Supplementary Table S7. List of that are heavily methylated in normal and become demethylated in HCC normal_ cancer_ direction name description type methylation methylation _meth Alpha-2-macroglobulin-like 1 Precursor (C3 and PZP-like alpha-2- A2ML1 macroglobulin domain-containing protein_coding protein 9) [Source:UniProtKB/Swiss- Prot;Acc:A8K2U0] 12 0.99 0.96 -1 Retinal-specific ATP-binding cassette transporter (ATP-binding cassette sub- family A member 4)(RIM ABC ABCA4 transporter)(RIM protein_coding protein)(RmP)(Stargardt disease protein) [Source:UniProtKB/Swiss- Prot;Acc:P78363] 1 0.96 0.96 -1 Hypothetical supported by BX648692 AC005692.1 protein_coding [Source:UniProtKB/TrEMBL;Acc:A4D1T 2] 7 0.99 0.97 -1 Putative uncharacterized protein AC005863.1 FLJ45831 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6ZS49] 17 0.97 1 -1 cDNA FLJ45743 fis, clone KIDNE2016464 (HCG2045177) AC009271.7 protein_coding [Source:UniProtKB/TrEMBL;Acc:Q6ZS 83] 18 1 0.91 -1 Putative uncharacterized protein AC009365.9-1 FLJ40288 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:A4D1N5] 7 0.91 0.84 -1 Putative uncharacterized protein AC013469.8-2 LOC643905 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8WXC7] 2 0.95 0.95 -1 Uncharacterized protein FLJ46481 AC105915.4 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6ZRC1] 4 0.97 0.94 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Protein GREB1 (Gene regulated in breast cancer 1 protein) AC110754.4 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q4ZG55] 2 0.96 0.86 -1 Protein GREB1 (Gene regulated in breast cancer 1 protein) AC110754.4 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q4ZG55] 2 0.88 0.87 0 UPF0640 protein AC112215.3-1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8WVI0] 3 0.96 0.9 -1 AC116655.7-2 NA pseudogene 4 1 1 -1 cDNA FLJ40448 fis, clone TESTI2040815 AC138028.1-3 protein_coding [Source:UniProtKB/TrEMBL;Acc:Q8N7 R2] 16 0.91 0.89 -1 Acrosin Precursor (EC 3.4.21.10) [Contains Acrosin chain;Acrosin ACR protein_coding heavy chain] [Source:UniProtKB/Swiss- Prot;Acc:P10323] 22 0.98 0.91 -1 Long-chain-fatty-acid--CoA ligase ACSBG1 (EC 6.2.1.3)(Acyl-CoA synthetase bubblegum family member ACSBG1 protein_coding 1)(hsBGM)(hsBG)(hBG1)(Lipodisin) [Source:UniProtKB/Swiss- Prot;Acc:Q96GR2] 15 0.99 0.97 -1 Long-chain-fatty-acid--CoA ligase 5 (EC 6.2.1.3)(Long-chain acyl-CoA ACSL5 synthetase 5)(LACS 5) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9ULC5] 10 0.96 0.94 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Beta--like protein 2 (Kappa-actin) ACTBL2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q562R1] 5 0.91 0.88 -1 Actin, gamma-enteric smooth muscle (Smooth muscle gamma-actin)(Gamma- ACTG2 2-actin)(Alpha-actin-3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P63267] 2 1 0.99 -1 Adenosine deaminase domain- containing protein 1 (Testis nuclear ADAD1 RNA-binding protein) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q96M93] 4 0.91 0.89 -1 ADAM 18 Precursor (A disintegrin and metalloproteinase domain 18)(Transmembrane metalloproteinase- ADAM18 like, disintegrin-like, and cysteine-rich protein_coding protein III)(tMDC III) [Source:UniProtKB/Swiss- Prot;Acc:Q9Y3Q7] 8 0.96 1 -1 Disintegrin and metalloproteinase domain-containing protein 2 Precursor (ADAM 2)(Fertilin subunit beta)(PH- ADAM2 30)(PH30)(PH30-beta)(Cancer/testis protein_coding antigen 15)(CT15) [Source:UniProtKB/Swiss- Prot;Acc:Q99965] 8 1 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth ADAM DEC1 Precursor (EC 3.4.24.-)(A disintegrin and metalloproteinase domain-like protein decysin 1)(ADAM- ADAMDEC1 protein_coding like protein decysin 1) [Source:UniProtKB/Swiss- Prot;Acc:O15204] 8 0.71 0.67 0 Adenosine A3 receptor ADORA3 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P33765] 1 0.99 0.98 -1 Cytosolic carboxypeptidase 4 (EC 3.4.17.-)(ATP/GTP-binding protein-like AGBL1 protein_coding 1) [Source:UniProtKB/Swiss- Prot;Acc:Q96MI9] 15 0.94 0.92 -1 Anterior gradient protein 2 homolog Precursor (hAG-2)(AG-2)(Secreted cement gland protein XAG-2 AGR2 protein_coding homolog)(HPC8) [Source:UniProtKB/Swiss- Prot;Acc:O95994] 7 0.99 0.92 -1 AL121755.23 NA retrotransposed 20 0.96 0.91 -1 AL132709.5-3 NA miRNA 14 0.93 0.9 -1 AL365217.10-1 NA pseudogene 6 0.97 0.93 -1 HCG2044975Putative uncharacterized protein ENSP00000357662 ; AL589787.16 protein_coding [Source:UniProtKB/TrEMBL;Acc:B7WP 59] 10 0.9 0.89 -1 Putative uncharacterized protein ENSP00000350482 AL773578.1 protein_coding [Source:UniProtKB/TrEMBL;Acc:B7WN N0] 21 0.92 0.77 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Arachidonate 12-lipoxygenase, 12R type (12R-lipoxygenase)(12R-LOX)(EC ALOX12B 1.13.11.-)(Epidermis-type lipoxygenase protein_coding 12) [Source:UniProtKB/Swiss- Prot;Acc:O75342] 17 0.99 1 -1 Arachidonate 5-lipoxygenase-activating protein (FLAP)(MK-886-binding protein) ALOX5AP protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P20292] 13 0.91 0.92 -1 Ameloblastin Precursor AMBN [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9NP70] 4 0.97 0.92 -1 Protein AMBP Precursor [Contains Alpha-1-microglobulin(Protein HC)(Complex-forming glycoprotein heterogeneous in charge)(Alpha-1 AMBP protein_coding microglycoprotein);Inter-alpha-trypsin inhibitor light chain(ITI-LC)(Bikunin)(HI- 30)(Uronic-acid-rich protein)(EDC1);Trypstati 9 0.97 0.85 -1 repeat domain-containing protein 23 (Diabetes-related ankyrin ANKRD23 repeat protein)(Muscle ankyrin repeat protein_coding protein 3) [Source:UniProtKB/Swiss- Prot;Acc:Q86SG2] 2 0.98 0.97 -1 Ankyrin repeat domain-containing ANKRD55 protein 55 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q3KP44] 5 1 0.99 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Ankyrin repeat domain-containing protein 7 (Testis-specific protein ANKRD7 protein_coding TSA806) [Source:UniProtKB/Swiss- Prot;Acc:Q92527] 7 1 1 -1 Anoctamin-2 (Transmembrane protein ANO2 16B) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9NQ90] 12 0.99 0.94 -1 Acidic leucine-rich nuclear phosphoprotein 32 family member C (Phosphoprotein 32-related protein ANP32C protein_coding 1)(Tumorigenic protein pp32r1) [Source:UniProtKB/Swiss- Prot;Acc:O43423] 4 0.91 0.88 -1 AP001525.6-2 NA miRNA 18 0.97 0.94 -1 AP003778.3-1 NA pseudogene 11 0.91 0.82 -1 Probable DNA dC->dU-editing APOBEC-3B (EC 3.5.4.-)(Phorbolin-1- APOBEC3B related protein)(Phorbolin-2/3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UH17] 22 0.88 0.88 0 Aquaporin-10 (AQP-10)(Small intestine AQP10 aquaporin) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q96PS8] 1 0.98 0.9 -1 Aquaporin-2 (AQP-2)(Aquaporin- CD)(AQP-CD)(Water channel protein for renal collecting duct)(ADH water AQP2 channel)(Collecting duct water channel protein_coding protein)(WCH-CD) [Source:UniProtKB/Swiss- Prot;Acc:P41181] 12 0.95 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Aquaporin-6 (AQP-6)(Aquaporin-2- like)(Kidney-specific aquaporin)(hKID) AQP6 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q13520] 12 0.99 0.98 -1 Rho guanine exchange factor 18 (114 kDa Rho-specific guanine nucleotide exchange factor)(p114-Rho- ARHGEF18 protein_coding GEF)(p114RhoGEF)(Septin-associated RhoGEF)(SA-RhoGEF) [Source:UniProtKB/Swiss- Prot;Acc:Q6ZSZ5] 19 0.93 0.93 -1 Ankyrin repeat and SOCS box protein 4 ASB4 (ASB-4) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9Y574] 7 0.95 0.81 -1 B1 bradykinin receptor (BK-1 receptor)(B1R) BDKRB1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P46663] 14 0.96 0.96 -1 Bestrophin-2 (Vitelliform macular dystrophy 2-like protein 1) BEST2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NFU1] 19 0.98 0.94 -1 Bombesin receptor subtype-3 (BRS-3) BRS3 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P32247] X 0.91 0.87 -1 Butyrophilin-like protein 9 Precursor BTNL9 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6UXG8] 5 0.93 0.8 -1 Putative uncharacterized protein C10orf113 C10orf113 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5VZT2] 10 0.95 0.94 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Protein SPATIAL (Stromal protein associated with thymii and lymph node C10orf27 protein_coding homolog) [Source:UniProtKB/Swiss- Prot;Acc:Q96M53] 10 0.9 0.93 -1 Uncharacterized protein C11orf44 C11orf44 Precursor [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8N8P7] 11 0.97 1 -1 Uncharacterized protein C11orf66 C11orf66 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q7Z5V6] 11 1 0.97 -1 Putative uncharacterized protein C14orf177 C14orf177 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q52M58] 14 0.94 0.92 -1 Uncharacterized protein C15orf60 C15orf60 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q7Z4M0] 15 0.97 0.89 -1 hypothetical protein LOC283870 C16orf79 [Source:RefSeq protein_coding peptide;Acc:NP_872369] 16 0.93 0.89 -1 Uncharacterized protein C17orf74 C17orf74 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q0P670] 17 0.99 0.97 -1 Putative uncharacterized protein C18orf62 C18orf62 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q3B7S5] 18 0.92 0.89 -1 Uncharacterized protein C1orf161 C1orf161 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8N8X9] 1 0.98 0.94 -1 Putative uncharacterized protein C1orf200 C1orf200 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5SR53] 1 0.9 0.87 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Uncharacterized protein C2orf57 C2orf57 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q53QW1] 2 0.93 0.96 -1 Uncharacterized protein C2orf71 C2orf71 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:A6NGG8] 2 0.95 0.95 -1 Protein GR6 [Source:UniProtKB/Swiss- C3orf27 protein_coding Prot;Acc:O15544] 3 0.95 0.93 -1 Putative uncharacterized protein C3orf56 C3orf56 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8N813] 3 0.91 0.94 -1 Uncharacterized protein C4orf19 C4orf19 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8IY42] 4 0.91 0.89 -1 ES cell-associated transcript 1 protein C6orf221 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q587J8] 6 0.93 0.89 -1 Exocrine differentiation and proliferation factor-like protein C8orf22 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8WWR9] 8 0.99 1 -1 Uncharacterized protein C9orf117 C9orf117 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5JU67] 9 0.96 0.96 -1 Uncharacterized protein C9orf152 C9orf152 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5JTZ5] 9 0.98 0.94 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Carbonic anhydrase 5A, mitochondrial Precursor (EC 4.2.1.1)(Carbonic anhydrase VA)(CA-VA)(Carbonate CA5A protein_coding dehydratase VA) [Source:UniProtKB/Swiss- Prot;Acc:P35218] 16 0.92 0.97 -1 Calcium-binding protein 5 (CaBP5) CABP5 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9NP86] 19 0.97 0.98 -1 Voltage-dependent L-type calcium channel subunit beta-2 (CAB2)(Calcium channel voltage-dependent subunit CACNB2 beta 2)(Lambert-Eaton myasthenic protein_coding syndrome antigen B)(MYSB) [Source:UniProtKB/Swiss- Prot;Acc:Q08289] 10 0.95 0.92 -1 Voltage-dependent calcium channel gamma-5 subunit (Neuronal voltage- CACNG5 gated calcium channel gamma-5 protein_coding subunit) [Source:UniProtKB/Swiss- Prot;Acc:Q9UF02] 17 1 0.98 -1 Calcium homeostasis modulator protein 1 (Protein FAM26C) CALHM1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8IU99] 10 0.93 0.89 -1 Calmodulin-like protein 6 (Calglandulin- CALML6 like protein) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8TD86] 1 0.95 0.96 -1 Calneuron-1 (Calcium-binding protein CALN1 CaBP8) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9BXU9] 7 0.97 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Caspase-5 Precursor (CASP-5)(EC 3.4.22.58)(ICH-3 protease)(TY protease)(ICE(rel)-III) [Contains CASP5 protein_coding -5 subunit p20;Caspase-5 subunit p10] [Source:UniProtKB/Swiss- Prot;Acc:P51878] 11 0.94 1 -1 C-C chemokine receptor type 3 (C-C CKR-3)(CC-CKR-3)(CCR- 3)(CCR3)(CKR3)( eotaxin CCR3 protein_coding receptor)(CD193 antigen) [Source:UniProtKB/Swiss- Prot;Acc:P51677] 3 0.93 0.91 -1 CD177_HUMAN Isoform 3 of Q8N6Q3 - Homo sapiens () CD177 protein_coding [Source:UniprotKB/SpliceVariant;Acc:Q 8N6Q3-3] 19 0.9 0.84 -1 C-type domain family 4 member K ()(CD207 antigen) CD207 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UJ71] 2 0.96 0.86 -1 CMRF35-like molecule 6 Precursor (CLM-6)(CMRF35-A1)(CMRF- 35)(CD300 antigen-like family member CD300C protein_coding C)(CD300c antigen) [Source:UniProtKB/Swiss- Prot;Acc:Q08708] 17 0.96 0.98 -1 Myeloid cell surface antigen CD33 Precursor (Sialic acid-binding Ig-like CD33 lectin 3)(Siglec-3)(gp67)(CD33 antigen) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P20138] 19 0.93 0.89 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

