Fig. 5

Identification of 14 CpG probe methylation signatures in training set (TCGA) for diffuse astrocytoma (DA) and oligodendroglioma (ODG). a Plot demonstrating classification error for 2817 CpG probes from PAM analysis in training set. The threshold value of 9.491 corresponded to 14 discriminatory CpG probes which classified DA (LGG IDH Mut with intact 1p/19q; n = 131) and ODG (LGG IDH Mut with 1p/19q codel; n = 86) LGG samples with classification error of 0.93%. b Heat map of the 14 CpG discriminatory probes identified from the PAM analysis between DA and ODG patient samples in the training set (TCGA). A dual color code was used where yellow indicates more methylation (hypermethylation) and blue indicates less methylation (hypomethylation). c PCA was performed using beta (methylation) values of 14 PAM-identified CpG probes between DA (n = 131) and WT (n = 86) LGG samples in training set. A scatter plot is generated using the first two principal components for each sample. The color code of the samples is as indicated. d The detailed cross-validation probabilities of 10-fold cross-validation for the samples of training set based on the beta values of 14 CpG probes are shown. For each sample, its probability as ODG (red color) and DA (green color) is shown and it was predicted by the PAM program as either ODG or DA in LGG samples based on which grade’s probability is higher. The original histological grade of the samples is shown on the top