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Table 1 List of the 14 CpG methylation signatures for LGG IDH mutant versus IDH WT in the training set and validation set (GSE58218)

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

    Training set (TCGA cohort) Validation set (GSE58218 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 cg00976453 KCNB1 0.795 0.037 0.758 1.31E−27 1.67E−27 0.806 0.162 0.644 1.18E−19 1.38E−19
2 cg02423318 NA 0.860 0.096 0.764 9.56E−28 1.67E−27 0.876 0.167 0.709 7.35E−21 2.87E−20
3 cg03300177 GNAO1 0.841 0.063 0.777 9.78E−28 1.67E−27 0.839 0.171 0.667 1.47E−20 2.95E−20
4 cg05866411 FGFRL1 0.784 0.102 0.682 8.35E−28 1.67E−27 0.681 0.208 0.473 3.96E−20 5.54E−20
5 cg07355841 TPPP3 0.835 0.055 0.781 1.25E−27 1.67E−27 0.819 0.184 0.635 1.93E−20 3.38E−20
6 cg08231710 MMP23A 0.874 0.127 0.747 9.35E−28 1.67E−27 0.809 0.293 0.516 1.47E−18 1.58E−18
7 cg08442798 NA 0.772 0.023 0.749 8.35E−28 1.67E−27 0.824 0.090 0.734 5.43E−21 2.87E−20
8 cg10064339 UCP2 0.779 0.042 0.737 8.35E−28 1.67E−27 0.805 0.115 0.690 8.82E−21 2.87E−20
9 cg10504751 GNAO1 0.846 0.067 0.779 1.23E−27 1.67E−27 0.846 0.173 0.673 2.61E−20 4.06E−20
10 cg11302533 NA 0.784 0.037 0.747 1.8E−27 1.94E−27 0.834 0.102 0.732 1.19E−20 2.87E−20
11 cg12565681 RHBDF2 0.834 0.053 0.781 1.44E−27 1.68E−27 0.822 0.295 0.527 5.87E−18 5.87E−18
12 cg20564913 FGFRL1 0.837 0.108 0.729 8.94E−28 1.67E−27 0.832 0.222 0.610 1.23E−20 2.87E−20
13 cg25499397 GPR62 0.822 0.076 0.746 8.35E−28 1.67E−27 0.798 0.272 0.527 1.12E−19 1.38E−19
14 cg25813864 RAPGEFL1 0.851 0.064 0.787 2.64E−27 2.64E−27 0.855 0.160 0.695 9.37E−21 2.87E−20
  1. NA not associated with any gene