Cupid: Simultaneous reconstruction of micrornatarget and cerna networks

Hua Sheng Chiu, David Llobet-Navas, Xuerui Yang, Wei Jen Chung, Alberto Ambesi-Impiombato, Archana Iyer, Hyunjae Ryan Kim, Elena G. Seviour, Zijun Luo, Vasudha Sehgal, Tyler Moss, Yiling Lu, Prahlad Ram, José Silva, Gordon B. Mills, Andrea Califano, Pavel Sumazin

Research output: Contribution to journalArticlepeer-review

81 Scopus citations


We introduce a method for simultaneous prediction of microRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA-target prediction accuracy as assessed by both mRNA and protein level measurements. Our biochemical assays support nearly 500 microRNA-target interactions with evidence for regulation in breast cancer tumors. Moreover, these assays constitute the most extensive validation platform for computationally inferred networks of microRNA-target interactions in breast cancer tumors, providing a useful benchmark to ascertain future improvements.

Original languageEnglish (US)
Pages (from-to)257-267
Number of pages11
JournalGenome Research
Issue number2
StatePublished - Feb 1 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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