Fig. 3: Global characterization of chromatin structure and its relationship with gene expression.

A Commonality of histone marks, open chromatin regions and gene expression patterns between samples. Color scale represents the percentage of patients sharing a particular genomic element status. Bar height represents a number of genomic elements (scaled to 100%). B Venn diagram shows intersection of the promoter regions marked by H3K4me3, H3K27ac and open chromatin sites detected with ATAC-seq. C Evolutionary conservation of the identified promoters (green) and enhancers (purple) measured by PhastCons 100-Way scores. Mean scores for the identified regulatory regions are compared to mean scores obtained for random genomic intervals. P values were calculated with one-sided Mann–Whitney U test. Data are represented as boxplots in which the box shows the quartiles of the dataset, the middle line is the median and the whiskers extends to the largest or smallest value no further than 1.5 × the inter-quartile range. D Correlation between H3K4me3 (green), H3K27ac (purple) and transcript expression. Normalized ChIP-seq coverage is plotted against an expression level of transcripts of protein coding genes, divided into quantiles. Data are represented as violin plots with a nested boxplot, where shape indicates the distribution of data. The box shows the quartiles of the dataset, the middle white dot is the median, whiskers extend to 1.5 × IQR past the low and high quartiles. E Hierarchical clustering of samples based on gene expression profiles. Shades of blue indicate tumor grade (from light = normal brain to dark = Grade IV and black PG). In the table on the right side the subtype of glioblastoma samples (GBM) is reported as well as assignment of glioma samples to one of Pan Glioma RNA Expression Clusters (LGr) as well as IDH1 gene mutation status (IDH). F Correlation between H3K27ac ChIP-seq coverage on enhancers and transcript expression. Numbers above bars indicate numbers of enhancers in each group. The p value has been estimated empirically as explained in “Methods”.