Additional file 1: Tables S1-S5. of High-throughput validation of ceRNA regulatory networks

Inferred ceRNA networks. Predicted interactions in the two tumor contexts: Table S1. for BRCA, and Table S2. for PRAD. Each table describes the coupled ceRNA pair, confidence level in the interaction, number of mediating miRNAs, and the identity of miRNA mediators. Tables S3-4. MCF7 and PC3 LINCS fold changes, describing gene-expression responses to perturbagens. For each LINCS gene profiled at a given time point after each perturbation, we provide the number of replicates (Luminex plates), observed fold change relative to control, and the standard error across plates. Table S5. BRCA and PRAD ceRNET validation using LINCS data. For each LINCS gene profiled at a given time point, we list (1) the number of predicted regulators that were silenced, (2) the size of the control set, which includes the gene’s profiling after shRNA-mediated silencing of genes that were not predicted to target it, (3) observed and expected U-statistics, (4) and Z-statistics and associated the p-values obtained from them. For each interaction at a given time point, we list the target fold change in response to the perturbation, and the percentile rank when comparing target fold changes to fold changes of all other profiled genes in response to the perturbation. We also provide the identity of shRNA hairpins used. (PDF 1kb)