Table S1 List of genes/proteins shared between NAFLD, fibrosis, and inflammation Gene 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 (interleukin 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 (tumor necrosis factor) 7124
IL6 IL6 (interleukin 6) 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 (interleukin 10) 3586
TLR2 TLR2 (toll like receptor 2) 7097
MIF MIF (macrophage migration inhibitory factor) 4282
CCL2 CCL2 (C-C motif chemokine ligand 2) 6347
IL33 IL33 (interleukin 33) 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 (interleukin 18) 3606
NFE2L2 NFE2L2 (nuclear factor, erythroid 2 like 2) 4780
TNFSF12 TNFSF12 (TNF superfamily member 12) 8742
IL22 IL22 (interleukin 22) 50616
MAPK14 MAPK14 (mitogen-activated protein kinase 14) 1432
SOCS3 SOCS3 (suppressor of cytokine signaling 3) 9021
IL32 IL32 (interleukin 32) 9235
HMOX1 HMOX1 (heme oxygenase 1) 3162
PTGS2 PTGS2 (prostaglandin-endoperoxide synthase 2) 5743
IL4 IL4 (interleukin 4) 3565
CXCL10 CXCL10 (C-X-C motif chemokine ligand 10) 3627
IL23A IL23A (interleukin 23 subunit alpha) 51561
MAPK1 MAPK1 (mitogen-activated protein kinase 1) 5594
IL13 IL13 (interleukin 13) 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 (interleukin 27) 246778
IL1RL1 IL1RL1 (interleukin 1 receptor like 1) 9173
NAMPT NAMPT (nicotinamide phosphoribosyltransferase) 10135
IL21 IL21 (interleukin 21) 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 (interleukin 2) 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 (endothelin 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 (Fas ligand) 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, apoptosis 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 (heat shock protein 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 (interferon lambda 3) 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 (platelet 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.