Figure 5

Gene expression profiling reveals altered RNA metabolism and developmental transcriptomic signatures in BAP1-deficient uveal melanoma cells. (a) Gene expression heatmap generated in Partek of significantly altered genes (P < 0.01) in BAP1-deficient stable cells compared to control stable cells after 4 weeks of shRNA expression. (b) The top six gene ontology categories represented by the significantly changing genes in BAP1-deficient cells. Significant Analysis of Microarrays (SAM) was performed and a cutoff of q < 10% was used to determine the most highly significant genes. Three of the genes in the ubiquitin system category are deubiquitinases (DUBs). (c) The top nine categories represented after gene set enrichment analysis (GSEA) of BAP1-deficient cells using a threshold of P < 0.005. GSEA was performed using a pre-ranked file generated after SAM analysis.