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

doi:10.1101/gr.178194.114

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 journal › Article › peer-review

89 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 language	English
Pages (from-to)	257-267
Number of pages	11
Journal	Genome Research
Volume	25
Issue number	2
DOIs	https://doi.org/10.1101/gr.178194.114
State	Published - 1 Feb 2015

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10.1101/gr.178194.114

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title = "Cupid: Simultaneous reconstruction of micrornatarget and cerna networks",

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.",

author = "Chiu, {Hua Sheng} and David Llobet-Navas and Xuerui Yang and Chung, {Wei Jen} and Alberto Ambesi-Impiombato and Archana Iyer and Kim, {Hyunjae Ryan} and Seviour, {Elena G.} and Zijun Luo and Vasudha Sehgal and Tyler Moss and Yiling Lu and Prahlad Ram and Jos{\'e} Silva and Mills, {Gordon B.} and Andrea Califano and Pavel Sumazin",

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year = "2015",

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doi = "10.1101/gr.178194.114",

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TY - JOUR

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T2 - Simultaneous reconstruction of micrornatarget and cerna networks

AU - Chiu, Hua Sheng

AU - Llobet-Navas, David

AU - Yang, Xuerui

AU - Chung, Wei Jen

AU - Ambesi-Impiombato, Alberto

AU - Iyer, Archana

AU - Kim, Hyunjae Ryan

AU - Seviour, Elena G.

AU - Luo, Zijun

AU - Sehgal, Vasudha

AU - Moss, Tyler

AU - Lu, Yiling

AU - Ram, Prahlad

AU - Silva, José

AU - Mills, Gordon B.

AU - Califano, Andrea

AU - Sumazin, Pavel

PY - 2015/2/1

Y1 - 2015/2/1

N2 - 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.

AB - 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.

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Cupid: Simultaneous reconstruction of micrornatarget and cerna networks

Abstract

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