ProteoMirExpress: Inferring MicroRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data

Jing Qin, Mulin Jun Li, Panwen Wang, Nai Sum Wong, Maria P. Wong, Zhengyuan Xia, George S.W. Tsao, Michael Q. Zhang, Junwen Wang

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein level and therefore can reveal the direct effects of miRNAs' translational repression. Here, we present a web server, ProteoMir- Express, that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks. With both types of high-throughput data from the users, ProteoMirExpress is able to discover not only miRNA targets that have decreased mRNA, but also subgroups of targets with suppressed proteins whose mRNAs are not significantly changed or with decreased mRNA whose proteins are not significantly changed, which are usually ignored by most current methods. Furthermore, both direct and indirect targets of miRNAs can be detected. Therefore, ProteoMirExpress provides more comprehensive miRNA-centered regulatory networks. We used several published data to assess the quality of our inferred networks and prove the value of our server. ProteoMirExpress is available online, with free access to academic users.

Original languageEnglish (US)
Pages (from-to)3379-3387
Number of pages9
JournalMolecular and Cellular Proteomics
Volume12
Issue number11
DOIs
StatePublished - Nov 2013

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology

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