CD40 ligand (CD40-L)(Tumor necrosis factor ligand superfamily member 5)(TNF-related activation protein)(TRAP)(T-cell antigen CD40LG protein_coding Gp39)(CD154 antigen) [Contains CD40 ligand, membrane form;CD40 ligand, soluble form] [Source:UniProtKB/Swiss- Prot;Acc:P29965] X 0.96 0.93 -1 B-cell differentiation antigen CD72 (Lyb- 2)(CD72 antigen) CD72 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P21854] 9 0.93 0.93 -1 Cadherin-16 Precursor (Kidney-specific cadherin)(Ksp-cadherin) CDH16 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O75309] 16 0.91 0.91 -1 Cadherin-17 Precursor (Liver-intestine cadherin)(LI-cadherin)(Intestinal CDH17 peptide-associated transporter HPT-1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q12864] 8 1 0.95 -1 Cadherin-like protein 26 Precursor (Cadherin-like protein VR20) CDH26 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8IXH8] 20 0.91 0.98 -1 CMT1A duplicated region transcript 4 CDRT4 protein [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8N9R6] 17 1 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth -related cell adhesion molecule 7 Precursor CEACAM7 (Carcinoembryonic antigen CGM2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q14002] 19 0.94 0.95 -1 Carcinoembryonic antigen-related cell adhesion molecule 8 Precursor (Carcinoembryonic antigen CGM6)(Non- CEACAM8 specific cross-reacting antigen NCA- protein_coding 95)(CD67 antigen)(CD66b antigen) [Source:UniProtKB/Swiss- Prot;Acc:P31997] 19 0.95 0.89 -1 chorionic gonadotropin, beta CGB1 polypeptide 1 [Source:RefSeq protein_coding peptide;Acc:NP_203695] 19 0.96 0.88 -1 Choriogonadotropin subunit beta Precursor (CG-beta)(Chorionic CGB5 gonadotrophin chain beta) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P01233] 19 0.96 0.93 -1 Choriogonadotropin subunit beta Precursor (CG-beta)(Chorionic CGB8 gonadotrophin chain beta) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P01233] 19 0.95 0.81 -1 Neuronal acetylcholine receptor subunit beta-3 Precursor CHRNB3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q05901] 8 0.97 0.96 -1 Claudin-14 [Source:UniProtKB/Swiss- CLDN14 protein_coding Prot;Acc:O95500] 21 0.97 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Claudin-18 [Source:UniProtKB/Swiss- CLDN18 protein_coding Prot;Acc:P56856] 3 0.9 0.92 -1 Claudin-19 [Source:UniProtKB/Swiss- CLDN19 protein_coding Prot;Acc:Q8N6F1] 1 0.94 0.96 -1 Claudin-4 (Clostridium perfringens enterotoxin receptor)(CPE- receptor)(CPE-R)(Williams-Beuren CLDN4 protein_coding syndrome chromosomal region 8 protein) [Source:UniProtKB/Swiss- Prot;Acc:O14493] 7 0.95 0.91 -1 -like protein 3 CLEC18C Precursor [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NCF0] 16 0.93 0.84 -1 C-type lectin domain family 4 member D (C-type lectin superfamily member CLEC4D 8)(C-type lectin-like receptor 6)(CLEC- protein_coding 6) [Source:UniProtKB/Swiss- Prot;Acc:Q8WXI8] 12 0.9 0.77 -1 C-type lectin domain family 4 member M (CD209 antigen-like protein 1)(Dendritic cell-specific ICAM-3- grabbing non-integrin 2)(DC- CLEC4M protein_coding SIGN2)(DC-SIGN-related protein)(DC- SIGNR)(Liver/lymph node-specific ICAM-3-grabbing non-integrin)(L- SIGN)(CD299 antigen) [Sour 19 0.99 0.91 -1 C-type lectin domain family 9 member CLEC9A A [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6UXN8] 12 1 1 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Dual specificity protein kinase CLK3 (EC 2.7.12.1)(CDC-like kinase 3) CLK3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P49761] 15 0.98 1 -1 Collagen alpha-3(VI) chain Precursor COL6A3 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P12111] 2 1 0.97 -1 -6 [Source:UniProtKB/Swiss- CORO6 protein_coding Prot;Acc:Q6QEF8] 17 0.94 0.95 -1 Ceruloplasmin Precursor (EC 1.16.3.1)(Ferroxidase) CP protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P00450] 3 0.93 0.73 -1 Beta/gamma crystallin domain- containing protein 3 CRYBG3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q68DQ2] 3 0.98 1 -1 Gamma-crystallin C (Gamma-C- crystallin)(Gamma-crystallin 2- CRYGC 1)(Gamma-crystallin 3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P07315] 2 1 0.98 -1 Putative uncharacterized protein CSAG4 Fragment CSAG4 protein_coding [Source:UniProtKB/TrEMBL;Acc:A8MQ T1] X 0.91 0.89 -1 Granulocyte colony-stimulating factor Precursor (G- CSF3 CSF)(Pluripoietin)(Filgrastim)(Lenogras protein_coding tim) [Source:UniProtKB/Swiss- Prot;Acc:P09919] 17 0.93 0.86 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Chondroitin sulfate N- acetylgalactosaminyltransferase 1 (CsGalNAcT-1)(EC 2.4.1.174)(Chondroitin beta-1,4-N- CSGALNACT1 protein_coding acetylgalactosaminyltransferase 1)(Beta4GalNAcT-1) [Source:UniProtKB/Swiss- Prot;Acc:Q8TDX6] 8 0.94 0.92 -1 Cystatin-SA Precursor (Cystatin- 2)(Cystatin-S5) CST2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P09228] 20 0.95 0.94 -1 C-terminal-binding protein 2 (CtBP2) CTBP2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P56545] 10 0.99 0.97 -1 Cortexin-3 (Kidney and -expressed CTXN3 protein) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q4LDR2] 5 0.94 0.92 -1 Uncharacterized protein CXorf48 (Tumor antigen BJ-HCC- CXorf48 20)(Cancer/testis antigen 55)(CT55) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8WUE5] X 0.94 0.95 -1 Kita-kyushu cancer antigen 1 (KK- LC-1)(Cancer/testis antigen 83)(CT83) CXorf61 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q5H943] X 0.97 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Cytochrome P450 11B1, mitochondrial Precursor (EC 1.14.15.4)(CYPXIB1)(P- CYP11B1 450c11)(P450C11)(Steroid 11-beta- protein_coding hydroxylase) [Source:UniProtKB/Swiss- Prot;Acc:P15538] 8 0.96 0.92 -1 Cytochrome P450 11B2, mitochondrial Precursor (EC 1.14.15.4)(EC 1.14.15.5)(CYPXIB2)(P- 450Aldo)(Aldosterone CYP11B2 synthase)(ALDOS)(Aldosterone- protein_coding synthesizing enzyme)(Steroid 18- hydroxylase)(P-450C18) [Source:UniProtKB/Swiss- Prot;Acc:P19099] 8 0.94 0.96 -1 Sperm antigen with calponin and coiled-coil domains 1 (Nuclear structure protein 5)(NSP5)(Sperm CYTSB protein_coding antigen HCMOGT-1) [Source:UniProtKB/Swiss- Prot;Acc:Q5M775] 17 0.98 0.95 -1 Dopamine beta-hydroxylase (EC 1.14.17.1)(Dopamine beta- monooxygenase) [Contains Soluble DBH protein_coding dopamine beta-hydroxylase] [Source:UniProtKB/Swiss- Prot;Acc:P09172] 9 0.95 0.94 -1 Dysbindin domain-containing protein 1 DBNDD1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9H9R9] 16 0.91 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Protein DDI1 homolog 1 DDI1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8WTU0] 11 0.92 0.86 -1 defensin 3 Precursor (HNP- 3)(HP-3)(HP3)(Defensin, alpha 3) [Contains HP 3-56;Neutrophil defensin DEFA3 protein_coding 2(HNP-2)(HP-2)(HP2)] [Source:UniProtKB/Swiss- Prot;Acc:P59666] 8 0.9 0.83 -1 Neutrophil defensin 4 Precursor (HNP- 4)(HP-4)(Defensin, alpha 4) DEFA4 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P12838] 8 0.97 0.98 -1 Dickkopf-related protein 4 Precursor (Dickkopf-4)(Dkk-4)(hDkk-4) [Contains DKK4 Dickkopf-related protein 4 short form] protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UBT3] 8 0.98 0.89 -1 Disks large-associated protein 2 (DAP- 2)(SAP90/PSD-95-associated protein DLGAP2 2)(SAPAP2)(PSD-95/SAP90-binding protein_coding protein 2) [Source:UniProtKB/Swiss- Prot;Acc:Q9P1A6] 8 0.94 0.92 -1 Disks large-associated protein 5 (DAP- 5)(Disks large-associated protein DLG7)(Discs large homolog DLGAP5 7)(Hepatoma up-regulated protein_coding protein)(HURP) [Source:UniProtKB/Swiss- Prot;Acc:Q15398] 14 0.64 0.56 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth DnaJ homolog subfamily B member 8 DNAJB8 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NHS0] 3 0.91 0.89 -1 Deoxyribonuclease-1 Precursor (EC 3.1.21.1)(Deoxyribonuclease I)(DNase DNASE1 I)(Dornase alfa) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P24855] 16 0.98 0.96 -1 Dipeptidase 1 Precursor (EC 3.4.13.19)(Microsomal dipeptidase)(Renal DPEP1 protein_coding dipeptidase)(hRDP)(Dehydropeptidase- I) [Source:UniProtKB/Swiss- Prot;Acc:P16444] 16 0.93 0.87 -1 Developmental pluripotency-associated protein 3 (Stella-related protein) DPPA3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6W0C5] 12 0.93 0.92 -1 Epidermal growth factor receptor kinase substrate 8-like protein 3 (Epidermal growth factor receptor EPS8L3 pathway substrate 8-related protein protein_coding 3)(EPS8-like protein 3) [Source:UniProtKB/Swiss- Prot;Acc:Q8TE67] 1 0.99 0.96 -1 Transcriptional regulator ERG (Transforming protein ERG) ERG protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P11308] 21 0.93 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Endothelial cell-specific molecule 1 Precursor (ESM-1 secretory ESM1 protein)(ESM-1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9NQ30] 5 0.8 0.66 -1 Eyes absent homolog 2 (EC 3.1.3.48) EYA2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O00167] 20 0.93 0.9 -1 Coagulation factor VII Precursor (EC 3.4.21.21)(Serum prothrombin conversion accelerator)(SPCA)(Proconvertin)(Epta F7 protein_coding cog alfa) [Contains Factor VII light chain;Factor VII heavy chain] [Source:UniProtKB/Swiss- Prot;Acc:P08709] 13 0.92 0.88 -1 Fatty acid-binding protein, liver (L- FABP1 FABP) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P07148] 2 0.94 0.9 -1 Protein FAM180A Precursor FAM180A [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6UWF9] 7 0.94 0.92 -1 Protein FAM90A1 FAM90A1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q86YD7] 12 0.97 0.95 -1 Protein FAM92B FAM92B [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6ZTR7] 16 0.91 0.92 -1 Immunoglobulin alpha Fc receptor Precursor (IgA Fc receptor)(CD89 FCAR protein_coding antigen) [Source:UniProtKB/Swiss- Prot;Acc:P24071] 19 0.9 0.71 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Low affinity immunoglobulin epsilon Fc receptor ( IgE receptor)(Fc- epsilon-RII)(BLAST-2)(Immunoglobulin FCER2 E-binding factor)(CD23 antigen) protein_coding [Contains Low affinity immunoglobulin epsilon Fc receptor membrane-bound form;Low affinity immunoglobulin eps 19 0.94 0.89 -1 -1 Precursor (Ficolin-A)(Ficolin- alpha)(M-ficolin)(Collagen/fibrinogen FCN1 domain-containing protein 1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O00602] 9 0.93 0.87 -1 Ficolin-2 Precursor (Ficolin-B)(Ficolin- beta)(L-ficolin)(Collagen/fibrinogen domain-containing protein 2)(Serum FCN2 lectin p35)(37 kDa elastin-binding protein_coding protein)(EBP-37)(Hucolin) [Source:UniProtKB/Swiss- Prot;Acc:Q15485] 9 0.94 0.89 -1 Fc receptor-like protein 3 Precursor (FcR-like protein 3)(FcRL3)(Fc receptor homolog 3)(FcRH3)(IFGP family protein FCRL3 3)(hIFGP3)(Immune receptor protein_coding translocation-associated protein 3)(SH2 domain-containing phosphatase anchor protein 2) [Source:UniProtKB/Swiss-P 1 0.91 0.8 -1 FYVE, RhoGEF and PH domain- containing protein 5 (Zinc finger FYVE FGD5 domain-containing protein 23) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6ZNL6] 3 0.93 0.93 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Fibroblast growth factor-binding protein 1 Precursor (FGF-binding protein 1)(FGF-BP1)(FGFBP-1)(FGF-BP)(17 kDa heparin-binding growth factor- FGFBP1 protein_coding binding protein)(17 kDa HBGF-binding protein)(HBp17) [Source:UniProtKB/Swiss- Prot;Acc:Q14512] 4 0.91 0.82 -1 A-interacting protein 1-like (130 kDa GPBP-interacting protein)(90 kDa GPBP-interacting protein)(Protein down- FILIP1L protein_coding regulated in ovarian cancer 1)(DOC-1) [Source:UniProtKB/Swiss- Prot;Acc:Q4L180] 3 0.98 0.92 -1 Probable polypeptide N- acetylgalactosaminyltransferase 8 (EC 2.4.1.41)(Polypeptide GalNAc transferase 8)(pp-GaNTase 8)(GalNAc- GALNT8 T8)(Protein-UDP protein_coding acetylgalactosaminyltransferase 8)(UDP-GalNAc:polypeptide N- acetylgalactosaminyltransferase 8) [Source:UniProtKB/ 12 0.9 0.85 -1 Gastrin Precursor [Contains Gastrin- 71(Gastrin component I);Gastrin- 52(G52);Big gastrin(Gastrin- 34)(G34)(Gastrin component GAST protein_coding II);Gastrin(Gastrin-17)(G17)(Gastrin component III);Gastrin-14(G14);Gastrin- 6(G6)] [Source:UniProtKB/Swiss- Prot;Acc:P01350] 17 0.99 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Growth hormone variant Precursor (GH- V)(Placenta-specific growth GH2 hormone)(Growth hormone 2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P01242] 17 0.93 0.92 -1 Glycerol kinase 2 (Glycerokinase 2)(GK 2)(EC 2.7.1.30)(Glycerol kinase, testis specific 2)(ATP:glycerol 3- GK2 protein_coding phosphotransferase) [Source:UniProtKB/Swiss- Prot;Acc:Q14410] 4 0.98 1 -1 Glucagon-like peptide 2 receptor Precursor (GLP-2 receptor)(GLP-2- GLP2R protein_coding R)(GLP-2R) [Source:UniProtKB/Swiss- Prot;Acc:O95838] 17 0.98 0.97 -1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 GNB3 (Transducin beta chain 3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P16520] 12 0.99 0.96 -1 Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 Precursor (GPI-anchored HDL- GPIHBP1 binding protein 1)(GPI-HBP1)(High protein_coding density lipoprotein-binding protein 1) [Source:UniProtKB/Swiss- Prot;Acc:Q8IV16] 8 0.96 0.92 -1 Neuronal membrane glycoprotein M6-b GPM6B (M6b) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q13491] X 0.91 0.89 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Putative G-protein coupled receptor 44 (Chemoattractant receptor-homologous molecule expressed on Th2 GPR44 protein_coding cells)(CD294 antigen) [Source:UniProtKB/Swiss- Prot;Acc:Q9Y5Y4] 11 0.95 0.91 -1 Probable G-protein coupled receptor 45 (PSP24-alpha)(PSP24-1) GPR45 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9Y5Y3] 2 0.98 0.96 -1 Probable G-protein coupled receptor 81 (G-protein coupled receptor 104) GPR81 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BXC0] 12 0.94 0.91 -1 GRAM domain-containing protein 1B GRAMD1B [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q3KR37] 11 0.95 0.91 -1 Rhodopsin kinase Precursor (RK)(EC 2.7.11.14)(G protein-coupled receptor GRK1 protein_coding kinase 1) [Source:UniProtKB/Swiss- Prot;Acc:Q15835] 13 0.93 0.91 -1 G protein-coupled receptor kinase 7 Precursor (EC 2.7.11.16)(G protein- GRK7 coupled receptor kinase GRK7) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8WTQ7] 3 0.9 0.95 -1 Metabotropic glutamate receptor 4 Precursor (mGluR4) GRM4 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q14833] 6 0.95 0.9 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Metabotropic glutamate receptor 5 Precursor (mGluR5) GRM5 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P41594] 11 0.93 0.71 -1 Gasdermin-A (Gasdermin-1) GSDMA [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q96QA5] 17 0.9 0.91 -1 Germ cell-specific gene 1 protein GSG1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q2KHT4] 12 0.96 0.89 -1 Heat-stable enterotoxin receptor Precursor (STA receptor)(hSTAR)(EC 4.6.1.2)(Intestinal guanylate GUCY2C protein_coding cyclase)(GC-C) [Source:UniProtKB/Swiss- Prot;Acc:P25092] 12 0.99 0.91 -1 Histone H2B type W-T (H2B histone family member W testis-specific) H2BFWT protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q7Z2G1] X 0.9 0.83 -1 Putative cancer susceptibility gene HEPN1 protein HEPN1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6WQI6] 11 0.95 0.79 -1 Hepatocyte nuclear factor 4-alpha (HNF- 4-alpha)( HNF- 4)(Nuclear receptor subfamily 2 group HNF4A protein_coding A member 1)(Transcription factor 14) [Source:UniProtKB/Swiss- Prot;Acc:P41235] 20 0.96 0.87 -1 Haptoglobin-related protein Precursor HP [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P00739] 16 0.9 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth hsa-mir-136 hsa-mir-136 miRNA [Source:miRBase;Acc:MI0000475] 14 0.92 0.93 -1 hsa-mir-139 hsa-mir-139 miRNA [Source:miRBase;Acc:MI0000261] 11 0.99 0.96 -1 hsa-mir-145 hsa-mir-145 miRNA [Source:miRBase;Acc:MI0000461] 5 0.9 0.9 -1 hsa-mir-153-2 hsa-mir-153-2 miRNA [Source:miRBase;Acc:MI0000464] 7 0.96 0.94 -1 hsa-mir-205 hsa-mir-205 miRNA [Source:miRBase;Acc:MI0000285] 1 0.9 0.89 -1 hsa-mir-208a hsa-mir-208a miRNA [Source:miRBase;Acc:MI0000251] 14 0.94 0.84 -1 hsa-mir-218-1 hsa-mir-218-1 miRNA [Source:miRBase;Acc:MI0000294] 4 1 0.96 -1 hsa-mir-218-2 hsa-mir-218-2 miRNA [Source:miRBase;Acc:MI0000295] 5 0.96 0.95 -1 hsa-mir-26a-2 hsa-mir-26a-2 miRNA [Source:miRBase;Acc:MI0000750] 12 0.94 0.89 -1 hsa-mir-296 hsa-mir-296 miRNA [Source:miRBase;Acc:MI0000747] 20 0.96 0.89 -1 hsa-mir-31 hsa-mir-31 miRNA [Source:miRBase;Acc:MI0000089] 9 0.97 0.95 -1 hsa-mir-371 hsa-mir-371 miRNA [Source:miRBase;Acc:MI0000779] 19 0.92 0.86 -1 hsa-mir-372 hsa-mir-372 miRNA [Source:miRBase;Acc:MI0000780] 19 0.91 0.87 -1 hsa-mir-373 hsa-mir-373 miRNA [Source:miRBase;Acc:MI0000781] 19 0.92 0.9 -1 hsa-mir-381 hsa-mir-381 miRNA [Source:miRBase;Acc:MI0000789] 14 0.96 0.87 -1 hsa-mir-432 hsa-mir-432 miRNA [Source:miRBase;Acc:MI0003133] 14 0.91 0.93 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth hsa-mir-453 hsa-mir-453 miRNA [Source:miRBase;Acc:MI0001727] 14 0.9 0.94 -1 hsa-mir-485 hsa-mir-485 miRNA [Source:miRBase;Acc:MI0002469] 14 0.9 0.93 -1 hsa-mir-487b hsa-mir-487b miRNA [Source:miRBase;Acc:MI0003530] 14 0.96 0.9 -1 hsa-mir-488 hsa-mir-488 miRNA [Source:miRBase;Acc:MI0003123] 1 0.99 0.9 -1 hsa-mir-494 hsa-mir-494 miRNA [Source:miRBase;Acc:MI0003134] 14 0.93 0.9 -1 hsa-mir-539 hsa-mir-539 miRNA [Source:miRBase;Acc:MI0003514] 14 0.95 0.93 -1 hsa-mir-592 hsa-mir-592 miRNA [Source:miRBase;Acc:MI0003604] 7 0.91 0.86 -1 hsa-mir-595 hsa-mir-595 miRNA [Source:miRBase;Acc:MI0003607] 7 0.96 0.98 -1 hsa-mir-598 hsa-mir-598 miRNA [Source:miRBase;Acc:MI0003610] 8 0.96 0.93 -1 hsa-mir-614 hsa-mir-614 miRNA [Source:miRBase;Acc:MI0003627] 12 0.95 0.85 -1 hsa-mir-622 hsa-mir-622 miRNA [Source:miRBase;Acc:MI0003636] 13 0.97 0.92 -1 hsa-mir-655 hsa-mir-655 miRNA [Source:miRBase;Acc:MI0003677] 14 0.92 0.96 -1 hsa-mir-668 hsa-mir-668 miRNA [Source:miRBase;Acc:MI0003761] 14 0.91 0.93 -1 hsa-mir-889 hsa-mir-889 miRNA [Source:miRBase;Acc:MI0005540] 14 0.94 0.93 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth 5-hydroxytryptamine receptor 3A Precursor (5-HT3R)(5-HT3A)(5-HT- 3)(Serotonin receptor 3A)(Serotonin- HTR3A protein_coding gated ion channel receptor) [Source:UniProtKB/Swiss- Prot;Acc:P46098] 11 0.93 0.87 -1 5-hydroxytryptamine receptor 3C Precursor (5-HT3C)(Serotonin receptor HTR3C protein_coding 3C) [Source:UniProtKB/Swiss- Prot;Acc:Q8WXA8] 3 0.96 0.9 -1 Insulin growth factor-like family member IGFL1 1 Precursor [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6UW32] 19 0.97 0.9 -1 Immunoglobulin superfamily member 10 Precursor (Calvaria mechanical IGSF10 force protein 608)(CMF608) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6WRI0] 3 0.9 0.87 -1 Interleukin-12 subunit beta Precursor (IL-12B)(IL-12 subunit p40)(Cytotoxic lymphocyte maturation factor 40 kDa IL12B subunit)(CLMF p40)(NK cell stimulatory protein_coding factor chain 2)(NKSF2) [Source:UniProtKB/Swiss- Prot;Acc:P29460] 5 0.95 0.94 -1 Interleukin-17B Precursor (IL- 17B)(Cytokine-like protein Zcyto7)(Neuronal interleukin-17-related IL17B protein_coding factor)(Interleukin-20)(IL-20) [Source:UniProtKB/Swiss- Prot;Acc:Q9UHF5] 5 0.91 0.89 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Interleukin-26 Precursor (AK155 IL26 protein) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9NPH9] 12 0.9 0.86 -1 Interleukin-2 receptor alpha chain Precursor (IL-2 receptor alpha subunit)(IL-2-RA)(IL2-RA)(p55)(TAC IL2RA protein_coding antigen)(CD25 antigen) [Source:UniProtKB/Swiss- Prot;Acc:P01589] 10 1 0.97 -1 Inhibin beta E chain Precursor (Activin INHBE beta-E chain) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P58166] 12 0.95 0.95 -1 Integrin beta-1-binding protein 2 ITGB1BP2 (Melusin) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9UKP3] X 0.96 0.85 -1 Integrin beta-2 Precursor (Cell surface adhesion glycoproteins LFA- 1/CR3/p150,95 subunit ITGB2 beta)(Complement receptor C3 subunit protein_coding beta)(CD18 antigen) [Source:UniProtKB/Swiss- Prot;Acc:P05107] 21 0.94 0.85 -1 Inter-alpha-trypsin inhibitor heavy chain H3 Precursor (Inter-alpha-inhibitor heavy chain 3)(ITI heavy chain H3)(ITI- ITIH3 HC3)(Serum-derived hyaluronan- protein_coding associated protein)(SHAP) [Source:UniProtKB/Swiss- Prot;Acc:Q06033] 3 0.99 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Kalirin (EC 2.7.11.1)(Huntingtin- associated protein-interacting protein)(Protein Duo)(Serine/threonine KALRN kinase with Dbl- and pleckstrin protein_coding homology domain) [Source:UniProtKB/Swiss- Prot;Acc:O60229] 3 0.99 0.99 -1 Potassium voltage-gated channel subfamily E member 4 (Minimum potassium ion channel-related peptide KCNE4 3)(Potassium channel subunit beta protein_coding MiRP3)(MinK-related peptide 3) [Source:UniProtKB/Swiss- Prot;Acc:Q8WWG9] 2 0.93 0.91 -1 Potassium voltage-gated channel subfamily H member 5 (Voltage-gated potassium channel subunit KCNH5 Kv10.2)(Ether-a-go-go potassium protein_coding channel 2)(hEAG2) [Source:UniProtKB/Swiss- Prot;Acc:Q8NCM2] 14 1 0.98 -1 ATP-sensitive inward rectifier potassium channel 15 (Potassium channel, inwardly rectifying subfamily J KCNJ15 member 15)(Inward rectifier K(+) protein_coding channel Kir4.2)(Kir1.3) [Source:UniProtKB/Swiss- Prot;Acc:Q99712] 21 0.94 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Potassium channel subfamily K member 18 (TWIK-related individual potassium channel)(TWIK-related KCNK18 protein_coding spinal cord potassium channel) [Source:UniProtKB/Swiss- Prot;Acc:Q7Z418] 10 0.95 0.96 -1 Calcium-activated potassium channel subunit beta-1 (Calcium-activated potassium channel, subfamily M subunit beta-1)(Calcium-activated KCNMB1 protein_coding potassium channel subunit beta)(Maxi K channel subunit beta-1)(BK channel subunit beta- 1)(BKbeta1)(BKbeta)(Hbeta1)(K(VCA 5 0.92 0.83 -1 Small conductance calcium-activated potassium channel protein 3 KCNN3 (SKCa3)(SK3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UGI6] 1 0.99 0.96 -1 Killer cell immunoglobulin-like receptor 2DS4 Precursor (MHC class I NK cell receptor)(Natural killer-associated KIR2DS4 transcript 8)(NKAT-8)(P58 natural killer protein_coding cell receptor clone CL-39)(p58 NK receptor)(CL-17)(CD158 antigen-like family member I)(CD158i antigen 19 0.97 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Killer cell immunoglobulin-like receptor 3DL1 Precursor (MHC class I NK cell receptor)(Natural killer-associated KIR3DL1 transcript 3)(NKAT-3)(p70 natural killer protein_coding cell receptor clones CL-2/CL-11)(HLA- BW4-specific inhibitory NK cell receptor)(CD158 antigen-like fam 19 1 1 -1 Kallikrein-11 Precursor (hK11)(EC 3.4.21.-)(Hippostasin)(Trypsin-like protease)(Serine protease 20) KLK11 [Contains Kallikrein-11 inactive chain protein_coding 1;Kallikrein-11 inactive chain 2] [Source:UniProtKB/Swiss- Prot;Acc:Q9UBX7] 19 0.94 0.94 -1 Kallikrein-4 Precursor (EC 3.4.21.- )(Prostase)(Kallikrein-like protein 1)(KLK-)(Enamel matrix serine KLK4 protein_coding proteinase 1)(Serine protease 17) [Source:UniProtKB/Swiss- Prot;Acc:Q9Y5K2] 19 0.98 0.97 -1 , type II cytoskeletal 1 (-1)(CK-1)(Keratin-1)(K1)(67 KRT1 kDa cytokeratin)(Hair alpha protein) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P04264] 12 0.98 0.99 -1 Keratin, type I cytoskeletal 14 (Cytokeratin-14)(CK-14)(Keratin- KRT14 protein_coding 14)(K14) [Source:UniProtKB/Swiss- Prot;Acc:P02533] 17 1 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Keratin, type I cytoskeletal 15 (Cytokeratin-15)(CK-15)(Keratin- KRT15 protein_coding 15)(K15) [Source:UniProtKB/Swiss- Prot;Acc:P19012] 17 0.97 0.95 -1 Keratin, type I cuticular Ha1 (, type I Ha1)(Keratin-31)(K31) KRT31 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q15323] 17 0.98 1 -1 Keratin, type I cuticular Ha4 (Hair keratin, type I Ha4)(Keratin-34)(K34) KRT34 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O76011] 17 0.97 0.96 -1 Keratin, type II cytoskeletal 5 (Cytokeratin-5)(CK-5)(Keratin-5)(K5)(58 KRT5 kDa cytokeratin) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P13647] 12 0.97 0.92 -1 Keratin, type II cytoskeletal 6B (Cytokeratin-6B)(CK 6B)(K6b keratin) KRT6B protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P04259] 12 1 0.95 -1 Keratin, type II cytoskeletal 75 (Cytokeratin-75)(CK-75)(Keratin- 75)(K75)(Type II keratin-18)(Type II KRT75 keratin-K6hf)(Keratin-6 hair protein_coding follicle)(hK6hf) [Source:UniProtKB/Swiss- Prot;Acc:O95678] 12 0.94 0.9 -1 Keratin, type II cuticular Hb4 (Type II hair keratin Hb4)(Keratin-84)(K84) KRT84 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9NSB2] 12 0.97 0.84 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Keratin, type II cuticular Hb5 (Type II hair keratin Hb5)(Keratin- KRT85 85)(K85)(K12.12) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P78386] 12 0.94 0.94 -1 Keratin-associated protein 10-1 (Keratin- associated protein 10.1)(High sulfur keratin-associated protein 10.1)(Keratin- KRTAP10-1 associated protein 18-1)(Keratin- protein_coding associated protein 18.1) [Source:UniProtKB/Swiss- Prot;Acc:P60331] 21 0.96 0.98 -1 Keratin-associated protein 10-10 (Keratin-associated protein 10.10)(High sulfur keratin-associated protein KRTAP10-10 10.10)(Keratin-associated protein 18- protein_coding 10)(Keratin-associated protein 18.10) [Source:UniProtKB/Swiss- Prot;Acc:P60014] 21 0.98 0.97 -1 Keratin-associated protein 10-11 (Keratin-associated protein 10.11)(High sulfur keratin-associated protein KRTAP10-11 10.11)(Keratin-associated protein 18- protein_coding 11)(Keratin-associated protein 18.11) [Source:UniProtKB/Swiss- Prot;Acc:P60412] 21 0.98 0.92 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Keratin-associated protein 10-7 (Keratin- associated protein 10.7)(High sulfur keratin-associated protein 10.7)(Keratin- KRTAP10-7 associated protein 18-7)(Keratin- protein_coding associated protein 18.7) [Source:UniProtKB/Swiss- Prot;Acc:P60409] 21 0.98 0.97 -1 Keratin-associated protein 11-1 (High sulfur keratin-associated protein 11.1) KRTAP11-1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8IUC1] 21 0.9 0.84 -1 Keratin-associated protein 12-1 (Keratin- associated protein 12.1)(High sulfur KRTAP12-1 keratin-associated protein 12.1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P59990] 21 0.99 0.94 -1 Keratin-associated protein 12-2 (Keratin- associated protein 12.2)(High sulfur KRTAP12-2 keratin-associated protein 12.2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P59991] 21 0.96 0.92 -1 Keratin-associated protein 13-2 KRTAP13-2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q52LG2] 21 0.95 0.88 -1 Keratin-associated protein 15-1 KRTAP15-1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q3LI76] 21 0.95 0.81 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Keratin-associated protein 17-1 (Keratin- associated protein 16.1) KRTAP17-1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BYP8] 17 0.94 0.91 -1 Keratin-associated protein 27-1 KRTAP27-1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q3LI81] 21 0.99 0.84 -1 Keratin-associated protein 5-4 (Keratin- associated protein 5.4)(Ultrahigh sulfur KRTAP5-4 keratin-associated protein 5.4) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6L8H1] 11 0.93 0.8 -1 Keratin-associated protein 9-2 (Keratin- associated protein 9.2)(Ultrahigh sulfur KRTAP9-2 keratin-associated protein 9.2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BYQ4] 17 0.96 0.87 -1 Keratin-associated protein 9-3 (Keratin- associated protein 9.3)(Ultrahigh sulfur KRTAP9-3 keratin-associated protein 9.3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BYQ3] 17 0.93 0.89 -1 Leukocyte-associated immunoglobulin- like receptor 2 Precursor (LAIR- LAIR2 2)(CD306 antigen) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6ISS4] 19 0.96 0.82 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Lipocalin-1 Precursor (Von Ebner gland protein)(VEG protein)(Tear LCN1 prealbumin)(TP)(Tear lipocalin)(Tlc) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P31025] 9 0.92 0.95 -1 Epididymal-specific lipocalin-10 LCN10 Precursor [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6JVE6] 9 0.94 0.93 -1 Leukemia inhibitory factor receptor Precursor (LIF receptor)(LIF-R)(CD118 LIFR protein_coding antigen) [Source:UniProtKB/Swiss- Prot;Acc:P42702] 5 1 0.95 -1 Leukocyte immunoglobulin-like receptor subfamily A member 3 Precursor (Leukocyte immunoglobulin-like receptor 4)(LIR-4)(Immunoglobulin-like LILRA3 protein_coding transcript 6)(ILT-6)( inhibitory receptor HM43/HM31)(CD85 antigen- like family member E)(CD85e antigen) [Sou 19 0.94 0.89 -1 Leukocyte immunoglobulin-like receptor subfamily A member 5 Precursor (Leukocyte immunoglobulin-like receptor 9)(LIR-9)(Immunoglobulin-like LILRA5 protein_coding transcript 11)(ILT-11)(CD85 antigen- like family member F)(CD85f antigen) [Source:UniProtKB/Swiss- Prot;Acc:A6NI73] 19 1 0.9 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Leukocyte immunoglobulin-like receptor subfamily B member 3 Precursor (Leukocyte immunoglobulin-like LILRB3 receptor 3)(LIR-3)(Immunoglobulin-like protein_coding transcript 5)(ILT-5)(Monocyte inhibitory receptor HL9)(CD85 antigen-like family member A)(CD85a antigen) [Source:Un 19 0.92 0.89 -1 Latrophilin-3 Precursor (Calcium- independent alpha-latrotoxin receptor LPHN3 3)(Lectomedin-3) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9HAR2] 4 0.92 0.77 -1 Leucine-rich repeat and transmembrane domain-containing LRTM1 protein 1 Precursor protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9HBL6] 3 0.97 0.9 -1 Latent-transforming growth factor beta- binding protein, isoform 1L Precursor (LTBP-1)(Transforming growth factor LTBP1 protein_coding beta-1-binding protein 1)(TGF-beta1- BP-1) [Source:UniProtKB/Swiss- Prot;Acc:Q14766] 2 0.98 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Lymphatic vessel endothelial hyaluronic acid receptor 1 Precursor (LYVE-1)(Cell surface retention sequence-binding protein 1)(CRSBP-1)(Hyaluronic acid LYVE1 protein_coding receptor)(Extracellular link domain- containing protein 1) [Source:UniProtKB/Swiss- Prot;Acc:Q9Y5Y7] 11 0.95 0.96 -1 Protein mab-21-like 1 MAB21L1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q13394] 13 0.94 0.86 -1 Melanoma-associated antigen 1 (MAGE-1 antigen)(Antigen MZ2- MAGEA1 E)(Cancer/testis antigen 1.1)(CT1.1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P43355] X 0.93 0.96 -1 Melanoma-associated antigen 11 (MAGE-11 antigen)(Cancer/testis MAGEA11 antigen 1.11)(CT1.11) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P43364] X 0.93 0.88 -1 Melanoma-associated antigen 12 (MAGE-12 antigen)(MAGE12F antigen)(Cancer/testis antigen MAGEA12 protein_coding 1.12)(CT1.12) [Source:UniProtKB/Swiss- Prot;Acc:P43365] X 0.92 0.9 -1 Melanoma-associated antigen C1 (MAGE-C1 antigen)(Cancer/testis MAGEC1 antigen 7.1)(CT7.1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O60732] X 0.93 0.92 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Melanoma-associated antigen C2 (MAGE-C2 antigen)(MAGE-E1 antigen)(Hepatocellular carcinoma- MAGEC2 associated antigen 587)(Cancer/testis protein_coding antigen 10)(CT10) [Source:UniProtKB/Swiss- Prot;Acc:Q9UBF1] X 1 0.97 0 Myoglobin [Source:UniProtKB/Swiss- MB protein_coding Prot;Acc:P02144] 22 1 0.96 -1 Melanocortin receptor 5 (MC5-R)(MC- MC5R 2) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P33032] 18 0.97 0.94 -1 Mitochondrial carrier triple repeat MCART2 protein 2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q3SY17] 18 0.96 0.97 -1 Meprin A subunit alpha Precursor (EC 3.4.24.18)(Endopeptidase-2)(N-benzoyl- L-tyrosyl-P-amino-benzoic acid MEP1A hydrolase subunit alpha)(PABA peptide protein_coding hydrolase)(PPH alpha) [Source:UniProtKB/Swiss- Prot;Acc:Q16819] 6 0.98 0.88 -1 Microfibrillar-associated protein 5 Precursor (MFAP-5)(Microfibril- MFAP5 associated glycoprotein 2)(MAGP- protein_coding 2)(MP25) [Source:UniProtKB/Swiss- Prot;Acc:Q13361] 12 0.98 0.93 -1 Microphthalmia-associated transcription MITF factor [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O75030] 3 0.99 0.89 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Makorin-3 (Zinc finger protein 127)(RING finger protein 63) MKRN3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q13064] 15 0.92 0.9 -1 Interstitial collagenase Precursor (EC 3.4.24.7)(Matrix metalloproteinase- 1)(MMP-1)(Fibroblast collagenase) MMP1 [Contains 22 kDa interstitial protein_coding collagenase;27 kDa interstitial collagenase] [Source:UniProtKB/Swiss- Prot;Acc:P03956] 11 0.92 0.92 0 Macrophage metalloelastase Precursor (HME)(EC 3.4.24.65)(Matrix metalloproteinase-12)(MMP- MMP12 protein_coding 12)(Macrophage elastase)(ME) [Source:UniProtKB/Swiss- Prot;Acc:P39900] 11 0.99 0.97 0 Collagenase 3 Precursor (EC 3.4.24.