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

BMC Bioinformatics

Table 1 The final list of 19 TFs after filtering according to their differential expression as well as differential DNA methylation and the level of correlation with the methylation in the associated CpG loci

Ensembl	TF gene symbol	TF protein name	correl	logFC I_stage vs. Control	logFC Cancer vs. Control	Methylation logFC Cancer vs. Control	CMA NEG_200bp	CMA POS_200bp	CMAcorrel_500bp	F-Match NEG_200bp	F-Match POS_200bp
ENSG00000198521	ZNF43	ZNF43	−0.763	− 0.706	− 0.711	0.296	+
ENSG00000257591	ZNF625	ZNF625	−0.667	−0.461	− 0.365	0.558	+
ENSG00000136997	MYC	c-Myc	−0.567	2.126	2.442	−0.682			+
ENSG00000197905	TEAD4	TEF-3	−0.453	1.829	2.335	−0.589			+		+
ENSG00000139515	PDX1	IPF-1	−0.407	2.565	2.869	0.541				+	+
ENSG00000125798	FOXA2	HNF-3beta	−0.364	0.821	1.312	−0.332	+	+
ENSG00000177426	TGIF1	TGIF	−0.282	1.003	1.511	−0.294	+				+
ENSG00000204103	MAFB	MafB	−0.244	−0.678	− 0.226	0.280		+
ENSG00000149948	HMGA2	HMGI-C	−0.242	0.533	1.016	−0.284		+			+
ENSG00000137309	HMGA1	HMGIY	−0.220	1.422	1.758	−0.328	+	+
ENSG00000169016	E2F6	E2F-6	−0.204	0.793	1.259	−0.420	+
ENSG00000196628	TCF4	ITF-2	−0.166	−0.429	0.021^a	0.332		+
ENSG00000159216	RUNX1	AML1	−0.057	0.911	1.525	−0.556	+
ENSG00000075426	FOSL2	Fra-2	−0.050	−0.559	− 0.027^a	−0.386	+			+
ENSG00000164749	HNF4G	HNF-4gamma	0.064	−0.708	− 0.209	− 0.365	+	+
ENSG00000129514	FOXA1	HNF-3alpha	0.183	−1.296	−0.768	− 0.430	+	+
ENSG00000156127	BATF	B-ATF	0.222	0.607	1.028	−0.416		+
ENSG00000176842	IRX5	IRX2a	0.355	0.890	1.155	0.400		+	+	+
ENSG00000113580	NR3C1	GR	0.548	−1.331	−0.931	− 0.588	+	+	+

^a The LogFC was not significant for the full Cancer vs Control comparison, but was highly significant for the Cancer stage I vs Control

ISSN: 1471-2105