globule-EGF factor 8 protein) 4240

FLT1 FLT1 (fms related tyrosine kinase 1) 2321

KLF6 KLF6 (Kruppel like factor 6) 1316

GHRL GHRL (ghrelin and obestatin prepropeptide) 51738

CCR2 CCR2 (C-C motif chemokine receptor 2) 729230

CTNNB1 CTNNB1 (catenin beta 1) 1499

AGT AGT (angiotensinogen) 183

ATF4 ATF4 (activating transcription factor 4) 468

CCR5 CCR5 [C-C motif chemokine receptor 5 (gene/pseudogene)] 1234

INS INS (insulin) 3630

SOD2 SOD2 (superoxide dismutase 2) 6648

DLL4 DLL4 (delta like canonical Notch ligand 4) 54567

CNR1 CNR1 (cannabinoid receptor 1) 1268

MERTK MERTK (MER proto-oncogene, tyrosine kinase) 10461

HSPA5 HSPA5 [heat shock protein family A (Hsp70) member 5] 3309

IGF1 IGF1 (insulin like growth factor 1) 3479

MPO MPO (myeloperoxidase) 4353

SERPINF1 SERPINF1 (serpin family F member 1) 5176

CLU CLU (clusterin) 1191

CTF1 CTF1 (cardiotrophin 1) 1489

ADIPOR2 ADIPOR2 (adiponectin receptor 2) 79602

CD44 CD44 (CD44 molecule (Indian blood group)) 960

C5 C5 (complement C5) 727

CEBPA CEBPA (CCAAT enhancer binding protein alpha) 1050

NR1I2 NR1I2 (nuclear receptor subfamily 1 group I member 2) 8856

SERPINA1 SERPINA1 (serpin family A member 1) 5265

TRIB3 TRIB3 (tribbles pseudokinase 3) 57761

ANXA2 ANXA2 (annexin A2) 302

GREM1 GREM1 (gremlin 1, DAN family BMP antagonist) 26585

ABCA1 ABCA1 (ATP binding cassette subfamily A member 1) 19

CYP7A1 CYP7A1 (cytochrome P450 family 7 subfamily A member 1) 1581

IGFBP1 IGFBP1 (insulin like growth factor binding protein 1) 3484

NGFR NGFR (nerve growth factor receptor) 4804

KDR KDR (kinase insert domain receptor) 3791

TIMP2 TIMP2 (TIMP metallopeptidase inhibitor 2) 7077

AOC3 AOC3 (amine oxidase, copper containing 3) 8639

ARG1 ARG1 (arginase 1) 383

HP HP (haptoglobin) 3240

AREG AREG (amphiregulin) 374

AGTR1 AGTR1 (angiotensin II receptor type 1) 185

CAV1 CAV1 (caveolin 1) 857

AHSG AHSG (alpha 2-HS glycoprotein) 197

GCLC GCLC (glutamate-cysteine ligase catalytic subunit) 2729

USP18 USP18 (ubiquitin specific peptidase 18) 11274

SCD SCD (stearoyl-CoA desaturase) 6319

ADIPOR1 ADIPOR1 (adiponectin receptor 1) 51094

EGFL7 EGFL7 (EGF like domain multiple 7) 51162

FAM3A FAM3A (family with sequence similarity 3 member A) 60343

HABP2 HABP2 (hyaluronan binding protein 2) 3026

VDR VDR (vitamin D receptor) 7421

FOXO1 FOXO1 (forkhead box O1) 2308

IFNL3 IFNL3 () 282617

KRT18 KRT18 (keratin 18) 3875

VWF VWF (von Willebrand factor) 7450

PLAUR PLAUR (plasminogen activator, urokinase receptor) 5329

SOD1 SOD1 (superoxide dismutase 1) 6647

EGF EGF (epidermal growth factor) 1950

LOX LOX (lysyl oxidase) 4015

SREBF2 SREBF2 (sterol regulatory element binding transcription factor 2) 6721

RBP4 RBP4 (retinol binding protein 4) 5950

PPARGC1A PPARGC1A (PPARG coactivator 1 alpha) 10891

PDGFB PDGFB ( derived growth factor subunit B) 5155

FGFR4 FGFR4 (fibroblast growth factor receptor 4) 2264

IGF2 IGF2 (insulin like growth factor 2) 3481

CHIT1 CHIT1 (chitinase 1) 1118

APLN APLN (apelin) 8862

HSPA4 HSPA4 [heat shock protein family A (Hsp70) member 4] 3308

IRS2 IRS2 (insulin receptor substrate 2) 8660

GPBAR1 GPBAR1 (G protein-coupled bile acid receptor 1) 151306

BSG BSG [basigin (ok blood group)] 682

RGN RGN (regucalcin) 9104

ACE2 ACE2 (angiotensin I converting enzyme 2) 59272

DKK1 DKK1 (dickkopf WNT signaling pathway inhibitor 1) 22943

RORA RORA (RAR related orphan receptor A) 6095 The search of genes/proteins was performed by literature-enrichment analysis offered by the Genie web server (http://cbdm.uni-mainz. de/genie), a tool that computes associations of genes with keywords (in our case NAFLD/NASH, inflammation and fibrosis as 3 separated concepts) using biomedical literature annotations and the intersection set from the 3 gene lists was obtained using the platform NetworkAnalyst from the Venn diagram (http://www.networkanalyst.ca). NAFLD, nonalcoholic fatty liver disease.