Table 3. Comparison of cumulative methylation levels of multiple CpG sites in each gene using different models.
| Gene | Model A | Model B | Model C | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cumulative methylation level | F | P | P | Cumulative methylation level | F | P | P | Cumulative methylation level | F | P | P | |||||||||||||
| N (n=10) | A (n=43) | T (n=43) | N vs. A | A vs. T | N vs. T | N (n=10) | A (n=43) | T (n=43) | N vs. A | A vs. T | N vs. T | N (n=10) | A (n=43) | T (n=43) | N vs. A | A vs. T | N vs. T | |||||||
| APC | 0.108 | 0.118 | 0.199 | 6.739 | 0.034 | 0.355 | 0.405 | 0.04 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| BNIP3 | 6.902 | 8.833 | 8.041 | 9.57 | 0.008 | 0.045 | 0.031 | 1 | 1.251 | 2.505 | 2.579 | 18.411 | <0.001 | <0.001 | 1 | <0.001 | 1.251 | 2.505 | 2.579 | 18.411 | <0.001 | <0.001 | 1 | <0.001 |
| BRCA1 | 22.537 | 22.669 | 20.809 | 14.314 | 0.001 | 1 | <0.001 | 0.475 | 10.075 | 9.99 | 9.038 | 32.385 | <0.001 | 1 | <0.001 | 0.001 | 0.88 | 0.898 | 0.896 | 6.655 | 0.036 | 0.03 | 1 | 0.114 |
| CCND1 | 0.134 | 0.144 | 0.133 | 7.392 | 0.025 | 0.265 | 0.033 | 1 | 0.004 | 0.008 | 0.008 | 8.725 | 0.013 | 0.013 | 1 | 0.017 | 0.004 | 0.008 | 0.008 | 8.725 | 0.013 | 0.013 | 1 | 0.017 |
| CDKN2A | 5.913 | 6.941 | 7.23 | 15.116 | 0.001 | 0.055 | 0.001 | 1 | 1.718 | 2.183 | 2.662 | 10.386 | 0.006 | 0.102 | 0.009 | 1 | 0.352 | 0.905 | 1.68 | 20.527 | <0.001 | <0.001 | 1 | <0.001 |
| HTATIP2 | 0.363 | 0.525 | 0.527 | 8.63 | 0.013 | 0.01 | 1 | 0.052 | 0.082 | 0.155 | 0.17 | 16.578 | <0.001 | <0.001 | 1 | <0.001 | 0.082 | 0.155 | 0.17 | 16.578 | <0.001 | <0.001 | 1 | <0.001 |
| ITGAV | 0.614 | 0.715 | 0.722 | 10.101 | 0.006 | 0.005 | 1 | 0.013 | 0.029 | 0.059 | 0.065 | 14.9 | 0.001 | 0.003 | 1 | <0.001 | 0.029 | 0.059 | 0.065 | 14.9 | 0.001 | 0.003 | 1 | <0.001 |
| NFKB1 | 0.687 | 0.777 | 0.942 | 1.731 | 0.421 | - | - | - | 0.007 | 0.042 | 0.058 | 14.347 | 0.001 | 0.001 | 1 | 0.001 | 0.007 | 0.042 | 0.058 | 14.347 | 0.001 | 0.001 | 1 | 0.001 |
| PIK3R1 | 1.291 | 1.357 | 1.969 | 2.422 | 0.298 | - | - | - | 0.057 | 0.153 | 0.213 | 22.693 | <0.001 | <0.001 | 0.576 | <0.001 | 0.041 | 0.142 | 0.204 | 25.481 | <0.001 | <0.001 | 0.376 | <0.001 |
| PRDM16 | 9.155 | 13.202 | 20.756 | 35.643 | <0.001 | 0.003 | 0.001 | <0.001 | 6.724 | 10.686 | 18.062 | 36.8949 | <0.001 | 0.003 | <0.001 | <0.001 | 5.86 | 9.867 | 17.251 | 37.181 | <0.001 | 0.002 | <0.001 | <0.001 |
| PTEN | 0.381 | 0.534 | 1.666 | 5.182 | 0.075 | - | - | - | 0.374 | 0.53 | 1.659 | 4.886 | 0.087 | - | - | - | 0.374 | 0.53 | 1.659 | 4.886 | 0.087 | - | - | - |
| PTX3 | 0.468 | 1.053 | 1.649 | 0.947 | 0.623 | - | - | - | 0.301 | 0.222 | 0.391 | 6.239 | 0.044 | 0.125 | 1 | 0.037 | 0.03 | 0.222 | 0.391 | 6.239 | 0.044 | 0.125 | 1 | 0.037 |
| RASSF1 | 2.535 | 3.482 | 8.962 | 3.598 | 0.165 | - | - | - | 1.804 | 2.71 | 6.898 | 2.871 | 0.238 | - | - | - | 1.803 | 2.71 | 6.898 | 2.871 | 0.238 | - | - | - |
| SOCS1 | 1.328 | 2.321 | 2.391 | 3.888 | 0.143 | - | - | - | 0.085 | 0.276 | 0.316 | 5.436 | 0.066 | - | - | - | 0.084 | 0.276 | 2.338 | 5.436 | 0.066 | - | - | - |
| TAP2 | 5.712 | 5.719 | 5.362 | 32.904 | <0.001 | 1 | <0.001 | 0.003 | 2.369 | 2.325 | 2.152 | 44.501 | <0.001 | 0.301 | <0.001 | <0.001 | - | - | - | - | - | - | - | - |
N: healthy control tissues; A: remote normal-appearing tissues; T: cancer tissue