- )(Matrix metalloproteinase-13)(MMP- MMP13 protein_coding 13) [Source:UniProtKB/Swiss- Prot;Acc:P45452] 11 1 0.98 -1 Membrane-spanning 4-domains subfamily A member 15 MS4A15 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8N5U1] 11 0.9 0.87 -1 Membrane-spanning 4-domains subfamily A member 5 (Testis- expressed transmembrane 4 MS4A5 protein_coding protein)(CD20 antigen-like 2)(CD20 antigen) [Source:UniProtKB/Swiss- Prot;Acc:Q9H3V2] 11 0.95 0.87 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth MutS protein homolog 4 MSH4 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O15457] 1 0.97 0.91 -1 Metallothionein-1B (MT- 1B)(Metallothionein-IB)(MT-IB) MT1B protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P07438] 16 0.92 0.92 -1 Myotubularin-related protein 11 (Cisplatin resistance-associated MTMR11 protein)(hCRA) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:A4FU01] 1 0.9 0.8 -1 Mucin-16 (MUC-16)(Ovarian carcinoma antigen CA125)(Ovarian cancer-related MUC16 tumor marker CA125)(CA-125) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8WXI7] 19 0.95 0.92 -1 Mucin-2 Precursor (MUC-2)(Intestinal MUC2 mucin-2) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q02817] 11 0.92 0.93 -1 Muscle, skeletal receptor tyrosine protein kinase Precursor (EC 2.7.10.1)(Muscle-specific tyrosine MUSK protein kinase receptor)(Muscle- protein_coding specific kinase receptor)(MuSK) [Source:UniProtKB/Swiss- Prot;Acc:O15146] 9 0.99 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Interferon-induced GTP-binding protein Mx2 (Myxovirus resistance protein 2)(Interferon-regulated resistance GTP- MX2 protein_coding binding protein MxB)(p78-related protein) [Source:UniProtKB/Swiss- Prot;Acc:P20592] 21 0.92 0.77 -1 -3 (Myosin heavy chain 3)(Myosin heavy chain, fast skeletal muscle, embryonic)(Muscle embryonic MYH3 protein_coding myosin heavy chain)(SMHCE) [Source:UniProtKB/Swiss- Prot;Acc:P11055] 17 0.96 0.88 -1 Myosin-6 (Myosin heavy chain 6)(Myosin heavy chain, cardiac muscle MYH6 alpha isoform)(MyHC-alpha) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P13533] 14 1 0.97 -1 Myosin regulatory light chain 2, ventricular/cardiac muscle isoform MYL2 (MLC-2v)(MLC-2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P10916] 12 0.94 0.93 -1 kinase family member 4 (EC 2.7.11.1)(Serine/threonine-protein MYLK4 protein_coding kinase SgK085)(Sugen kinase 85) [Source:UniProtKB/Swiss- Prot;Acc:Q86YV6] 6 0.91 0.83 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Myosin-Ia (Brush border myosin I)(BBM- I)(BBMI)(Myosin I heavy chain)(MIHC) MYO1A protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UBC5] 12 1 1 -1 Myotilin ( protein)(Myofibrillar titin-like Ig domains MYOT protein)(57 kDa cytoskeletal protein) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UBF9] 5 0.95 0.86 -1 Myelin transcription factor 1 (MyT1)(MyTI)(Proteolipid protein- MYT1 binding protein)(PLPB1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q01538] 20 0.98 0.95 -1 Myelin transcription factor 1-like protein (MyT1L protein)(MyT1-L) MYT1L protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UL68] 2 1 0.92 -1 Ephexin-1 (Eph-interacting exchange protein)(Neuronal guanine nucleotide NGEF exchange factor) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8N5V2] 2 0.9 0.96 -1 Nicotinic acid receptor 1 (G-protein coupled receptor 109A)(G-protein NIACR2 coupled receptor HM74A) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8TDS4] 12 1 0.94 -1 NK6 homeobox 3 [Source:RefSeq NKX6-3 protein_coding peptide;Acc:NP_689781] 8 0.9 0.89 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth NACHT, LRR and PYD domains- containing protein 5 (Mater protein NLRP5 protein_coding homolog) [Source:UniProtKB/Swiss- Prot;Acc:P59047] 19 0.93 0.9 -1 NACHT, LRR and PYD domains- containing protein 7 (PYRIN-containing APAF1-like protein 3)(Nucleotide- NLRP7 protein_coding binding oligomerization domain protein 12) [Source:UniProtKB/Swiss- Prot;Acc:Q8WX94] 19 0.96 0.93 -1 Nucleoside diphosphate kinase A (NDP kinase A)(NDK A)(EC 2.7.4.6)(Tumor metastatic process-associated protein)(Metastasis inhibition factor NME1-NME2 protein_coding nm23)(nm23-H1)(Granzyme A- activated DNase)(GAAD) [Source:UniProtKB/Swiss- Prot;Acc:P15531] 17 0.93 0.84 -1 Nicotinamide mononucleotide adenylyltransferase 2 (NMN NMNAT2 adenylyltransferase 2)(EC 2.7.7.1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BZQ4] 1 1 1 -1 Neuromedin-S Precursor NMS [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5H8A3] 2 0.94 0.7 -1 Neuromedin-U receptor 2 (NMU-R2)(G- protein coupled receptor TGR-1)(G- NMUR2 protein coupled receptor FM-4) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9GZQ4] 5 0.94 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Neuropeptides B/W receptor type 2 (G- protein coupled receptor 8) NPBWR2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P48146] 20 0.95 0.9 -1 Nuclear receptor-interacting protein 2 NRIP2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9BQI9] 12 0.9 0.89 -1 5'-nucleotidase domain-containing NT5DC2 protein 2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9H857] 3 0.96 0.9 -1 Neurotrophin-3 Precursor (NT- 3)(Neurotrophic factor)(HDNF)(Nerve NTF3 growth factor 2)(NGF-2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P20783] 12 0.94 0.98 -1 Netrin-G2 Precursor (Laminet-2) NTNG2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q96CW9] 9 0.96 0.97 -1 Odorant-binding protein 2a Precursor OBP2A (OBPIIa) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9NY56] 9 0.93 0.92 -1 Teneurin-3 (Ten-3)(Tenascin-M3)(Ten- m3)(Protein Odd Oz/ten-m homolog 3) ODZ3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9P273] 4 0.98 0.87 -1 Opsin-5 (Neuropsin)(G-protein coupled receptor 136)(G-protein coupled OPN5 receptor PGR12)(Transmembrane protein_coding protein 13) [Source:UniProtKB/Swiss- Prot;Acc:Q6U736] 6 0.98 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Opticin Precursor (Oculoglycan) OPTC [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9UBM4] 1 0.99 0.96 -1 10A3 (Olfactory receptor OR11-97)(HTPCRX12) OR10A3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P58181] 11 0.91 0.79 -1 Olfactory receptor 10G4 (Olfactory receptor OR11-278) OR10G4 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGN3] 11 0.96 0.91 -1 Olfactory receptor 10G7 (Olfactory receptor OR11-283) OR10G7 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGN6] 11 0.94 0.91 -1 Olfactory receptor 10G8 (Olfactory receptor OR11-282) OR10G8 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGN5] 11 0.99 0.88 -1 Olfactory receptor 10H1 (Olfactory receptor OR19-27) OR10H1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9Y4A9] 19 0.94 0.88 -1 Olfactory receptor 10H5 (Olfactory receptor OR19-25)(Olfactory receptor OR10H5 protein_coding OR19-26) [Source:UniProtKB/Swiss- Prot;Acc:Q8NGA6] 19 0.97 0.94 -1 Olfactory receptor 11L1 OR11L1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NGX0] 1 0.93 0.87 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Olfactory receptor 13C3 (Olfactory receptor OR9-8) OR13C3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGS6] 9 1 0.93 -1 Olfactory receptor 13C8 OR13C8 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NGS7] 9 1 1 -1 Olfactory receptor 13F1 (Olfactory receptor OR9-6) OR13F1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGS4] 9 0.96 0.88 -1 Olfactory receptor 14A16 (Olfactory receptor 5AT1)(Olfactory receptor OR1- OR14A16 protein_coding 45) [Source:UniProtKB/Swiss- Prot;Acc:Q8NHC5] 1 1 0.98 -1 Olfactory receptor 1B1 (Olfactory receptor OR9-26)(Olfactory receptor 9- OR1B1 protein_coding B)(OR9-B) [Source:UniProtKB/Swiss- Prot;Acc:Q8NGR6] 9 0.91 0.98 -1 Olfactory receptor 1C1 (Olfactory receptor OR1-42)(Olfactory receptor OR1C1 protein_coding TPCR27) [Source:UniProtKB/Swiss- Prot;Acc:Q15619] 1 0.96 0.9 -1 Olfactory receptor 1E2 (Olfactory receptor 17-93/17-135/17-136)(OR17- OR1E2 93)(OR17-135)(OR17-136) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P47887] 17 1 1 -1 Olfactory receptor 1I1 (Olfactory receptor 19-20)(OR19-20) OR1I1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O60431] 19 0.95 0.93 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Olfactory receptor 1K1 OR1K1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NGR3] 9 0.98 0.98 -1 Olfactory receptor 1L1 (Olfactory receptor 9-C)(OR9-C) OR1L1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NH94] 9 0.9 0.79 -1 Olfactory receptor 1L3 (Olfactory receptor OR9-28)(Olfactory receptor 9- OR1L3 protein_coding D)(OR9-D) [Source:UniProtKB/Swiss- Prot;Acc:Q8NH93] 9 0.93 0.8 -1 Olfactory receptor 1L6 OR1L6 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NGR2] 9 1 0.99 -1 Olfactory receptor 1M1 (Olfactory receptor OR19-5)(Olfactory receptor 19- OR1M1 protein_coding 6)(OR19-6) [Source:UniProtKB/Swiss- Prot;Acc:Q8NGA1] 19 0.99 0.97 -1 Olfactory receptor 1S1 (Olfactory receptor OR11-232) OR1S1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NH92] 11 0.94 0.9 -1 Olfactory receptor 2B11 OR2B11 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5JQS5] 1 0.99 0.95 -1 Olfactory receptor 2D2 (Olfactory receptor OR11-88)(Olfactory receptor OR2D2 11-610)(OR11-610)(HB2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9H210] 11 0.95 0.88 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Olfactory receptor 2M2 (OST423) OR2M2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q96R28] 1 0.92 0.86 -1 Olfactory receptor 2T29 OR2T29 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NH02] 1 0.92 0.87 -1 Olfactory receptor 2T33 (Olfactory receptor OR1-56) OR2T33 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NG76] 1 0.9 0.77 -1 Olfactory receptor 2T5 (Olfactory receptor OR1-62) OR2T5 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6IEZ7] 1 0.91 0.83 -1 Olfactory receptor 2V2 (Olfactory receptor OR5-3) OR2V2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q96R30] 5 0.95 0.94 -1 Olfactory receptor 2Y1 (Olfactory receptor OR5-2) OR2Y1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGV0] 5 0.96 0.9 -1 Olfactory receptor 2Z1 (Olfactory receptor OR19-4) OR2Z1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NG97] 19 0.93 0.86 -1 Olfactory receptor 4D1 (Olfactory receptor TPCR16) OR4D1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q15615] 17 0.92 0.85 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Olfactory receptor 51B2 (Odorant receptor HOR5'beta3) OR51B2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9Y5P1] 11 0.91 0.83 -1 Olfactory receptor 51B5 (Olfactory receptor OR11-37)(Odorant receptor OR51B5 protein_coding HOR5'beta5) [Source:UniProtKB/Swiss- Prot;Acc:Q9H339] 11 0.97 0.78 -1 Olfactory receptor 51L1 (Olfactory receptor OR11-31) OR51L1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGJ5] 11 0.97 0.83 -1 Olfactory receptor 5A1 (Olfactory receptor OR11-249)(OST181) OR5A1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGJ0] 11 1 0.96 -1 Olfactory receptor 5D18 (Olfactory receptor OR11-143)(Olfactory receptor OR5D18 protein_coding OR11-152) [Source:UniProtKB/Swiss- Prot;Acc:Q8NGL1] 11 0.96 0.89 -1 Olfactory receptor 6B2 (Olfactory receptor OR2-1) OR6B2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6IFH4] 2 0.96 0.92 -1 Olfactory receptor 6K2 (Olfactory receptor OR1-17) OR6K2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGY2] 1 0.94 0.81 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Olfactory receptor 6K6 (Olfactory receptor OR1-21) OR6K6 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGW6] 1 0.97 0.8 -1 Olfactory receptor 6T1 (Olfactory receptor OR11-277) OR6T1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGN1] 11 0.98 0.94 -1 Olfactory receptor 7C2 (Olfactory receptor OR19-22)(Olfactory receptor OR7C2 19-18)(OR19-18) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O60412] 19 1 0.95 -1 Olfactory receptor 8B12 (Olfactory receptor OR11-317) OR8B12 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGG6] 11 0.91 0.86 -1 Olfactory receptor 8B8 (Olfactory receptor TPCR85)(Olfactory-like OR8B8 receptor JCG8) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q15620] 11 0.92 0.97 -1 Olfactory receptor 8S1 OR8S1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8NH09] 12 0.93 0.87 -1 Olfactory receptor 9A2 (Olfactory receptor OR7-2) OR9A2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NGT5] 7 0.92 0.81 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Protein-arginine deiminase type-6 (EC 3.5.3.15)(Protein-arginine deiminase PADI6 type VI)(Peptidylarginine deiminase VI) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6TGC4] 1 0.98 0.97 -1 Glycodelin Precursor (GD)(Pregnancy- associated endometrial alpha-2 globulin)(PAEG)(PEG)(Placental protein 14)(PP14)(Progesterone- PAEP associated endometrial protein_coding protein)(Progestagen-associated endometrial protein) [Source:UniProtKB/Swiss- Prot;Acc:P09466] 9 0.9 0.9 -1 G antigen family C member 1 (GAGE- 9)(Prostate-associated gene 4 PAGE4 protein)(PAGE-4)(PAGE-1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O60829] X 0.95 0.9 0 Poly(rC)-binding protein 3 (Alpha-CP3) PCBP3 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P57721] 21 0.94 0.99 -1 Purkinje cell protein 4 (Brain-specific antigen PCP-4)(Brain-specific PCP4 polypeptide PEP-19) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P48539] 21 0.96 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (GMP- PDE6A PDE alpha)(EC 3.1.4.35)(PDE V-B1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P16499] 5 0.92 0.91 -1 PDZ domain-containing protein 2 (PDZ domain-containing protein 3)(Activated in prostate cancer protein) [Contains PDZD2 protein_coding Processed PDZ domain-containing protein 2] [Source:UniProtKB/Swiss- Prot;Acc:O15018] 5 0.97 0.96 -1 Gastricsin Precursor (EC 3.4.23.3)(Pepsinogen C) PGC protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P20142] 6 0.98 0.96 -1 Phosphoglycerate kinase 2 (EC 2.7.2.3)(Phosphoglycerate kinase, PGK2 testis specific) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P07205] 6 0.92 0.89 -1 Peptidoglycan recognition protein I-beta Precursor (PGRP-I-beta)(Peptidoglycan recognition protein intermediate PGLYRP4 beta)(PGLYRPIbeta)(Peptidoglycan protein_coding recognition protein 4) [Source:UniProtKB/Swiss- Prot;Acc:Q96LB8] 1 0.98 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Phosphatase and actin regulator 3 (Scaffold-associated PP1-inhibiting PHACTR3 protein)(Scapinin) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q96KR7] 20 0.98 0.93 -1 PH domain leucine-rich repeat protein phosphatase-like (PHLPP-like)(EC PHLPPL 3.1.3.16)(PHLPP2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6ZVD8] 16 0.97 0.97 -1 Paired immunoglobulin-like type 2 receptor alpha Precursor (Inhibitory receptor PILR-alpha)(Cell surface PILRA protein_coding receptor FDF03) [Source:UniProtKB/Swiss- Prot;Acc:Q9UKJ1] 7 0.98 0.94 -1 Phospholipase B1, membrane- associated Precursor (Phospholipase B)(hPLB)(Phospholipase B/lipase)(PLB/LIP) [Includes PLB1 protein_coding Phospholipase A2(EC 3.1.1.4);Lysophospholipase(EC 3.1.1.5)] [Source:UniProtKB/Swiss- Prot;Acc:Q6P1J6] 2 0.96 0.93 -1 Peripheral myelin protein 22 (PMP- 22)(Growth arrest-specific protein PMP22 protein_coding 3)(GAS-3) [Source:UniProtKB/Swiss- Prot;Acc:Q01453] 17 0.98 0.95 -1 Pancreatic lipase-related protein 2 Precursor (PL-RP2)(EC 3.1.1.3) PNLIPRP2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P54317] 10 0.97 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Liprin-alpha-4 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha- PPFIA4 protein_coding 4)(PTPRF-interacting protein alpha-4) [Source:UniProtKB/Swiss- Prot;Acc:O75335] 1 0.99 0.99 -1 Protein phosphatase 1 regulatory subunit 14D (Gastrointestinal and brain- PPP1R14D specific PP1-inhibitory protein 1)(GBPI- protein_coding 1) [Source:UniProtKB/Swiss- Prot;Acc:Q9NXH3] 15 0.98 0.94 -1 Pancreatic prohormone Precursor (Pancreatic polypeptide)(PP)(Obinepitide) [Contains PPY Pancreatic hormone(PH);Pancreatic protein_coding icosapeptide(PI)] [Source:UniProtKB/Swiss- Prot;Acc:P01298] 17 0.99 0.95 -1 Basic salivary proline-rich protein 3 Precursor (Parotid salivary glycoprotein PRB3 G1)(Proline-rich protein G1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q04118] 12 0.94 0.94 -1 Perforin-1 Precursor (P1)(Lymphocyte pore-forming protein)(PFP)(Cytolysin) PRF1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P14222] 10 0.96 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Perforin-1 Precursor (P1)(Lymphocyte pore-forming protein)(PFP)(Cytolysin) PRF1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P14222] 10 0.96 0.95 -1 Transmembrane gamma- carboxyglutamic acid protein 3 Precursor (Proline-rich gamma- PRRG3 carboxyglutamic acid protein 3)(Proline- protein_coding rich Gla protein 3) [Source:UniProtKB/Swiss- Prot;Acc:Q9BZD7] X 0.97 0.99 -1 Serine protease 33 Precursor (EC 3.4.21.-)(Serine protease EOS) PRSS33 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8NF86] 16 0.99 1 -1 Polyserase-2 Precursor (EC 3.4.21.- )(Polyserine protease 2)(Serine PRSS36 protein_coding protease 36) [Source:UniProtKB/Swiss- Prot;Acc:Q5K4E3] 16 0.96 0.97 -1 Pregnancy-specific beta-1-glycoprotein 1 Precursor (PSBG-1)(Pregnancy- specific beta-1 glycoprotein C/D)(PS- beta-C/D)(Fetal liver non-specific cross- PSG1 protein_coding reactive antigen 1/2)(FL-NCA- 1/2)(PSG95)(CD66 antigen-like family member F)(CD66f antigen)(CD66 antigen) [S 19 0.97 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

