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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

From: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

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
  1. 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
  2. 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