MOESM1 of DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation

Additional file 1: Table S1. Numbers of genes in three datasets Absher, Kirby and TCGA (with overlap) that can be assigned to the four groups of regulation patterns, based on DNA methylation of the probes and expression of the associated gene: UPUP (gain of methylation — upregulated expression), UPDOWN (gain of methylation — downregulated expression), DOWNUP (loss of methylation — upregulated expression) and DOWNDOWN (loss of methylation — downregulated expression). Table S2. Number of genes, associated with multiple probes, in Absher, Kirby and TCGA datasets for all four established groups of gene regulation patterns: UPUP, UPDOWN, DOWNUP and DOWNDOWN. Genes that are associated with both hypermethylated and hypomethylated probes are defined as inconsistent and indicated in the table. Table S3. Probes in TCGA combined methylation/gene expression dataset for UPUP-only and UPDOWN-only groups that can be assigned to different groups, according to their probe DNA methylation and associated gene expression correlation. In addition, number of genes, associated with the probes in each correlation group, are displayed. Table S4. Number of probes in the TCGA methylation dataset for UPUP-only and UPDOWN-only groups that are located in different distances from the TSSs of the associated genes. Table S5. Number of probes in the TCGA DNA methylation dataset for UPUP-only and UPDOWN-only regulation pattern groups that are located in CGIs, their shores, shelves or all locations. Number of genes that the probes can be associated with is also displayed. Table S6. Top 10 most significantly hypermethylated genes in UPUP-only and UPDOWN-only regulation pattern groups. Figure S1. Hypermethylated probes associated with genes following UPUP-only and UPDOWN-only are located 50 to 2000 bp upstream or downstream from the TSS of the genes. Figure S2. UCSC Genome Browser window for the gene GSC (Goosecoid) together with methylation fold changes for each visualized position in the same order.