A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

(A) Determining the optimal method(s) (most sensitive and specific) to infer miRNA-mediated regulation from coexpressed genes. The methods tested were (1) Weeder coupled to miRvestigator (Weeder–miRvestigator) (black line), (2) enrichment of PITA-predicted miRNA target genes (blue line), (3) enrichment of TargetScan-predicted target genes (green line), (4) enrichment of miRSVR-predicted target genes (orange line), and (5) enrichment of miRanda-predicted target genes (red line). (B) Overlap of coexpression signatures between putative miRNA regulators predicted by the three methods (Weeder–miRvestigator, PITA, and TargetScan) in FIRM. Pairwise overlap of coexpression signatures between methods is statistically significant (Weeder–miRvestigator vs. PITA: 0.045; Weeder–miRvestigator vs. TargetScan: 0.019; PITA vs. TargetScan: 7.4 × 10⁻²²). All three methods identified miR-29a/b/c as the regulator for the lung adenocarcinoma coexpression signature AD Lung Beer 31.