Table 2.
Selected 23 genes as potential master-regulators prioritized according to the level of differential gene expression in different cancer stages and in metastatic cancer and also according to the level of the differential DNA methylation in cancer versus control sets
| Master molecule name | Gene symbol | Meth probes: Illumina ID | correl | logFC I_stage vs. Normal | Cancer_vs_Normal logFC | Meth_logFC | Number of target TFsa | Master-regulator Score |
|---|---|---|---|---|---|---|---|---|
| MKP-2 | DUSP4 | cg13635007 | − 0.018 | 1.694 | 2.309 | −0.408 | 13 | 0.751 |
| c-Myc | MYC | cg00163372 | −0.498 | 2.126 | 2.442 | −0.682 | 13 | 0.725 |
| IL-17A | IL17A | cg11924517 | −0.145 | 1.083 | 0.889 | −0.747 | 13 | 0.649 |
| MT1-MMP | MMP14 | cg05931439 | −0.212 | 0.793 | 1.439 | −0.486 | 13 | 0.619 |
| eNOS | NOS3 | cg08018731 | −0.059 | 1.460 | 1.958 | −0.631 | 13 | 0.560 |
| TGFbeta-2A | TGFB2 | cg06899755 | −0.171 | 0.645 | 0.946 | 0.296 | 13 | 0.556 |
| IGF-2 | IGF2 | cg02425416 | −0.025 | 0.760 | 1.353 | −0.419 | 13 | 0.517 |
| col1A1 | COL1A1 | cg18618815 | −0.142 | 1.340 | 2.085 | −0.428 | 13 | 0.502 |
| Matrin | MMP7 | cg01813071 | −0.055 | 4.505 | 4.814 | −0.367 | 13 | 0.498 |
| CTLA-4 | CTLA4 | cg08460026 | −0.110 | 0.892 | 1.022 | −0.699 | 13 | 0.496 |
| amphiregulin-NTF | AREG | cg02334660 | −0.438 | 1.649 | 1.711 | −0.644 | 13 | 0.494 |
| alpha-enolase | ENO1 | cg06972019 | −0.405 | 0.783 | 1.148 | −0.653 | 13 | 0.480 |
| CXCR2 | CXCR2 | cg06547715 | 0.005 | 1.156 | 1.036 | −0.570 | 13 | 0.479 |
| calcitonin | CALCA | cg01421342 | 0.052 | 0.834 | 1.043 | 0.309 | 13 | 0.455 |
| IRAK-2 | IRAK2 | cg09386682 | −0.419 | 1.292 | 1.614 | −0.444 | 13 | 0.446 |
| WT1 | WT1 | cg01952234 | −0.227 | 0.412 | 1.004 | 0.346 | 13 | 0.415 |
| IL-11 | IL11 | cg26367719 | 0.082 | 1.789 | 2.039 | −0.568 | 13 | 0.401 |
| Wnt-2 | WNT2 | cg07697895 | 0.128 | 2.171 | 2.494 | 0.288 | 13 | 0.385 |
| CD86b | CD86 | cg00697440 | 0.141 | −0.153 | 0.105 | −0.584 | 13 | 0.384 |
| GROalpha | CXCL1 | cg00419314 | −0.145 | 3.922 | 3.903 | −0.313 | 11 | 0.378 |
| trip6 | TRIP6 | cg00374672 | −0.292 | 0.949 | 1.356 | −0.610 | 11 | 0.363 |
| mgat5 | MGAT5 | cg20063095 | −0.209 | 0.570 | 1.162 | −0.459 | 13 | 0.343 |
| Fcgamma RIIIB | FCGR3B | cg04567009 | 0.048 | 1.709 | 1.727 | −0.573 | 11 | 0.284 |
a 13 target TFs: AML1a, E2F-6, Fra-2, GR-alpha, HMGI-C, HMGIY, HNF-3beta, HNF-4gamma, ITF-2-A-, SEF2-1A, TGIF, c-Myc, IPF-1; 11 target TFs: AML1a, E2F-6, Fra-2, GR-alpha, HMGI-C, HMGIY, HNF-3beta, HNF-4gamma, TGIF, c-Myc, IPF-1
b CD89 did not achieve statistical significant levels of gene expression Fold Changes but was selected here due to its highly significant level of methylation Fold Change