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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
  1. NA not associated with any gene