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

Kel, Alexander; Boyarskikh, Ulyana; Stegmaier, Philip; Leskov, Leonid S.; Sokolov, Andrey V.; Yevshin, Ivan; Mandrik, Nikita; Stelmashenko, Daria; Koschmann, Jeannette; Kel-Margoulis, Olga; Krull, Mathias; Martínez-Cardús, Anna; Moran, Sebastian; Esteller, Manel; Kolpakov, Fedor; Filipenko, Maxim; Wingender, Edgar

doi:10.1186/s12859-019-2687-7

BMC Bioinformatics

Table 3 Selected set of 47 potential DNA methylation biomarkers

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

ID	CHR	Position (hg19)	Gene symbol (gene)	Methylation Caner_vs_Control LogFC	Expression Cancer_vs_Control logFC	Correlation	Enriched TF^a	Master-regulator^b
cg02612618	19	22,018,605	ZNF43	0.296	−0.711	−0.743	+
cg07945582	7	26,206,579	NFE2L3	−0.534	2.858	−0.518	+
cg00163372	8	128,752,988	MYC	−0.682	2.442	−0.498	+	+
cg02915837	12	3,069,243	TEAD4	−0.306	2.335	−0.453	+
cg02334660	4	75,312,483	AREG	−0.644	1.711	−0.438		+
cg09386682	3	10,207,069	IRAK2	−0.444	1.614	−0.419		+
cg06972019	1	8,937,448	ENO1	−0.653	1.148	−0.405		+
cg01777575	20	22,566,140	FOXA2	−0.332	1.312	−0.307	+
cg19377250	7	100,463,206	TRIP6	−0.712	1.356	−0.292		+
cg01952234	11	32,457,130	WT1	0.346	1.004	−0.227		+
cg05931439	14	23,305,957	MMP14	−0.486	1.439	−0.212		+
cg20063095	2	134,977,141	MGAT5	−0.459	1.162	−0.209		+
cg17726575	2	11,606,945	E2F6	−0.420	1.259	−0.204	+
cg18696576	6	34,203,630	HMGA1	−0.328	1.758	−0.190	+
cg06899755	1	218,520,325	TGFB2	0.296	0.946	−0.171		+
cg01742897	18	53,257,019	TCF4	0.184	0.021	−0.166	+
cg15555970	18	3,452,317	TGIF1	−0.294	1.511	−0.161	+
cg00419314	4	74,735,092	CXCL1	−0.313	3.903	−0.145		+
cg11924517	6	52,050,597	IL17A	−0.747	0.889	−0.145		+
cg18618815	17	48,275,324	COL1A1	−0.428	2.085	−0.142		+
cg08460026	2	204,732,474	CTLA4	−0.699	1.022	−0.110		+
cg00425708	12	66,217,779	HMGA2	−0.284	1.016	−0.105	+
cg08018731	7	150,687,961	NOS3	−0.631	1.958	−0.059		+
cg01813071	11	102,401,616	MMP7	−0.367	4.814	−0.055		+
cg02425416	11	2,163,808	IGF2	−0.419	1.353	−0.025		+
cg13635007	8	29,210,154	DUSP4	−0.408	2.309	−0.018		+
cg07330438	21	37,258,460	RUNX1	−0.556	1.525	−0.011	+
cg06547715	2	218,990,976	CXCR2	−0.570	1.036	0.005		+
cg08836542	2	28,618,831	FOSL2	−0.386	−0.027	0.006	+
cg02059626	8	76,319,264	HNF4G	−0.365	−0.209	0.026	+
cg04567009	1	161,600,769	FCGR3B	−0.573	1.727	0.048		+
cg01421342	11	14,995,754	CALCA	0.309	1.043	0.052		+
cg26367719	19	55,875,605	IL11	−0.568	2.039	0.082		+
cg01830294	7	116,963,492	WNT2	0.132	2.494	0.128		+
cg01664670	20	39,316,308	MAFB	0.280	−0.226	0.140	+
cg01824511	14	38,064,456	FOXA1	−0.430	−0.768	0.141	+
cg00697440	3	121,795,768	CD86	−0.584	0.105	0.141		+
cg01589587	14	76,002,440	BATF	−0.416	1.028	0.222	+
cg24093411	5	133,449,651	TCF7	0.387	2.022	0.321	+
cg02991571	13	28,501,126	PDX1	0.541	2.869	0.353	+
cg06613263	5	142,779,552	NR3C1	−0.588	−0.931	0.410	+
cg03130910	1	234,908,226	BMP3	−1.107	−2.482	0.601
cg05259836	6	74,290,516	PYY	−0.813	−5.604	0.601
cg24032190	15	67,442,893	ADH1B	−1.071	−3.781	0.603
cg04786142	1	234,908,381	NR5A2	−1.075	−1.644	0.606
cg03800922	6	74,290,220	CA1	−0.842	−6.934	0.610
cg26541218	7	47,826,387	KLF4	−0.771	−1.938	0.617

^aThe column “Enriched TF” marks genes that encode TFs whose sites found enriched around CpG loci
^bThe column “Master regulator” marks genes that encode master-regulator molecules identified in the study

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com