ProteoMirExpress: inferring microRNA-centered regulatory networks from high-throughput proteomic and transcriptome data

Abstract

MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein levels, and therefore can reveal the direct effects of miRNAs’ translational repression. Here, we present a web server, ProteoMirExpress that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks. With both high throughput data from the users, ProteoMirExpress is able to discover not only miRNA targets that have mRNA decreased, but also subgroups of targets whose proteins are suppressed but mRNAs are not significantly changed or whose mRNAs are decreased but proteins are not significantly changed, which were 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 use several published data to assess the quality of our inferred networks and prove the value of our server. ProteoMirExpress is available at http://jjwanglab.org/ProteoMirExpress, with free access to academic users.