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 Mills, Andrea Califano, Pavel Sumazin

Research output: Contribution to journalArticle

43 Citations (Scopus)

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 - Jan 1 2015
Externally publishedYes

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MicroRNAs
Breast Neoplasms
Benchmarking
RNA
Cell Line
Messenger RNA
Proteins

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Chiu, H. S., Llobet-Navas, D., Yang, X., Chung, W. J., Ambesi-Impiombato, A., Iyer, 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

Cupid : Simultaneous reconstruction of micrornatarget and cerna networks. / Chiu, Hua Sheng; Llobet-Navas, David; Yang, Xuerui; Chung, Wei Jen; Ambesi-Impiombato, Alberto; Iyer, Archana; Kim, Hyunjae Ryan; Seviour, Elena G.; Luo, Zijun; Sehgal, Vasudha; Moss, Tyler; Lu, Yiling; Ram, Prahlad; Silva, José; Mills, Gordon; Califano, Andrea; Sumazin, Pavel.

In: Genome Research, Vol. 25, No. 2, 01.01.2015, p. 257-267.

Research output: Contribution to journalArticle

Chiu, HS, Llobet-Navas, D, Yang, X, Chung, WJ, Ambesi-Impiombato, A, Iyer, A, Kim, HR, Seviour, EG, Luo, Z, Sehgal, V, Moss, T, Lu, Y, Ram, P, Silva, J, Mills, G, Califano, A & Sumazin, P 2015, 'Cupid: Simultaneous reconstruction of micrornatarget and cerna networks', Genome Research, vol. 25, no. 2, pp. 257-267. https://doi.org/10.1101/gr.178194.114
Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A et al. Cupid: Simultaneous reconstruction of micrornatarget and cerna networks. Genome Research. 2015 Jan 1;25(2):257-267. https://doi.org/10.1101/gr.178194.114
Chiu, Hua Sheng ; Llobet-Navas, David ; Yang, Xuerui ; Chung, Wei Jen ; Ambesi-Impiombato, Alberto ; Iyer, Archana ; Kim, Hyunjae Ryan ; Seviour, Elena G. ; Luo, Zijun ; Sehgal, Vasudha ; Moss, Tyler ; Lu, Yiling ; Ram, Prahlad ; Silva, José ; Mills, Gordon ; Califano, Andrea ; Sumazin, Pavel. / Cupid : Simultaneous reconstruction of micrornatarget and cerna networks. In: Genome Research. 2015 ; Vol. 25, No. 2. pp. 257-267.
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