Table 1.
List of genes commonly silenced by DNA hypermethylation in primary hepatocellular carcinoma tumor samples
| Gene | Cellular function | Freq | Ref. |
| 14-3-3 ε | Cell cycle, mitogenic signaling | 89% | [47] |
| APC | Cell proliferation, migration, apoptosis | 44%-71% | [48-52] |
| ARHI | Cell proliferation and invasion | 47% | [53] |
| ASS | Cell cycle and cell invasion | - | [54] |
| BASP1 | Apoptosis | 50% | [55] |
| BLU | Apoptosis | 81% | [56] |
| CADM1 | Cell adhesion and cell differentiation | 41% | [57] |
| CASP8 | Apoptosis | 34% | [58] |
| CAV1 | Cell cycle and proliferation | 56% | [59] |
| CCND2 | Cell cycle | 24%-68% | [48,50] |
| CDH1 | Cell adhesion and metastasis | 34% | [52] |
| CDKN2A | Cell cycle | 30%-70% | [49,50,60,61] |
| CFTR | Intercellular transport | 77%-98% | [50,62] |
| CHFR | Cell cycle, protein degradation | 35% | [63] |
| COX-2 | Immune response, cell migration | 35% | [64] |
| CSRP1 | Cell proliferation and differentiation | 56% | [59] |
| DKK1 | Cell proliferation | 36% | [52] |
| DKK3 | Cell differentiation, embryonic development | - | [65] |
| DLC-1 | Cell proliferation | 24%-35% | [52,66] |
| DLEC1 | Cell proliferation | 71% | [67] |
| E2F1 | Cell proliferation, migration, and differentiation | 71% | [68] |
| FAM43B | Cell proliferation | 60% | [69] |
| FBLN1 | Cell adhesion and migration | 50% | [70] |
| FHIT | Cell proliferation and apoptosis | 65% | [56] |
| GSTP1 | Cell metabolism and detoxification | 70%-76% | [50,60,61,71] |
| HAI-2/PB | Cell proliferation and invasion | 80% | [72] |
| HDPR1 | Cell proliferation, differentiation, cellular signaling | 51% | [73] |
| HINT1 | Apoptosis | 55% | [74] |
| IGFBP-3 | Cell proliferation and growth | 33% | [75] |
| KL | Cell proliferation and growth | 81% | [76] |
| KLK10 | Cell proliferation, survival, and cellular signaling | 55% | [77] |
| LIFR | Signal transduction | 48% | [78] |
| MAGE-A1 | Cell differentiation, embryonic development | 53% | [79] |
| MAGE-A3 | Cell differentiation, embryonic development | 74% | [79] |
| MAT1A | Cell metabolism | 85% | [80] |
| MT1G | Cell proliferation and apoptosis | 60% | [81] |
| MTM1 | Cell differentiation | 100% | [82] |
| MTSS1 | Cell migration and metastasis | 80% | [83] |
| MUC2 | Immune system | 62% | [84] |
| NORE1B | Cell proliferation and growth | 62% | [85] |
| NQO1 | Cell metabolism | 50% | [86] |
| OXGR1 | Cell growth and metabolism | 78% | [77] |
| p14ARF | Cell proliferation and apoptosis | 40%-42% | [68,71] |
| p15INK4B | Cell cycle | 22%-61% | [71,87] |
| P16 | Cell cycle | 37%-83% | [48,71,87] |
| P21 | Cell cycle | 63% | [68] |
| P27 | Cell cycle | 48% | [68] |
| P300 | Cell proliferation and differentiation | 68% | [68] |
| P53 | Cell proliferation, apoptosis, and DNA repair | 14% | [68] |
| P73 | DNA repair and apoptosis | 35% | [71] |
| PCDH10 | Cell adhesion and migration | 76% | [88] |
| PER3 | DNA repair | 60% | [89] |
| PRDM2 | Cell metabolism | - | [90] |
| PTEN | Cell proliferation and migration | 16%-22% | [87,91] |
| RASSF1A | Cell proliferation, migration, and apoptosis | 64%-88% | [48,51] |
| RB | Cell cycle, apoptosis | 24%-32% | [68,87] |
| RECK | Cell invasion and metastasis | 55% | [92] |
| RELN | Cell adhesion | 37% | [93] |
| RIZ1 | Cell proliferation and apoptosis | 29%-67% | [48,94,95] |
| RUNX-3 | Apoptosis | 38%-48% | [50-52] |
| SFRP1 | Cell proliferation and differentiation | 37%-45% | [51,52,96] |
| SFRP2 | Cell proliferation and differentiation | 48%-54% | [97] |
| SFRP5 | Cell proliferation and differentiation | 39% | [96] |
| SLIT2 | Cell migration | 83% | [98] |
| SOCS1 | Cell growth and survival | 39%-72% | [9,48,90,99] |
| SOX1 | Cell proliferation | 57% | [100] |
| SOX17 | Cell differentiation and embryonic development | 82% | [101] |
| SPARC | Cell growth and invasion | 75% | [102] |
| SPINT2 | Cell proliferation and growth | 60% | [50] |
| SRD5A2 | Cell proliferation and androgenic physiology | 50% | [55] |
| Survivin | Apoptosis and cell proliferation | 33% | [58] |
| TFPI2 | Matrix remodelling | 47% | [103] |
| TIP30 | Apoptosis and metastasis | 47% | [104] |
| UCHL1 | Cell metabolism and protein degradation | 44% | [105] |
| UNC5C | Cell migration | 26% | [106] |
| Vimentin | Cell migration and signaling | 56% | [107] |
| WIF-1 | Cell proliferation | 49%-61% | [52,65,108] |
| WT1 | Cell proliferation and survival | 54% | [68] |
| ZHX2 | Cell proliferation, differentiation, and development | 47% | [109] |
Freq: Frequency of hypermethylation.