Fig. 3

Contribution of genomic features exposes differential chromatin modifications using VPA and SAHA. a, b Distribution plots show the read count (log2 read abundance determined by edgeR) compared with fold change (log2FC). Transcripts subject to significant change are shown in red (adjusted P < 0.05) and non-significant change shown in black for cells exposed to VPA and SAHA. For each transcript, the fold change between RNA-seq data sets from stimulated and unstimulated cells was plotted against the combined read count for the corresponding gene. Significant differences in mRNA levels are shown in red and non-significant change shown in black for VPA- and SAHA-stimulated cells. The overlap of genomic features and regions of differential histone modification in VPA and SAHA exposed cells are also shown. ChIP-seq peaks were analysed for genomic features using odds ratio testing compared to ChIP input data selected as reference. VPA-stimulated genomic features are shown for c H3K9/14ac, d H3K4me3 and e H3K9me3. SAHA-stimulated genomic features are shown for f H3K9/14ac, g H3K4me3 and h H3K9me3