Fig. 2
Comparison of the transcriptomic effects of vemurafenib on HDF and MaMel cells. A Venn diagram showing the number of DEGs (q < 0.05) on BRAFV600E mutant malignant melanoma cells (MaMel21 and MaMel63a) and BRAFWT HDF cells after 18 h and 24 h of treatment with 2 µM of vemurafenib, respectively. B UpSet plot showing the number of up- and down-regulated genes for each cell line. The subsets of genes that are affected in an inverse direction in HDF and MaMel cells are highlighted in red. C Pearson correlation of the log2 fold changes (FC) within the subset of commonly deregulated genes in all the studied cell lines (n = 456). The duration of the stimulation for each cell line is indicated in parenthesis. D Dot plot of significantly over-represented biological processes (q < 0.1) within the subsets of negatively correlated DEGs in HDF and MaMel cells. The size of every dot represents the number of DEGs within every process. The level of transparency of the dots corresponds to the ratio of the number of DEGs to the total number of genes within every gene set. E Heatmap displaying the genes with the highest significant fold changes within the subset of commonly deregulated genes in all the studied cell lines. Fold change values of vemurafenib-treated cells with respect to DMSO control are depicted by a colorimetric scale (red: up-regulated, blue: down-regulated). F Correlation matrix of the FC after vemurafenib treatment in different BRAFV600E positive melanoma cell lines and HDF, for the subsets of negatively correlated DEGs in HDF and MaMel cells (n = 268). The correlation level is annotated and represented by the colorimetric scale. Only significant correlations (p < 0.05) are colored. The stimulation time and inhibitor concentration applied to each cell line is indicated in parenthesis