Table 3. Top 10 hyper-methylated DNA methylated regions based on 10% difference between Cancer and Control (-1000 ≤ distance to transcription start site [TSS] ≤ +1000 base-pair DNA).
| Gene | Regions | DMR location | Distance To TSS | Methylation Difference | Gene Name or Role | |||
|---|---|---|---|---|---|---|---|---|
| Start | End | % | p | q | ||||
| PCNXL3 | CDS | 65,402,926 | 65,403,007 | -774 | 39.49 | 3.20E-13 | 1.63E-11 | Homeostasis/metabolism phenotype |
| MIR4285 | Utr5 | 101,936,380 | 101,936,461 | 13 | 38.53 | 4.00E-07 | 2.85E-06 | MicroRNA 4285 |
| NLGN2 | CDS | 7,311,698 | 7,311,857 | 198 | 34.28 | 9.29E-05 | 2.72E-04 | Mediates cell-cell interactions and modulates insulin secretion |
| MIR3648 | Utr5 | 9,825,819 | 9,826,028 | 0 | 33.93 | 5.21E-21 | 3.53E-18 | MicroRNA 3648 |
| HOXA4 | CDS | 27,169,637 | 27,170,022 | 378 | 31.68 | 2.04E-03 | 3.40E-03 | Sequence-specific DNA binding transcription factor activity |
| CLDN23 | CDS | 8,560,299 | 8,560,499 | 635 | 31.19 | 1.56E-04 | 4.17E-04 | Structural molecule activityidentical protein binding |
| TONSL | CDS | 145,661,276 | 145,661,402 | -275 | 31.03 | 3.44E-10 | 7.12E-09 | Transcription corepressor activity |
| GNAS | Promoter | 57,464,802 | 57,465,121 | 624 | 28.79 | 3.48E-04 | 8.05E-04 | Insulin-like growth factor receptor binding |
| TUBB8 | Intron | 95,010 | 95,073 | 106 | 27.79 | 4.90E-04 | 1.07E-03 | Structural constituent of cytoskeleton |
| MIR1247 | Promoter | 102,028,543 | 102,0l28,738 | 857 | 27.63 | 5.44E-05 | 1.75E-04 | MicroRNA 1247 |
Note: CDS: coding DNA sequence; Utr5: five prime untranslated.