Figure 5

DMG and H3-WT patients have different methylation patterns of homeobox genes. (A) Heatmap representation of the significant differentially methylated probes comparing H3-WT (blue; N = 4) and H3K27M DMG (purple; N = 28). The beta value is a range between 0–1 with 0 (blue) being unmethylated, 1 (red) methylated and 0.5 (white). (B) Volcano plot of the differentially methylated probes comparing H3-WT midline gliomas and H3K27M DMG samples, where the x-axis is the log₂-fold change (logFC) and y-axis the adjusted p-value (log₁₀ scaled). Probes are highlighted as not significant (black), logFC > =|1| (blue), adjusted p-value < 0.05 (red) and both logFC > =|1| and adjusted p-value < 0.05 (green). Genes with a positive fold-change are more methylated and a negative fold-change is more unmethylated in H3-WT compared to H3K27M DMG samples. The three significantly differentially methylated EZHIP probes (unmethylated H3-WT) are labelled and significant homeobox family genes that were significantly differently methylated (methylated H3-WT) are also highlighted. (C) Relative TPM expression (y-axis) for each sample of the HOX family genes that were identified as differentially methylated between H3-WT (blue) and H3K27M DMG (purple) samples (NS = not significant) (D) GO enrichment analysis significant results from the significantly differentially methylated probes. The x-axis is the adjusted p-value (log₁₀ scaled), and the y-axis is the GO term. GO enrichment terms are coloured according to; biological processes (pink), cellular components (green) and molecular function (blue).