Fig 2: Expression profiles of CHL-1, A375, and MEL224 cell lines with transfected GLI1, GLI2 and GLI3. (A) MDS plot of A375 cell line. (B) Upset plot of differentially expressed genes across all cell lines and GLI proteins. (C) Heatmap of expression of top DEGs sorted by logFC across all cell lines. (D) Gene enrichment analysis of DEGs across cell lines, transfection with GLI1-3 vs. control. Upper half of the plot shows KEGG pathway analysis, while the lower part shows categories of diseases. On x-axis: normalized enrichment scores. Size of the circles denote ratio of DE genes in pathways. Color denotes significance, with gray and blue circles denoting non-significant enrichments and red denotes significant enrichment.

Fig 3: HH-GLI pathway activity in melanoma cell lines. (A) Western blot analysis of relative protein expression levels of GLI1, GLI2, GLI3 and PTCH1 in a panel of 14 melanoma cell lines. FL refers to the full-length protein, while R refers to the repressor form. (B) Average gene expression of GLI1, GLI2, GLI3 and PTCH1 relative to the housekeeping gene RPLP0 summarized according to the mutational background of the tested panel of melanoma cell lines. (C) Heatmap showing MTT proliferation assay on 14 melanoma cell lines. Cells were treated with three different HH-GLI pathway inhibitors in five doses, during 24, 48 and 72 h. Green color indicates high cell viability and red color indicates low viability (cell death). The uncropped blots are shown in File S1.