Table 3.
Selected 24 CpG Sites Based on 1,000 three-fold Cross-validations Distinguishing HCC Tumors from Adjacent Tissues with their Mean Methylation Levels in Tumor and Adjacent Tissues and the Differences*
| Symbol | Target ID | Consensus frequency | Mean β in Tumor | Mean β in Adjacent | Mean β difference | Adjusted P Value † | Function |
|---|---|---|---|---|---|---|---|
| BMP4 | cg14310034 | 1,000 | 0.55 | 0.14 | 0.41 | 5.36E-16 | Bone morphogenetic protein 4 |
| C6orf206 | cg04600618 | 985 | 0.44 | 0.16 | 0.28 | 4.08E-09 | Radial spoke head 9 homolog |
| CCDC37 | cg00891278 | 980 | 0.60 | 0.31 | 0.29 | 5.07E-12 | Coiled-coil domain containing 37 |
| CDKL2 | cg24432073 | 1,000 | 0.46 | 0.11 | 0.35 | 8.03E-13 | Cyclin dependent |
| CDKL2 | cg14988503 | 999 | 0.39 | 0.04 | 0.35 | 1.31E-10 | kinase |
| CDKN2A | cg07752420 | 1,000 | 0.49 | 0.20 | 0.30 | 1.92E-11 | Cyclin dependent |
| CDKN2A | cg09099744 | 1,000 | 0.50 | 0.08 | 0.42 | 8.69E-14 | kinase inhibitor |
| CDKN2A | cg10895543 | 1,000 | 0.48 | 0.14 | 0.34 | 2.36E-11 | |
| CDKN2A | cg12840719 | 1,000 | 0.39 | 0.14 | 0.25 | 2.26E-10 | |
| CDKN2A | cg11653709 | 994 | 0.46 | 0.21 | 0.25 | 3.17E-10 | |
| CFTR | cg25509184 | 1,000 | 0.59 | 0.31 | 0.28 | 4.23E-11 | Cystic fibrosis transmembrane conductance regulator |
| DAB2IP | cg05684891 | 1,000 | 0.61 | 0.21 | 0.40 | 3.58E-17 | GTPase-activating protein |
| DNM3 | cg23391785 | 993 | 0.55 | 0.18 | 0.36 | 2.75E-10 | Dynamin 3 |
| HIST1H3G | cg02909790 | 1,000 | 0.49 | 0.17 | 0.32 | 5.28E-10 | H3 histone family |
| HIST1H3J | cg17718302 | 1,000 | 0.37 | 0.05 | 0.31 | 2.36E-08 | H3 histone family |
| NKX6-2 | cg09260089 | 1,000 | 0.43 | 0.13 | 0.30 | 2.59E-10 | NK6 related transcription factor |
| PBX4 | cg19996355 | 999 | 0.47 | 0.15 | 0.32 | 2.46E-09 | Pre-B-cell leukemia homeobox 4 |
| RAB31 | cg17982102 | 988 | 0.38 | 0.14 | 0.24 | 7.14E-10 | Member Ras oncogene family |
| SPDY1 | cg04786857 | 1,000 | 0.55 | 0.19 | 0.36 | 1.79E-14 | Speedy homologue 1 |
| STEAP4 | cg00564163 | 999 | 0.49 | 0.19 | 0.31 | 1.68E-09 | Tumor necrosis factor |
| ZFP41 | cg12680609 | 1,000 | 0.51 | 0.12 | 0.39 | 3.25E-15 | Zinc finger protein 41homologue |
| ZNF154 | cg08668790 | 1,000 | 0.51 | 0.12 | 0.39 | 4.67E-12 | Zinc finger |
| ZNF154 | cg21790626 | 1,000 | 0.51 | 0.08 | 0.43 | 1.14E-12 | protein 154 |
| ZNF540 | cg03975694 | 1,000 | 0.53 | 0.24 | 0.30 | 2.03E-12 | Zinc finger protein 540 |
*
Sites were selected based on a mean difference in methylation levels between tumor and adjacent tissues of at least 20%; more than 60% of tumors have methylation levels greater than 2 standard deviation above the mean in all non tumor tissues and with mean levels of methylation in adjacent tissues <40%
†
After Bonferroni adjustment