Vila-Casadesús Maria, Gironella Meritxell, Lozano Juan José
Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.
Gastrointestinal and Pancreatic Oncology Group, Hospital Clínic of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.
PLoS One. 2016 Mar 11;11(3):e0151127. doi: 10.1371/journal.pone.0151127. eCollection 2016.
MicroRNAs (miRNAs) are small RNAs that regulate the expression of target mRNAs by specific binding on the mRNA 3'UTR and promoting mRNA degradation in the majority of cases. It is often of interest to know the specific targets of a miRNA in order to study them in a particular disease context. In that sense, some databases have been designed to predict potential miRNA-mRNA interactions based on hybridization sequences. However, one of the main limitations is that these databases have too many false positives and do not take into account disease-specific interactions. We have developed an R package (miRComb) able to combine miRNA and mRNA expression data with hybridization information, in order to find potential miRNA-mRNA targets that are more reliable to occur in a specific physiological or disease context. This article summarizes the pipeline and the main outputs of this package by using as example TCGA data from five gastrointestinal cancers (colon cancer, rectal cancer, liver cancer, stomach cancer and esophageal cancer). The obtained results can be used to develop a huge number of testable hypotheses by other authors. Globally, we show that the miRComb package is a useful tool to deal with miRNA and mRNA expression data, that helps to filter the high amount of miRNA-mRNA interactions obtained from the pre-existing miRNA target prediction databases and it presents the results in a standardised way (pdf report). Moreover, an integrative analysis of the miRComb miRNA-mRNA interactions from the five digestive cancers is presented. Therefore, miRComb is a very useful tool to start understanding miRNA gene regulation in a specific context. The package can be downloaded in http://mircomb.sourceforge.net.
微小RNA（miRNA）是一类小RNA，它们通过特异性结合mRNA的3'非翻译区（3'UTR）来调控靶mRNA的表达，并且在大多数情况下会促进mRNA的降解。为了在特定疾病背景下研究miRNA，了解其特定靶标通常很有意义。从这个意义上讲，一些数据库已被设计用于基于杂交序列预测潜在的miRNA-mRNA相互作用。然而，主要限制之一是这些数据库存在太多假阳性结果，并且没有考虑疾病特异性相互作用。我们开发了一个R包（miRComb），它能够将miRNA和mRNA表达数据与杂交信息相结合，以便找到在特定生理或疾病背景下更有可能出现的潜在miRNA-mRNA靶标。本文以来自五种胃肠道癌症（结肠癌、直肠癌、肝癌、胃癌和食管癌）的TCGA数据为例，总结了该包的流程和主要输出结果。其他作者可以利用所得结果提出大量可检验的假设。总体而言，我们表明miRComb包是处理miRNA和mRNA表达数据的有用工具，有助于筛选从现有的miRNA靶标预测数据库中获得的大量miRNA-mRNA相互作用，并以标准化方式（pdf报告）呈现结果。此外，还对五种消化系统癌症的miRComb miRNA-mRNA相互作用进行了综合分析。因此，miRComb是在特定背景下开始理解miRNA基因调控的非常有用的工具。该包可从http://mircomb.sourceforge.net下载。
