Supplementary Table S6 from BAP1 Loss Is Associated with DNA Methylomic Repatterning in Highly Aggressive Class 2 Uveal Melanomas

BAP1KDvsWT_HyperMethDecGE: All significantly hypermethylated probes from hypermethylated/downregulated genes (p < 0.05) with an absolute value (log2(RNA fold change)) > 1 and absolute value (methylation Delta Beta value) > 0.01 in BAP1KDvsWT 92.1 and Mel202 cells. BAP1KDvsWT_HypoMethIncGE: All significantly hypomethylated probes from hypomethylated/upregulated genes (p < 0.05) with an absolute value (log2(RNA fold change)) > 1 and absolute value (methylation Delta Beta value) > 0.01 in BAP1KDvsWT 92.1 and Mel202 cells. BAP1KD_HyperMethDecGE_ChrLoc: Chromosomal loci enriched (FDR < 0.05) for hypermethylated/downregulated genes in BAP1KDvsWT 92.1 and Mel202 cells. BAP1KD_HypoMethIncGE_ChrLoc: Chromosomal loci enriched (FDR < 0.05) for hypomethylated/upregulated genes in BAP1KDvsWT 92.1 and Mel202 cells. BAP1KD_HyperMethDecGE_KEGG: Functional (KEGG and REACTOME) pathways enriched (FDR < 0.05) for hypermethylated/downregulated genes in BAP1KDvsWT 92.1 and Mel202 cells. BAP1KD_HypoMethIncGE_KEGG: Functional (KEGG and REACTOME) pathways enriched (FDR < 0.05) for hypomethylated/upregulated genes in BAP1KDvsWT 92.1 and Mel202 cells. BAP1KD_TCGA_HyperMethDecGE_Gene: All significantly hypermethylated probes (FDR < 0.05) from hypermethylated/downregulated genes shared in common between the shBAP1KD (p < 0.05) and TCGA (FDR < 0.05) datasets. BAP1KD_TCGA_HypoMethIncGE_Gene: All significantly hypomethylated probes (FDR < 0.05) from hypomethylated/upregulated genes shared in common between the shBAP1KD (p < 0.05) and TCGA (FDR < 0.05) datasets.