Pregnancy-specific beta-1-glycoprotein 11 Precursor (PSBG-11)(PSBG-13) PSG11 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UQ72] 19 0.95 0.89 -1 Pregnancy-specific beta-1-glycoprotein 3 Precursor (PSBG- PSG3 3)(Carcinoembryonic antigen SG5) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q16557] 19 0.95 0.94 -1 Pregnancy-specific beta-1-glycoprotein 10 Precursor (PSBG-10)(PSBG-12) PSG6 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q15235] 19 1 0.96 -1 Receptor-type tyrosine-protein phosphatase R Precursor (EC 3.1.3.48)(Protein-tyrosine phosphatase PTPRR protein_coding PCPTP1)(NC-PTPCOM1)(Ch- 1PTPase) [Source:UniProtKB/Swiss- Prot;Acc:Q15256] 12 0.92 0.8 -1 Parvalbumin alpha PVALB [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P20472] 22 0.92 0.94 -1 Ras GTPase-activating protein nGAP (RAS protein activator-like 1) RASAL2 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UJF2] 1 0.95 0.93 -1 Recoverin (Cancer-associated retinopathy protein)(Protein CAR) RCVRN protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P35243] 17 1 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Regenerating islet-derived protein 3 gamma Precursor (Reg III- gamma)(Pancreatitis-associated REG3G protein_coding protein 1B)(PAP IB) [Source:UniProtKB/Swiss- Prot;Acc:Q6UW15] 2 0.92 0.87 -1 Ret finger protein-like 1 (RING finger RFPL1 protein 78) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O75677] 22 0.97 0.93 -1 Ret finger protein-like 2 (RING finger RFPL2 protein 79) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O75678] 22 0.94 0.91 -1 Ret finger protein-like 3 RFPL3 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O75679] 22 0.95 0.87 -1 Ret finger protein-like 4B (RING finger RFPL4B protein 211) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q6ZWI9] 6 1 1 -1 Retrotransposon gag domain- containing protein 1 (Tumor antigen BJ- RGAG1 protein_coding HCC-23) [Source:UniProtKB/Swiss- Prot;Acc:Q8NET4] X 1 0.96 -1 RIMS-binding protein 2 (RIM-BP2) RIMBP2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O15034] 12 0.9 0.77 -1 RING finger protein 17 (Tudor domain- containing protein 4) RNF17 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BXT8] 13 0.95 0.92 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth RING finger protein 186 RNF186 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9NXI6] 1 0.93 0.92 -1 processed_pseudoge RP11-344N17.6 NA ne X 0.96 0.97 -1 processed_pseudoge RP11-344N17.9 NA ne X 0.98 0.95 -1 processed_pseudoge RP11-501J20.3 NA ne 10 0.95 0.96 -1 processed_pseudoge RP11-552E4.2 NA ne X 1 0.98 -1 processed_pseudoge RP11-552J9.9 NA ne X 1 1 -1 Kazrin [Source:UniProtKB/Swiss- RP1-21O18.1 protein_coding Prot;Acc:Q674X7] 1 0.97 0.88 -1 retinitis pigmentosa 1-like 1 RP1L1 [Source:RefSeq protein_coding peptide;Acc:NP_849188] 8 0.96 0.99 -1 processed_pseudoge RP3-461P17.4 NA ne 20 0.9 0.93 -1 Retrotransposon-like protein 1 (Retrotransposon-derived protein PEG11)(Paternally expressed gene 11 RTL1 protein)(Mammalian retrotransposon protein_coding derived protein 1) [Source:UniProtKB/Swiss- Prot;Acc:A6NKG5] 14 0.91 0.93 -1 Receptor-transporting protein 3 (Transmembrane protein 7) RTP3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BQQ7] 3 0.93 0.92 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Relaxin receptor 1 (Relaxin family peptide receptor 1)(Leucine-rich repeat- RXFP1 containing G-protein coupled receptor protein_coding 7) [Source:UniProtKB/Swiss- Prot;Acc:Q9HBX9] 4 0.93 0.94 -1 Protein S100-A5 (S100 calcium-binding protein A5)(Protein S-100D) S100A5 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P33763] 1 0.98 0.97 -1 Protein S100-B (S100 calcium-binding protein B)(S-100 protein subunit S100B beta)(S-100 protein beta chain) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P04271] 21 1 0.99 -1 Sarcoma antigen 1 (Cancer/testis antigen 14)(CT14) SAGE1 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9NXZ1] X 0.96 0.89 -1 Epidermal retinal dehydrogenase 2 (RDH-E2)(EPHD-2)(EC 1.1.1.-)(Retinal SDR16C5 short chain dehydrogenase reductase protein_coding 2)(retSDR2) [Source:UniProtKB/Swiss- Prot;Acc:Q8N3Y7] 8 0.98 0.97 -1 Protein Z-dependent protease inhibitor Precursor (PZ-dependent protease SERPINA10 inhibitor)(PZI)(Serpin A10) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9UK55] 14 0.95 0.94 -1 Antithrombin-III Precursor (ATIII) SERPINC1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P01008] 1 0.96 0.85 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Heparin cofactor 2 Precursor (Heparin cofactor II)(HC-II)(Protease inhibitor SERPIND1 leuserpin 2)(HLS2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P05546] 22 0.93 0.83 -1 Serine/threonine-protein kinase Sgk2 (EC 2.7.11.1)(Serum/- SGK2 regulated kinase 2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9HBY8] 20 0.94 0.9 -1 Sialic acid-binding Ig-like lectin 12 Precursor (Siglec-12)(Sialic acid- SIGLEC12 binding Ig-like lectin-like 1)(Siglec-L1) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q96PQ1] 19 0.9 0.88 -1 Sialic acid-binding Ig-like lectin 15 Precursor (Siglec-15)(CD33 antigen- SIGLEC15 like 3)(CD33 antigen) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q6ZMC9] 18 0.94 0.96 -1 Sialic acid-binding Ig-like lectin 8 Precursor (Siglec-8)( family member 2)(SAF- SIGLEC8 protein_coding 2)(CDw329)(CD329 antigen) [Source:UniProtKB/Swiss- Prot;Acc:Q9NYZ4] 19 0.93 0.84 -1 Sialic acid-binding Ig-like lectin 9 Precursor (Siglec-9)(Protein FOAP-9) SIGLEC9 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9Y336] 19 0.94 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth SRC-like-adapter (Src-like-adapter protein 1)(hSLAP) SLA protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q13239] 8 0.92 0.87 -1 Solute carrier family 10 member 6 (Sodium-dependent organic anion SLC10A6 protein_coding transporter) [Source:UniProtKB/Swiss- Prot;Acc:Q3KNW5] 4 0.96 0.96 -1 Putative sodium-coupled neutral transporter 8 SLC38A8 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:A6NNN8] 16 0.94 0.92 -1 Sodium/glucose cotransporter 5 (Na(+)/glucose cotransporter 5)(Solute SLC5A10 carrier family 5 member 10) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:A0PJK1] 17 0.96 0.93 -1 Sodium/myo-inositol cotransporter 2 (Na+/myo-inositol cotransporter 2)(Sodium/glucose cotransporter SLC5A11 KST1)(Sodium-dependent glucose protein_coding cotransporter)(Solute carrier family 5 member 11) [Source:UniProtKB/Swiss- Prot;Acc:Q8WWX8] 16 0.92 0.89 -1 Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) (Amino acid SLC6A14 transporter ATB0+)(Solute carrier protein_coding family 6 member 14) [Source:UniProtKB/Swiss- Prot;Acc:Q9UN76] X 0.96 0.86 0 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Sodium- and chloride-dependent transporter XTRP2 (Solute carrier SLC6A18 family 6 member 18) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q96N87] 5 0.98 0.94 -1 B(0,+)-type amino acid transporter 1 (B(0,+)AT)(Glycoprotein-associated amino acid transporter b0,+AT1)(Solute SLC7A9 protein_coding carrier family 7 member 9) [Source:UniProtKB/Swiss- Prot;Acc:P82251] 19 0.9 0.85 -1 Sodium/calcium exchanger 3 Precursor (Na(+)/Ca(2+)-exchange protein 3) SLC8A3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P57103] 14 1 0.96 -1 Mothers against decapentaplegic homolog 9 (Mothers against DPP SMAD9 homolog 9)(SMAD 9)(Smad9)(Madh6) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:O15198] 13 0.94 0.92 -1 Sclerostin Precursor SOST [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9BQB4] 17 0.96 0.95 -1 Sperm protein associated with the nucleus on the X chromosome N1 SPANXN1 (SPANX-N1)(SPANX family member protein_coding N1) [Source:UniProtKB/Swiss- Prot;Acc:Q5VSR9] X 0.99 1 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Sperm protein associated with the nucleus on the X chromosome N5 SPANXN5 (SPANX-N5)(SPANX family member protein_coding N5) [Source:UniProtKB/Swiss- Prot;Acc:Q5MJ07] X 1 1 -1 Serine protease inhibitor Kazal-type 7 Precursor (Esophagus cancer-related SPINK7 gene 2 protein)(ECRG-2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P58062] 5 0.9 0.88 -1 SPRY domain-containing protein 5 (Tripartite motif-containing protein 51) SPRYD5 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BSJ1] 11 0.96 0.81 -1 Protein SSX1 (Synovial sarcoma, X breakpoint 1)(Cancer/testis antigen SSX1 protein_coding 5.1)(CT5.1) [Source:UniProtKB/Swiss- Prot;Acc:Q16384] X 0.94 0.99 -1 Protein SSX10 SSX10 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:A6NEJ1] X 0.96 0.97 -1 Protein SSX3 (Cancer/testis antigen SSX3 5.3)(CT5.3) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q99909] X 0.98 0.95 -1 Protein SSX5 SSX5 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O60225] X 1 0.98 -1 Protein SSX6 SSX6 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q7RTT6] X 0.96 0.93 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Protein SSX7 SSX7 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q7RTT5] X 1 1 -1 Protein SSX9 SSX9 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q7RTT3] X 0.96 0.97 -1 -4 (Stathmin-like protein STMN4 B3)(RB3) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9H169] 8 0.96 0.98 -1 Stonin-1 (Stoned B-like factor) STON1-GTF2A1L [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9Y6Q2] 2 0.9 0.85 -1 Synapsin-3 (Synapsin III) SYN3 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O14994] 22 0.94 0.91 -1 Synaptogyrin-1 SYNGR1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O43759] 22 0.94 0.96 -1 Synaptotagmin-14-like protein (Synaptotagmin XIV-like SYT14L protein)(Synaptotagmin XIV-derived protein_coding protein) [Source:UniProtKB/Swiss- Prot;Acc:Q58G82] 4 0.93 0.95 -1 Synaptotagmin-like protein 2 (Exophilin- SYTL2 4) [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9HCH5] 11 0.91 0.95 -1 Taste receptor type 2 member 38 (T2R38)(T2R61)(PTC bitter taste TAS2R38 protein_coding receptor) [Source:UniProtKB/Swiss- Prot;Acc:P59533] 7 0.94 0.95 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth TBC1 domain family member 26 TBC1D26 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q86UD7] 17 1 0.96 -1 RNA polymerase II transcription factor SIII subunit A2 (Elongin- A2)(EloA2)(Transcription elongation TCEB3B protein_coding factor B polypeptide 3B) [Source:UniProtKB/Swiss- Prot;Acc:Q8IYF1] 18 0.91 0.97 -1 T-complex protein 10A homolog 2 (T- complex protein 10A-2)(TCP10A- TCP10L 2)(TCP10-like) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8TDR4] 21 1 0.95 -1 Homeobox protein TGIF2LX (TGFB- induced factor 2-like protein, X- linked)(TGF(beta)induced transcription TGIF2LX protein_coding factor 2-like protein)(TGIF-like on the X) [Source:UniProtKB/Swiss- Prot;Acc:Q8IUE1] X 0.98 0.97 -1 Protein-glutamine gamma- glutamyltransferase 6 (EC 2.3.2.13)(Transglutaminase-3- TGM6 protein_coding like)(TGase-3-like)(Transglutaminase Y) [Source:UniProtKB/Swiss- Prot;Acc:O95932] 20 1 1 -1 Transmembrane protein PMP22CD (PMP22 claudin domain-containing TMEM225 protein_coding protein) [Source:UniProtKB/Swiss- Prot;Acc:Q6GV28] 11 0.92 0.83 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Transmembrane protease, serine 13 (EC 3.4.21.-)(Membrane-type mosaic TMPRSS13 serine protease)(Mosaic serine protein_coding protease) [Source:UniProtKB/Swiss- Prot;Acc:Q9BYE2] 11 0.99 0.93 -1 Transmembrane protease, serine 4 (EC 3.4.21.-)(Membrane-type serine TMPRSS4 protease 2)(MT-SP2) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9NRS4] 11 1 0.99 -1 Tumor necrosis factor receptor superfamily member 13B (Transmembrane activator and CAML TNFRSF13B protein_coding interactor)(CD267 antigen) [Source:UniProtKB/Swiss- Prot;Acc:O14836] 17 0.96 0.94 -1 Tumor protein D55 (hD55)(Tumor protein D52-like 3)(Testis development TPD52L3 protein NYD-SP25) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q96J77] 9 1 1 -1 Thyroid peroxidase Precursor (TPO)(EC 1.11.1.8) TPO protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P07202] 2 0.98 0.89 -1 Thyrotropin-releasing hormone receptor (TRH-R)(Thyroliberin receptor) TRHR protein_coding [Source:UniProtKB/Swiss- Prot;Acc:P34981] 8 0.99 0.98 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Tripartite motif-containing protein 54 (Muscle-specific RING finger protein 3)(MURF-3)(MuRF3)(Muscle-specific TRIM54 RING finger protein)(MuRF)(RING protein_coding finger protein 30) [Source:UniProtKB/Swiss- Prot;Acc:Q9BYV2] 2 0.94 0.93 -1 Tripartite motif-containing protein 55 (Muscle-specific RING finger protein TRIM55 2)(MURF-2)(MuRF2)(RING finger protein_coding protein 29) [Source:UniProtKB/Swiss- Prot;Acc:Q9BYV6] 8 1 0.91 -1 Tripartite motif-containing protein 34 (Interferon-responsive finger protein TRIM6-TRIM34 1)(RING finger protein 21) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9BYJ4] 11 0.91 0.91 -1 Short transient receptor potential channel 7 (TrpC7)(TRP7 protein) TRPC7 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q9HCX4] 5 0.99 0.95 -1 Transient receptor potential cation channel subfamily V member 5 (TrpV5)(Osm-9-like TRP channel 3)(OTRPC3)(Epithelial calcium channel TRPV5 protein_coding 1)(ECaC1)(ECaC)(Calcium transport protein 2)(CaT2) [Source:UniProtKB/Swiss- Prot;Acc:Q9NQA5] 7 0.99 1 -1 Testis-specific gene 13 protein TSGA13 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q96PP4] 7 0.95 0.9 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Tetraspanin-18 (Tspan-18) TSPAN18 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q96SJ8] 11 0.97 0.91 -1 Tubby protein homolog TUB [Source:UniProtKB/Swiss- protein_coding Prot;Acc:P50607] 11 1 0.99 -1 T-cell receptor beta V gene segment U66060.1-17 [Source:IMGT/GENE-DB;Acc:TRBV12- IG_V_gene 3] 7 0.93 0.74 -1 Ubiquitin-conjugating enzyme E2 U (EC 6.3.2.19)(Ubiquitin-protein ligase UBE2U U)(Ubiquitin carrier protein U) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q5VVX9] 1 0.94 0.91 -1 Urocortin-3 Precursor (Urocortin III)(Ucn III)(Stresscopin) UCN3 protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q969E3] 10 1 0.98 -1 UDP-glucuronosyltransferase 1-8 Precursor (EC 2.4.1.17)(UDP- glucuronosyltransferase UGT1A8 1A8)(UDPGT)(UGT1*8)(UGT1- protein_coding 08)(UGT1.8)(UGT-1H)(UGT1H) [Source:UniProtKB/Swiss- Prot;Acc:Q9HAW9] 2 0.92 0.9 -1 Uromodulin-like 1 Precursor (Olfactorin) UMODL1 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q5DID0] 21 1 0.98 -1 Protein unc-45 homolog B (UNC- 45B)(SMUNC45) UNC45B protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q8IWX7] 17 0.99 0.92 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Probable serine protease UNQ9391/PRO34284 Precursor (EC UNQ9391 protein_coding 3.4.21.-) [Source:UniProtKB/Swiss- Prot;Acc:Q6UWB4] 8 0.91 0.88 -1 Ubiquitin carboxyl-terminal hydrolase 17-like protein 2 (EC 3.1.2.15)(Ubiquitin thioesterase 17-like protein 2)(Ubiquitin- USP17 specific-processing protease 17-like protein_coding protein 2)(Deubiquitinating enzyme 17- like protein 2)(Deubiquitinating protein 3)(DUB-3) [Source 8 0.93 0.92 -1 Inactive ubiquitin carboxyl-terminal hydrolase 50 (Inactive ubiquitin-specific USP50 protein_coding peptidase 50) [Source:UniProtKB/Swiss- Prot;Acc:Q70EL3] 15 1 1 -1 Villin-like protein VILL [Source:UniProtKB/Swiss- protein_coding Prot;Acc:O15195] 3 0.93 0.93 -1 V-set and immunoglobulin domain- containing protein 1 Precursor (Cell VSIG1 surface A33 antigen)(Glycoprotein A34) protein_coding [Source:UniProtKB/Swiss- Prot;Acc:Q86XK7] X 0.98 0.75 -1 WD repeat-containing protein 42B WDR42B [Source:UniProtKB/Swiss- protein_coding Prot;Acc:A6NGE4] X 0.92 0.91 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth

