Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, China;
Mol Cell Proteomics. 2013 Nov;12(11):3379-87. doi: 10.1074/mcp.O112.019851. Epub 2013 Aug 7.
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, ProteoMirExpress, 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.
微小 RNA（miRNAs）通过翻译抑制和 RNA 降解来调节基因表达。最近开发的高通量蛋白质组学方法可在蛋白质水平上测量基因表达变化，因此可以揭示 miRNAs 翻译抑制的直接作用。在这里，我们介绍了一个名为 ProteoMirExpress 的网络服务器，它将蛋白质组学和 mRNA 表达数据集成在一起，以推断 miRNA 为中心的调控网络。使用用户提供的两种类型的高通量数据，ProteoMirExpress 不仅能够发现 mRNA 减少的 miRNA 靶标，还能够发现其蛋白质受到抑制但 mRNA 没有显著变化的靶标亚组，或者发现其 mRNA 减少但其蛋白质没有显著变化的靶标亚组，这些靶标亚组通常被大多数当前方法所忽略。此外，还可以检测 miRNA 的直接和间接靶标。因此，ProteoMirExpress 提供了更全面的 miRNA 为中心的调控网络。我们使用了一些已发表的数据来评估我们推断的网络的质量，并证明了我们服务器的价值。ProteoMirExpress 可在线使用，对学术用户免费开放。
