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 Alpha-2-macroglobulin-like protein 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 gene 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 light 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-actin-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 Ankyrin 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 enzyme 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 nucleotide 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-