Fig. 5

Chromatin accessibility profiles in HDF after vemurafenib treatment. Stimulation was done with 2 µM of vemurafenib (PLX4032, or PLX for short), or analog volume of vehicle (DMSO), for the indicated duration. A The UpSet plot shows the number of accessibility peaks identified for each condition. The bar plot below shows the annotation of over-represented biological processes for the genes within the subsets of peaks that are not detected after different time-points of stimulation with vemurafenib. The significance threshold for biological over-representation (q < 0.05) is indicated by the dashed red line. B Scatter plot showing the fold changes (FC) in chromatin accessibility for 21,800 peaks after vemurafenib treatment in comparison to the corresponding time-matched DMSO control. The FDR adjusted significance of the changes (q-value) for every region are represented by the level of transparency of the corresponding points, with significantly increased or reduced accessibility regions (q < 0.1) colored in red and blue, respectively. C Enriched transcription factor binding motifs within promoter peaks, after 18 h of stimulation with vemurafenib in comparison to DMSO control. Enrichment is estimated for binned sets of peaks, based on their FC in chromatin accessibility, as indicated by the top annotation of the heatmaps (purple: bins of peaks with higher accessibility under DMSO, green: bins of peaks with higher accessibility under vemurafenib). The heatmaps display the levels of enrichment (left) and significance (right) for each motif. The dendrogram represents the clustering of the motifs based on their sequence similarity