Figure 3.

Changes in CAMs gene expression due to BAP1 reexpression. A, Scatter plots showing fold change mRNA expression values for BAP1 mutant versus BAP1 reexpression or BAP1 mutant versus BAP1 wild-type comparisons from four independent datasets (14, 53) for the KEGG CAMs gene set. Red dots indicate genes with log₂ fold changes greater than 1 and BHFDR value of less than 0.05. B, A BAP1-mutant uveal melanoma cell line (53) was transfected with wild-type or mutant BAP1 to produce proficient and deficient reexpressing samples, respectively. Each of the mutant reexpressing and parental samples were compared against the wild-type reexpressing samples. Rank list plots showing the fold change values for genes in the KEGG CAMs pathway for parental (left), mutant A95P reexpressing (middle), and mutant C91W reexpressing (right) samples compared against BAP1 wild-type reexpressing samples. C, Expression of BAP1 in BAP1 mutant cell cline, MP46, was confirmed by Western blot analysis, and protein expression of E-cadherin decreased in MP46-BAP1 cells. MP46-GFP was used as a control. Representative Western blots from triplicate experiments are shown.