CupidTool
Cupid: simultaneous reconstruction of miRNA-target and ceRNA networks
...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. Likelihoods for each predictive feature are computed based on a positive gold standard set.
Step 3: Cupid assesses whether inferred targets compete for predicted miRNA regulators.