Fig. 5

Comparison of IFNγ and ERK-induced gene expression for M230 and M238 melanoma lines. (A) Plot showing the overlap of different ERK-regulated (M230_ERK and M238_ERK) and IFNγ-regulated (M230_IFNγ and M238_IFNγ) gene sets defined by differential expression analysis. (B) Schematic showing how the different gene lists were derived for calculating overlaps and enriched gene sets. (C) Table showing the number of differentially expressed genes in each subset for the M230 and M238 melanoma lines. These gene sets were used to determine the pathway and transcription factor binding site enriched in each subset. Heatmaps were generated using the negative log10 of adjusted P-values for a union set of the top 10 enriched (D) reactome pathways and (E) transcription factor (TF) binding sites for each subset. All M230 gene sets are labeled in green and M238 in purple color text. (F) Heatmaps showing the FPKM expression values for 24 stress response genes for each sample in the M230 (left panel) and M238 (right panel) melanoma lines. The two columns per sample represent data from two independent experiments. See also Figs S10-S12 and Supplementary Table 3