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 journalArticle

    45 Scopus citations

    Abstract

    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
    Volume25
    Issue number2
    DOIs
    StatePublished - Feb 1 2015

    ASJC Scopus subject areas

    • Genetics
    • Genetics(clinical)

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    Chiu, H. S., Llobet-Navas, D., Yang, X., Chung, W. J., Ambesi-Impiombato, A., Iyer, A., Kim, H. R., Seviour, E. G., Luo, Z., Sehgal, V., Moss, T., Lu, Y., Ram, P., Silva, J., Mills, G. B., Califano, A., & Sumazin, P. (2015). Cupid: Simultaneous reconstruction of micrornatarget and cerna networks. Genome Research, 25(2), 257-267. https://doi.org/10.1101/gr.178194.114