CupidTool
Cupid: simultaneous reconstruction of miRNA-target and ceRNA networks
...We showed that our integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines.
Cupid is implemented in 3 steps:
Step 1: re-evaluate candidate miRNA binding sites in 3’ UTRs, as inferred by TargetScan, miRanda and PITA by integrating their scores, location in the 3’ UTR, and cross-species conservation.
Step2: interactions are predicted by integrating information about selected sites, their multiplicity, and the statistical dependency between the expression profiles of miRNA and putative targets. ...