Cupid: simultaneous reconstruction of miRNA-target and ceRNA networks

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:

o  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.

o  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.

o  Step 3: Cupid assesses whether inferred targets compete for predicted miRNA regulators.



o  Hua-Sheng Chiu*, David Llobet-Navas*, et. al., Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Research. 2015 Feb;25(2):257-67

o  Pavel Sumazin*, Xuerui Yang*, Hua-Sheng Chiu*, et. al., An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 2011 Oct 14;147(2):370-81

o  Hua-Sheng Chiu*, María Rodríguez Martínez*, et. al., Genomic alterations dysregulate cancer genes by modulating microRNA activity. (in revision)



Ø   Download Cupid v1.0 and its user guide

Ø   Download Cupid poster presented in Symposia on Cancer Research 2014 Illuminating Genomic Dark Matter "NcRNA in Disease and Cancer"




Regulatory Circuits Lab @ Texas Children’s Hospital (affiliated with Baylor College of Medicine)

1102 Bates Ave (Feigin Center), Houston, Texas 77030

Contact: Dr. Pavel Sumazin or Dr. Hua-Sheng Chiu
Last update:
7/2/2015 10:39:34 AM


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