Fig. 4
From: High-throughput validation of ceRNA regulatory networks
Statistical evaluation. We plot p-values and average fold changes of target ceRNA expression following silencing of their predicted regulators, compared to silencing of all other genes in both BRCA and PRAD ceRNETs, at two profiling time points in a MCF7 and b PC3 cells. Results for targets with six or more perturbed ceRNA regulators are shown. To estimate p values for each ceRNA target, we collected all tested regulators and compared average fold-change responses following silencing of inferred ceRNA regulators (FCpos) vs. silencing of all other genes (FCneg) in the network; see Figs. 1, 2 and 3 for illustrative example cancer genes. In total, 91% and 92% (50% and 47% significantly, at p < 0.05 by U test) of ceRNA targets, predicted in breast and prostate cancer, were downregulated in response to ceRNA regulator silencing in MCF7 and PC3, respectively. In total, 342 tested ceRNA targets were significantly down-regulated and none were significantly up-regulated. Comparing the number of targets with significantly low FCpos and FCneg fold changes by Mann–Whitney U-test suggests an FDR < 0.01 for overall network validation