Extended Data Fig. 6: PRC2 target DNAme underlies the classification of GBM tumors by bulk DNAme.
From: Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states
a, Two-dimensional representation of single cells assigned to previously described LGm classes39, visualized as triangle plots (where each vertex corresponds to one LGm class) across 7 GBM samples (n = 867 cells [malignant and non-malignant] that passed quality control based on scDNAme). Mean DNAme at promoters of PRC2 targets46 (top), mean DNAme at promoters of housekeeping genes1, and number of tiles per cell (bottom) are overlaid for each triangle plot. b, Comparison between mean genome wide DNAme (defined as the mean DNAme across windows of 1,000 bp around 450K array probes, Methods) and mean DNAme at promoters (TSS ± 1Kb) of PRC2 targets46 for the 478 TCGA GBM samples that were classified as LGm4-6 by Ceccarelli et al.39. LGm classes assignment for each sample is shown. c, Left: mean genome wide DNAme for TCGA GBM samples (n = 478) previously classified as either LGm4, LGm5, or LGm6 by Ceccarelli et al.39 Right: mean DNAme at promoters (TSS ± 1Kb) of PRC2 targets46 for TCGA GBM samples (n = 478) previously classified as either LGm4, LGm5, or LGm6 by Ceccarelli et al.39. P values were determined by two-sided Mann-Whitney U test (c). Boxplots represent the median, bottom and upper quartiles, whiskers correspond to 1.5 times the interquartile range.
