Chiu et. al., Genome Research 2014
Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions.
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. 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.
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