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Table 3 List of the 14 CpG methylation signatures for oligodendroglioma (ODG) versus diffuse astrocytoma (DA) 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 ODG Average β in DA β = (avg β in ODG−avg β in DA) p value FDR Average β in ODG Average β in DA β = (avg β in ODG−avg β in DA) p value FDR
1 cg00873351 CD300LB 0.755 0.227 0.528 1.67E−32 3.9E−32 0.576 0.225 0.351 1.92E−22 2.99E−22
2 cg03492827 NA 0.647 0.192 0.455 8.18E−34 5.73E−33 0.701 0.286 0.415 3.01E−26 2.11E−25
3 cg04437966 FLJ37543 0.500 0.088 0.412 3.99E−33 1.39E−32 0.459 0.102 0.357 2.33E−25 8.16E−25
4 cg07250222 FGFR2 0.753 0.186 0.567 8.68E−30 8.68E−30 0.795 0.301 0.494 5.03E−21 7.04E−21
5 cg07847030 TCF7L1 0.730 0.163 0.567 6.78E−31 1.06E−30 0.798 0.368 0.429 2.62E−19 2.62E−19
6 cg07893801 PLCG1 0.807 0.312 0.495 1.28E−32 3.59E−32 0.737 0.378 0.359 1.61E−20 2.04E−20
7 cg08935418 PTPRN2 0.735 0.231 0.505 6.25E−30 6.73E−30 0.771 0.313 0.458 4.01E−23 7.53E−23
8 cg09772154 FGFR2 0.733 0.194 0.540 5.94E−30 6.73E−30 0.779 0.308 0.472 6.35E−20 6.84E−20
9 cg10363569 PRKAG2 0.675 0.162 0.513 5.1E−30 6.5E−30 0.574 0.196 0.377 5.22E−20 6.09E−20
10 cg12210255 NA 0.662 0.139 0.523 2.53E−33 1.18E−32 0.699 0.237 0.462 1.8E−24 5.05E−24
11 cg13412754 MAPKAP1 0.782 0.311 0.471 4.67E−32 9.34E−32 0.736 0.340 0.396 1.74E−25 8.1E−25
12 cg13598010 NA 0.778 0.175 0.603 1.89E−34 2.65E−33 0.790 0.254 0.536 5.09E−27 7.13E−26
13 cg19093820 GPR156 0.210 0.716 −0.506 3.56E−31 6.23E−31 0.211 0.655 −0.444 4.3E−23 7.53E−23
14 cg23759393 PTPRN2 0.722 0.203 0.518 1.08E−30 1.51E−30 0.790 0.300 0.490 8.76E−24 2.04E−23
  1. NA not associated with any gene