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

BMC Bioinformatics

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 TFs^a	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
CD86^b	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

ISSN: 1471-2105