Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks

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 p...

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Detalles Bibliográficos
Autores principales: 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 B., Califano, Andrea, Sumazin, Pavel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315299/
https://www.ncbi.nlm.nih.gov/pubmed/25378249
http://dx.doi.org/10.1101/gr.178194.114
Descripción
Sumario: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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