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Fig. 6 | Cell Communication and Signaling

Fig. 6

From: Dynamic transcriptome analysis reveals signatures of paradoxical effect of vemurafenib on human dermal fibroblasts

Fig. 6

Relation of chromatin accessibility and gene expression changes in HDF after vemurafenib treatment. A Multivariate regression models for gene-sets (KEGG pathways) showing a significant relation between gene expression changes after vemurafenib treatment, with the changes in accessibility of promoter peaks (log2 FC ATAC), and the length of stimulation (TP). The plot shows the standardized β coefficients of the independent variables for each regression models. The size of every dot represents the significance of each coefficient, and the whiskers indicate the SE. The plot only shows those gene-sets where the model, and the β coefficients are significant (q < 0.05, and p < 0.05, respectively). B Distribution of accessibility peaks within DEGs (q < 0.05), after different durations (indicated on top of the plot) of stimulation with vemurafenib in comparison to DMSO control. C Sequence logo for the motifs identified within accessibility peaks located in, or nearby DEGs. The stimulation time with vemurafenib, and the number of occurrences of each motif is indicated on top of the logo. D Accessibility within promoter regions and transcription start sites (TSS) of DEGs (q < 0.05). For each stimulation time-point (indicated in brackets) the heatmaps display the coverage of ATAC-seq reads (left, and middle), and the fold changes in accessibility (FC acc.) in vemurafenib- (PLX, for short) treated HDF, compared to DMSO control. The FC in gene expression (FC exp.) is indicated as a left annotation for each stimulation time-point. Top annotations show the mean coverage along promoter regions for each of the defined clusters (red: closed, green: permissive, blue: open)

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