Regulome Explorer analysis, TCGA data retrieval, and functional enrichment analysis

The Regulome Explorer tool is freely available at http://explorer.cancerregulome.org/. It contains gene expression, DNA methylation, CNVs, SNPs, miRNA expression, and clinical data for the samples available through TCGA (http://cancergenome.nih.gov/) on July 2016. The analysis was performed with 333 PCa clinical samples. Using a gene name (or more), the tool retrieves all the data that significantly correlate with the data available for the query gene(s). Statistical significance of each pairwise association (i.e., LSD1 vs. all and DNMT1 vs. all) is assessed using rank-ordered data and a statistical test appropriate to each data type pair, e.g., Fisher’s test (categorical-categorical), F statistic (continuous-continuous), and ANOVA (continuous-categorical). The top 20 significantly correlated genes were used to query the freely accessible cBioPortal tool to query the TCGA provisional (491 samples under “All Complete Tumors”) and Metastatic Michigan (61 samples under “tumors with sequencing and CNA”) data (http://www.cbioportal.org/index.do). Functional enrichment analysis was run with the Broad’s molecular signature database (http://software.broadinstitute.org/gsea/index.jsp) with a false discovery rate (FDR) < 0.05.