WAP four-disulfide core domain protein 12 Precursor (Putative protease WFDC12 inhibitor WAP12)(Whey acidic protein protein_coding 2) [Source:UniProtKB/Swiss- Prot;Acc:Q8WWY7] 20 0.94 0.97 -1 Probable histone-lysine N- methyltransferase NSD2 (EC 2.1.1.43)(Nuclear SET domain- containing protein 2)(Wolf-Hirschhorn WHSC1 protein_coding syndrome candidate 1 protein)(Multiple myeloma SET domain-containing protein)(Protein trithorax-5) [Source:UniProtKB/Swiss-Prot;Acc:O96 4 0.97 0.95 -1 Protein Wnt-5b Precursor WNT5B [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9H1J7] 12 0.9 0.88 -1 Y_RNA Y RNA [Source:RFAM;Acc:RF00019] misc_RNA 8 0.93 0.92 -1 Zinc finger BED domain-containing ZBED2 protein 2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9BTP6] 3 0.64 0.71 0 Zinc finger BED domain-containing ZBED2 protein 2 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q9BTP6] 3 0.64 0.71 0 Zinc finger protein 385C ZNF385C [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q66K41] 17 0.99 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC normal_ cancer_ direction name description type chromosome methylation methylation _meth Zinc finger protein 423 (Olf1/EBF- associated zinc finger protein)(hOAZ)(Smad- and Olf- ZNF423 protein_coding interacting zinc finger protein) [Source:UniProtKB/Swiss- Prot;Acc:Q2M1K9] 16 0.95 0.98 -1 Zinc finger protein 595 ZNF595 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8IYB9] 4 0.94 0.96 -1 Zinc finger protein 645 ZNF645 [Source:UniProtKB/Swiss- protein_coding Prot;Acc:Q8N7E2] X 0.97 0.93 -1 zinc finger protein 718 (ZNF718), ZNF718 mRNA [Source:RefSeq protein_coding DNA;Acc:NM_001039127] 4 0.94 0.96 -1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.95 2.51 2.59 0 LCP -4.99

