Fig. 4: Differential DNA methylation, expression, and mutation patterns in BPDCN subtypes C1 and C2.
a Top part of the heatmap shows mutational patterns of 14 genes previously identified as significantly enriched between the two clusters [6]. The bottom part shows beta values (DNA methylation levels) of CpG sites where an absolute mean difference above 0.25 was observed between C1 and C2. b Volcano plot of beta values showing log2 fold-changes and p values with gene annotations for significantly different CpGs (p < 0.0001). c Gene set enrichment analysis results of DNA methylation data against REACTOME gene sets (p < 0.05). d Volcano plot of expression profiles showing log2 fold-changes and p values with gene annotations for significant differentially expressed tumor suppressors genes, oncogenes, and genes involved in cell adhesion/cell cycle (p < 0.0001). e Gene set enrichment analysis of RNA-seq data against REACTOME gene sets (padj < 0.001, absolute enrichment >0.3). f Transcription factors with significantly different inferred activity (p < 0.05) in C1 (light blue) and C2 (dark blue). g Pathway activities in C1 (light blue) and C2 (dark blue) with significantly different pathway activities shown in red font (p < 0.05). h, i FFPE-ATAC-seq estimates of chromatin accessibility for CDK6 and STAT5A for four BPDCN cases belonging to subcluster C1. CDK6 is located on the minus strand and STAT5B on the plus strand, respectively.
