Clinical Epigenetics

Table 4 List of the 13 CpG methylation signatures for GBM IDH mutant versus IDH WT in the training set and validation set (GSE36278)

From: DNA methylation signatures for 2016 WHO classification subtypes of diffuse gliomas

			Training set (TCGA cohort)					Validation set (GSE36278 cohort)
No.	CpG ID	Gene name	Average β in mutant	Average β in WT	∆β = (avg β in mutant−avg β in WT)	p value	FDR	Average β in mutant	Average β in WT	∆β = (avg β in mutant−avg β in WT)	p value	FDR
1	cg02629106	PCDP1	0.845	0.113	0.732	0.00093	0.00163	0.76	0.18	0.58	4E−08	2.6E−07
2	cg03539765	LOC144571	0.746	0.127	0.618	0.00093	0.00163	0.63	0.18	0.45	2.7E−07	5.9E−07
3	cg08173692	PRR18	0.791	0.091	0.699	0.00093	0.00163	0.79	0.24	0.54	9.1E−06	1.1E−05
4	cg10366093	YPEL4	0.710	0.189	0.520	0.00102	0.00163	0.67	0.25	0.42	1.2E−06	2.3E−06
5	cg12662576	NA	0.780	0.172	0.608	0.00125	0.00163	0.76	0.29	0.48	2.7E−07	5.9E−07
6	cg15198101	SRRM3	0.695	0.109	0.586	0.00102	0.00163	0.79	0.15	0.64	1.7E−08	2.2E−07
7	cg15389472	GLUL	0.786	0.162	0.624	0.00184	0.00184	0.66	0.24	0.42	8.6E−06	1.1E−05
8	cg15454486	OBFC2A	0.823	0.231	0.592	0.00125	0.00163	0.71	0.32	0.39	3.1E−06	4.5E−06
9	cg16264705	ATP5G2	0.665	0.132	0.533	0.00167	0.00181	0.74	0.23	0.51	2.4E−07	5.9E−07
10	cg16725050	TUBA4B	0.769	0.214	0.556	0.00125	0.00163	0.78	0.32	0.46	2.7E−07	5.9E−07
11	cg16917193	NA	0.736	0.150	0.586	0.00138	0.00163	0.72	0.23	0.49	1.1E−05	1.2E−05
12	cg21000447	CHADL	0.626	0.077	0.549	0.00125	0.00163	0.70	0.19	0.51	3.1E−06	4.5E−06
13	cg25664381	NA	0.808	0.166	0.642	0.00138	0.00163	0.66	0.22	0.44	0.00016	0.00016

NA not associated with any gene

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