0.97 2.46 2.51 0 LCP -4.48

NA NA NA 0 ICP -4.69

NA NA NA 0 ICP -5.87

1.06 3.37 3.28 0 LCP -3.67

0.99 4.82 4.84 0 ICP -3.8

NA NA NA 0 ICP -5.39

NA NA NA 0 ICP -6.49 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.95 3.02 3.11 0 ICP -5.39

2.03 3.95 2.93 0 LCP -5.09

NA NA NA 1 HCP -4.87 NA NA NA 0 ICP -4.5

NA NA NA 0 ICP -5.45

0.81 3.73 4.03 0 LCP -3.97

0.92 3.03 3.15 0 ICP -4.73

NA NA NA -1 ICP -3.43 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -5.44

2.43 5.17 3.89 0 LCP -5.62

0.98 2.71 2.74 0 ICP -2.79

0.93 2.61 2.71 0 ICP -2.84

0.91 2.04 2.18 0 ICP -3.76 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

5.63 5.82 3.33 1 LCP -3.57

NA NA NA 0 LCP -5.36

NA NA NA 0 LCP -4.03

NA NA NA 0 LCP -5.95 NA NA NA 0 LCP -2.23 NA NA NA 0 ICP -3.8 1.01 6.46 6.45 0 HCP -3.61

NA NA NA 0 ICP -4.34

NA NA NA 0 LCP -4.11 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.96 2.81 2.88 0 HCP -4.57

1.26 7.27 6.94 0 LCP -4.31

1.47 3.91 3.35 0 LCP -4.97

0.56 12.19 13.02 -1 ICP -3.07

1.07 3.76 3.67 0 LCP -4.48

0.28 3.99 5.83 -1 ICP -3.16 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.96 2.16 2.22 0 ICP -3.81

1.01 2.58 2.56 0 LCP -2.62

0.97 2.23 2.28 0 ICP -5.84 NA NA NA 0 HCP -5.2 NA NA NA 0 LCP -4.81

3.91 5.28 3.31 0 ICP -1.12

NA NA NA 0 LCP -3.77

0.93 3.78 3.89 1 LCP -3.72 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.85 3.39 3.62 0 LCP -4.8

NA NA NA -1 ICP -3.28

0.81 2.78 3.1 0 ICP -4.75

0.97 2.98 3.02 0 LCP -5.23

0.84 2.83 3.07 0 ICP -4.76

0.98 2.26 2.29 0 LCP -4.52

0.92 4.58 4.7 0 LCP -5.42

NA NA NA 0 LCP -5.68 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.9 2.69 2.84 0 LCP -5.21

0.94 2.56 2.64 0 LCP -5.33

NA NA NA 0 ICP -3.2

NA NA NA 0 ICP -2.9

0.96 2.61 2.66 0 ICP -5.72

0.81 3.87 4.18 0 ICP -3.58

1.02 2.18 2.15 0 LCP -5.89

0.96 1.97 2.03 0 ICP -4.99

0.99 2.67 2.68 0 ICP -3.5

0.71 5.06 5.55 -1 HCP -3.76 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.89 3.65 3.82 0 ICP -3.71

0.95 3.14 3.22 0 LCP -5.56

0.9 3.42 3.58 -1 ICP -4.73

0.87 2.26 2.47 0 ICP -5.57

0.82 6.87 7.15 0 ICP -2.52

0.81 3.32 3.63 -1 ICP -5.45

0.97 2.57 2.62 0 ICP -5.32

0.75 4.92 5.33 0 LCP -4.86

NA NA NA 0 ICP -3.76 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.3 5.59 7.35 -1 ICP -5.05

0.98 2.76 2.8 0 ICP -2.78

NA NA NA 0 ICP -5.75

0.89 4.03 4.21 0 LCP -5.64

NA NA NA 0 ICP -3.49

0.92 2.6 2.72 0 ICP -5.23

NA NA NA 0 ICP -3.06 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.04 3.17 3.11 0 LCP -4.02

0.94 2.66 2.76 0 LCP -2.83

NA NA NA 0 LCP -2.05

0.96 2.61 2.67 0 LCP -3.73

0.86 3.67 3.88 0 LCP -6.38

0.74 5.33 5.76 0 LCP -5.32 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.93 4.25 4.35 0 ICP -5.74

NA NA NA 0 LCP -3.19

0.86 3.59 3.8 0 LCP -2.52

NA NA NA 0 LCP -5.27

NA NA NA 0 LCP -4

0.79 4.13 4.48 0 LCP -3.9 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.89 2.02 2.19 0 ICP -5.12

0.86 2.27 2.49 0 LCP -5.02

NA NA NA 0 ICP -2.18

NA NA NA 0 ICP -4.53

NA NA NA 0 ICP -3.16

1.02 3.01 2.99 0 ICP -3.94

0.73 5.49 5.95 0 ICP -5.11 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.41 3.88 3.39 0 LCP -3.94

1.02 3.71 3.69 0 LCP -4.88

NA NA NA 0 LCP -5.95

NA NA NA 0 LCP -2.71

1.01 2.62 2.61 0 LCP -4.87

0.1 4.4 7.74 0 LCP -3.98

NA NA NA 0 ICP -3.18 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.25 6.03 5.71 0 LCP -3.67

NA NA NA 0 ICP -5.59

NA NA NA 0 HCP -4.86

0.31 8.43 10.14 -1 ICP -2.79

0.95 6.48 6.55 0 LCP -4.9

0.84 3.02 3.27 0 LCP -5

NA NA NA 0 LCP -5.41

0.9 4.95 5.11 0 ICP -5.49 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.95 2.75 2.83 0 LCP -5.53

1 3.04 3.04 0 LCP -5.11

NA NA NA 0 ICP -5.36

0.95 2.21 2.28 0 LCP -4

1.08 3.49 3.38 0 ICP -3.7

1.29 2.64 2.28 0 ICP -5.11 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.94 3.9 3.98 0 LCP -4.04

0.75 4.32 4.73 0 LCP -3.26

1.04 2.58 2.52 0 ICP -4.31

0.42 3.69 4.94 -1 LCP -5.87

NA NA NA 1 ICP -3.68 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.93 2.58 2.68 0 ICP -3.92

NA NA NA 0 ICP -2.03

0.89 3.55 3.71 0 ICP -5.39

1.11 3.02 2.87 0 ICP -4.47

0.85 2.21 2.45 -1 ICP -5.65

7.98 5.89 2.89 1 ICP -3.81 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.89 2.57 2.74 0 ICP -4.1

0.9 5.37 5.53 0 LCP -4.89

NA NA NA 0 LCP -4.93

0.99 2.07 2.09 0 ICP -4.13

1.96 4.62 3.64 1 ICP -5.83

0.8 3.04 3.36 0 LCP -5.03 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

4.97 5.2 2.89 1 LCP -4.89

NA NA NA 0 LCP -5.78

0.44 8.78 9.97 -1 LCP -4.81

NA NA NA 0 LCP -4.83

NA NA NA 0 ICP -5.09

1.1 2.93 2.79 0 ICP -4.03

NA NA NA 0 ICP -4.55

0.9 2.13 2.28 0 ICP -4.39 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.97 2.61 2.65 0 ICP -3.76

0.75 4.63 5.04 0 LCP -5.91

0.09 5.01 8.5 0 LCP -5.64

NA NA NA 0 LCP -4.56

0.81 3.57 3.87 0 ICP -4.55 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.85 3.97 4.19 -1 LCP -3.25

0.89 2.18 2.35 0 ICP -2.95

1.02 3.11 3.09 0 ICP -2.51

1.2 3.9 3.64 0 LCP -4.4 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -3.26

0.99 2.6 2.62 0 LCP -3.78

1.03 2.65 2.61 0 ICP -5.68

0.91 4.63 4.77 -1 LCP -5.68

0.98 4.08 4.11 0 HCP -5.67

NA NA NA 0 ICP -3.95 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.05 4.35 4.28 0 ICP -3.97

0.94 3.45 3.53 0 LCP -4.46

1.1 5.5 5.37 0 ICP -5.71

NA NA NA 0 LCP -5.46

0.93 3.63 3.73 0 ICP -5.05

0.99 2.3 2.31 0 ICP -4.42

0.85 4.32 4.55 0 ICP -5.03 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.1 3.07 2.92 0 ICP -5.53

NA NA NA 0 LCP -3.34

0.9 2.52 2.67 0 LCP -4.41

1.63 3.25 2.54 0 LCP -3.59

NA NA NA 0 ICP -5.71

NA NA NA 0 LCP -2.64

0.74 3.07 3.52 0 LCP -4.97

NA NA NA 0 ICP -2.11 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 HCP -4.33

