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Cupid: simultaneous reconstruction of
miRNA-target and ceRNA networks |
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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. 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"” References: o
Hua-Sheng Chiu*, María
Rodríguez Martínez* et al. 2018. The number of titrated microRNA species dictates
ceRNA regulation. Nucleic Acids
Research (accepted). o
Hua-Sheng Chiu et
al. 2017. High-throughput
validation of ceRNA regulatory networks. BMC Genomics 18: 418. 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 |
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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
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