NA NA NA 0 LCP -3.19

NA NA NA 0 LCP -2.64

NA NA NA 0 ICP -3.83

NA NA NA 0 LCP -4.62

NA NA NA 0 ICP -4.75

NA NA NA 0 ICP -5.45

NA NA NA 0 ICP -5.45

NA NA NA 0 LCP -4.1

NA NA NA 0 ICP -3.91

NA NA NA 0 LCP -4.08

NA NA NA 0 ICP -5.08

NA NA NA 0 ICP -5.34

NA NA NA 0 HCP -6.59

NA NA NA 0 ICP -3.87

NA NA NA 0 HCP -4.21 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.49

NA NA NA 0 LCP -3.69

NA NA NA 0 ICP -4.79

NA NA NA 0 LCP -2.9

NA NA NA 0 ICP -3.8

NA NA NA 0 ICP -4.06

NA NA NA 0 ICP -3.66

NA NA NA 0 ICP -4.07

NA NA NA 0 ICP -3.66

NA NA NA 0 LCP -2.12

NA NA NA 0 ICP -3.75

NA NA NA 0 ICP -5.09

NA NA NA 0 LCP -3.39

NA NA NA 0 ICP -3.45 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.87 2.83 3.03 -1 LCP -3.86

0.83 3.42 3.7 -1 ICP -3.37

NA NA NA 0 LCP -4.18

0.75 2.74 3.15 -1 LCP -3.59

0.97 2.18 2.22 0 LCP -4.72

1.01 2.9 2.89 0 ICP -4.12 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.94 1.99 2.08 0 LCP -3.91

1.15 3.63 3.42 0 LCP -3.59

0.73 8.1 8.55 0 ICP -2.78

0.82 3.76 4.05 -1 ICP -5.22

NA NA NA 0 ICP -4.64

NA NA NA 0 LCP -4.65 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.02 2.71 2.68 0 ICP -5.56

1.04 2.71 2.65 0 ICP -5.5

NA NA NA 0 LCP -3.54

NA NA NA 0 LCP -3.1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -5.36

0.97 2.53 2.58 0 ICP -4.5

NA NA NA 0 ICP -4.87

0.84 3.7 3.95 0 ICP -4.45 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.94 3.47 3.55 -1 ICP -2.64

0.9 3.97 4.13 0 LCP -3.69

0.97 5.41 5.45 -1 ICP -3.46

0.93 2.87 2.98 0 LCP -5.2

1.21 2.92 2.65 0 LCP -5.02 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.39

0.93 2.33 2.43 0 LCP -5.33

0.98 2.47 2.5 0 LCP -5.06

0.88 2.98 3.16 0 LCP -6.08

0.97 4.08 4.12 0 LCP -3.77

0.92 3.6 3.71 0 LCP -5.46

NA NA NA 0 LCP -5.04 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1 3.45 3.44 0 LCP -5.86

NA NA NA 0 LCP -4.64

NA NA NA 0 LCP -4.92

NA NA NA 0 ICP -3.98 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -5.27

0.9 2.95 3.1 0 LCP -5.48

NA NA NA 0 LCP -4.53

NA NA NA 0 LCP -5.69

NA NA NA 0 LCP -5.88

NA NA NA 0 ICP -4.3 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.99 3.26 3.27 0 LCP -5.53

NA NA NA 0 ICP -5.45

NA NA NA 0 ICP -4.46

NA NA NA 0 LCP -4.53

NA NA NA 0 LCP -4.51

1.36 3.85 3.41 0 ICP -4.56 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.87 3.08 3.27 0 LCP -4.33

NA NA NA 0 ICP -3.88

0.42 3.43 4.69 0 ICP -2.46

0.77 4.07 4.45 0 ICP -4.52

0.98 2.78 2.81 -1 LCP -4.33 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -2.7

NA NA NA 0 ICP -3.36

0.94 3.2 3.3 0 LCP -5.97

0.78 5.19 5.55 0 LCP -4.59 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.19 5.78 8.21 -1 LCP -2.15

1.33 2.9 2.49 0 LCP -4.58

2.48 4.44 3.13 0 LCP -4.62

0.98 2.27 2.3 0 LCP -4.81

2.18 3.54 2.42 0 LCP -5.41

1.96 3.45 2.48 1 ICP -4.36 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.72 3.9 3.12 1 LCP -3.43

0.89 3.18 3.35 0 LCP -4.38

1.02 2.63 2.59 0 HCP -5.2

1.14 4.32 4.13 0 ICP -2.3

4.98 5.06 2.74 1 ICP -4.08

1.25 3.05 2.73 0 ICP -4.79

0.97 2.13 2.17 0 ICP -5.13 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.12 2.96 2.8 0 ICP -4.88

1.86 3.62 2.73 1 LCP -4.47

9.18 6.01 2.81 1 LCP -3.73

0.94 2.73 2.82 0 LCP -5.4

NA NA NA 0 ICP -2.59

0.83 2.72 2.99 -1 LCP -3.59 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.97 2.48 2.53 0 ICP -3.97

NA NA NA 0 LCP -5.42

1.32 5.56 5.16 0 HCP -4.94

NA NA NA 0 LCP -2.99

NA NA NA 0 LCP -3.25

0.92 2.46 2.57 0 LCP -5.1 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.15 6.77 6.56 0 LCP -4.11

0.9 3.26 3.41 0 ICP -3.73

1 2.22 2.23 0 LCP -5.66

0.86 2.51 2.73 -1 LCP -4.12

1.01 3.06 3.04 0 LCP -3.18 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.03 3.35 3.3 0 LCP -3.47

0.73 2.62 3.09 -1 LCP -5.7

1.06 2.85 2.76 0 ICP -5.66

1 2.54 2.54 0 ICP -6.16

1.01 6.7 6.69 0 ICP -3.96

NA NA NA 0 ICP -3.93

NA NA NA 0 ICP -4.47 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.03 2.7 2.65 0 ICP -2.2

NA NA NA 0 ICP -3.29

NA NA NA 0 ICP -5.34

NA NA NA 0 ICP -2.87

NA NA NA 0 ICP -4.53

0.9 3.42 3.57 0 LCP -3.74 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.97 2.56 2.61 0 ICP -4.3

0.85 3.57 3.79 0 LCP -4.53

1.91 4.09 3.16 1 LCP -4.87

NA NA NA 0 ICP -5

0.87 2.69 2.88 0 ICP -4.33

0.87 3.83 4.03 0 ICP -4.66

0.99 2.29 2.3 0 ICP -5.9

0.88 3.24 3.42 0 LCP -4.71 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.95 3.63 3.71 0 LCP -4.42

1.03 2.64 2.59 0 LCP -4.72

NA NA NA 0 LCP -3.59

NA NA NA 0 LCP -4.45

NA NA NA 0 LCP -4.22

NA NA NA 0 LCP -3.3

1.05 2.86 2.79 0 ICP -2.7

NA NA NA 0 ICP -4.7 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -6.69

NA NA NA 0 ICP -4.21

NA NA NA 0 LCP -6.57

NA NA NA 0 LCP -4.7

NA NA NA 0 LCP -3.34

0.99 2.64 2.66 0 LCP -3.64

NA NA NA 0 LCP -2.65

1.01 3.84 3.83 0 LCP -4.03 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -3.37

NA NA NA 0 ICP -4.03

NA NA NA 0 LCP -3.19

NA NA NA 0 ICP -3.83

NA NA NA 0 LCP -3.91

NA NA NA 0 LCP -3.84

NA NA NA 0 ICP -4.86

NA NA NA 0 LCP -4.7 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -4.26

NA NA NA 0 LCP -2.86

NA NA NA 0 LCP -5

NA NA NA 0 LCP -2.18

NA NA NA 0 ICP -3.81

NA NA NA 0 LCP -6.44

NA NA NA 0 ICP -3.41

0.91 3.38 3.52 0 LCP -5.68 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -5.02

NA NA NA 0 LCP -5.12

NA NA NA 0 ICP -5.71

NA NA NA 0 ICP -2.13

NA NA NA 0 ICP -5.39

NA NA NA 0 ICP -4.8

NA NA NA 0 LCP -4.96 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -5.38

NA NA NA 0 LCP -5.01

0.81 3.87 4.18 -1 ICP -3.2

NA NA NA 0 LCP -2.9

0.95 3.52 3.59 0 LCP -5.04

NA NA NA 0 ICP -3.91

NA NA NA 0 LCP -5.17 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.49

NA NA NA 0 LCP -5.68

2.33 4.13 2.91 0 LCP -4.24

NA NA NA 0 LCP -4.05

0.94 2.65 2.75 -1 ICP -5.28 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.89 2.62 2.78 0 ICP -2.16

NA NA NA 0 ICP -5.1

1.17 3.4 3.17 0 HCP -4.2

0.88 3.43 3.62 0 LCP -4.25

0.91 3.56 3.7 0 LCP -5.98 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.31

NA NA NA 0 LCP -3.58

1.04 3.91 3.86 0 LCP -2.73

1.06 4.3 4.22 0 LCP -4.28

NA NA NA -1 LCP -2.3

0.89 2.11 2.28 0 ICP -4.92 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.84

1 4.03 4.03 0 LCP -2.88

1 2.74 2.74 0 LCP -2.21

0.79 3.8 4.13 0 LCP -3.39

0.84 4.5 4.76 0 LCP -5.16 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -5.16

0.99 3.25 3.27 0 LCP -4.46

NA NA NA 0 LCP -3.59

0.91 4.26 4.4 0 ICP -4.14

1.08 4.05 3.94 0 LCP -2.59 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -3.79

1.01 2.3 2.29 -1 ICP -4.33

0.92 3.05 3.17 0 LCP -4.59

NA NA NA 0 ICP -3.89

0.51 2.8 3.78 0 LCP -3.76

1.29 6.08 5.71 1 HCP -4.64

0.91 3.04 3.18 0 LCP -3.61 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -5.05

0.9 2.06 2.21 0 LCP -2.61

NA NA NA 0 LCP -2.93

0.78 3.68 4.03 0 LCP -2.94

NA NA NA 0 ICP -4.29

NA NA NA 0 LCP -2.61

0.94 2.81 2.9 -1 ICP -4.69

0.97 2.35 2.39 0 ICP -5.13 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.85 3.23 3.46 -1 LCP -4.65

NA NA NA 0 ICP -4.81

NA NA NA 0 ICP -4.71

NA NA NA 0 LCP -5.36

NA NA NA 0 ICP -5.25

NA NA NA 0 ICP -4.54

NA NA NA 0 ICP -5.42

1.02 2.79 2.76 0 LCP -5.53

NA NA NA 0 LCP -2.55

NA NA NA 0 ICP -4.36

0.39 7.06 8.42 -1 LCP -4.75 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 ICP -2.69

NA NA NA 0 HCP -3.07

0.97 1.95 1.99 -1 HCP -4.38

NA NA NA 0 ICP -3.5

1.37 2.95 2.5 0 LCP -5.35

0.4 9.16 10.5 -1 LCP -2.83

0.42 10.24 11.49 -1 LCP -5.36 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.58 10.9 11.69 0 LCP -5.11

0.89 6.23 6.39 0 ICP -3.8

NA NA NA 0 ICP -4.26

NA NA NA 0 LCP -2.14

NA NA NA 0 LCP -5.38

0.81 3.49 3.79 0 LCP -3.95 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.81 6.33 6.64 0 LCP -4.14

NA NA NA 0 ICP -5.99

NA NA NA 0 LCP -2.2

1.18 4.57 4.33 0 ICP -6.28

1.02 3.85 3.83 0 LCP -5.66

1.83 3.07 2.21 0 LCP -4 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.87 3.19 3.39 0 ICP -5.38

0.79 7.41 7.74 0 ICP -5.97

NA NA NA 0 LCP -5.03

NA NA NA 0 ICP -3.51

0.9 2.3 2.44 0 LCP -5.55

NA NA NA 0 LCP -2.74 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.89

0.87 2.38 2.58 0 LCP -5.17

0.9 2.56 2.71 0 LCP -6.92

1.97 3.46 2.49 1 LCP -3.8

NA NA NA 0 LCP -4.81

1.12 3.67 3.5 0 LCP -4.71

0.89 3.2 3.37 0 LCP -5.25

1.6 3.48 2.81 0 LCP -3.36 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -4.54

NA NA NA 0 LCP -4.81

1 2.77 2.77 0 LCP -2.12

0.98 2.18 2.21 0 HCP -4.22

NA NA NA 0 LCP -3.69

NA NA NA 0 LCP -4.18

NA NA NA 0 ICP -3.7

0.94 2.78 2.86 0 ICP -3.47

0.97 2.94 2.99 0 LCP -5.27 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA 0 LCP -3.98

0.98 2.32 2.34 0 ICP -3.89

NA NA NA -1 ICP -5.54

NA NA NA 0 ICP -3.66

0.9 3.02 3.17 0 LCP -4.25

0.99 2.88 2.89 0 ICP -4.3 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.91 3.5 3.64 0 LCP -5.66

0.98 4 4.03 0 LCP -3.2

0.83 4.09 4.35 0 ICP -3.57

0.95 2.83 2.89 0 ICP -6.42

1.07 2.71 2.61 0 ICP -5.16

0.93 2.77 2.88 0 LCP -5.23 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

NA NA NA -1 LCP -3.14

0.94 4.73 4.82 0 LCP -4.32

NA NA NA 0 LCP -2.59

0.91 2.65 2.79 0 ICP -5.31

NA NA NA 0 LCP -3.47

NA NA NA 0 HCP -4.15 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.81 4.84 5.15 0 LCP -4.63

0.95 3.15 3.21 0 LCP -5.47

NA NA NA 0 LCP -2.22

1.08 2.24 2.13 0 ICP -4.39

0.89 3.59 3.77 0 ICP -4.45

NA NA NA 0 LCP -4.4

0.9 2.31 2.47 0 ICP -4.77

1.03 2.48 2.45 0 LCP -4.94 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.04 2.48 2.42 0 LCP -2.95

NA NA NA 0 ICP -4.02

NA NA NA 0 LCP -3.8

NA NA NA 0 LCP -2.24

1.11 2.96 2.81 0 ICP -5.68

NA NA NA 0 ICP -4.62 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

1.11 4.19 4.04 1 LCP -4.25

1.15 2.94 2.74 1 HCP -3.4

0.88 3.51 3.69 0 LCP -3.85

NA NA NA 0 ICP -2.82

1.71 3.87 3.09 0 LCP -2.02

1.71 3.87 3.09 0 LCP -2.02

NA NA NA 0 LCP -3.99 Supplementary Table S7. List of genes that are heavily methylated in normal liver and become demethylated in HCC cancer_ normal_e direction_ diff_expr cpg diff_meth expr xpr expr

0.96 3.77 3.84 0 LCP -4.98

NA NA NA 0 HCP -2.74

0.76 2.78 3.18 -1 ICP -5.03

1.05 3.38 3.3 0 HCP -2.74