Qiu Chengxiang, Wang Juan, Cui Qinghua
Department of Biomedical Informatics, Peking University Health Science Center, Beijing, 100191, China.
BMC Syst Biol. 2011;5 Suppl 2(Suppl 2):S9. doi: 10.1186/1752-0509-5-S2-S9. Epub 2011 Dec 14.
In recent years, a number of tools have been developed to explore microRNAs (miRNAs) by analyzing their target genes. However, a reverse problem, that is, inferring patterns of protein-coding genes through their miRNA regulators, has not been explored. As various miRNA annotation data become available, exploring gene patterns by analyzing the prior knowledge of their miRNA regulators is becoming more feasible.
In this study, we developed a tool, miR2Gene, for this purpose. Various sets of miRNAs, according to prior rules such as function, associated disease, tissue specificity, family, and cluster, were integrated with miR2Gene. For given genes, miR2Gene evaluates the enrichment of the predicted miRNAs that regulate them in each miRNA set. This tool can be used for single genes, multiple genes, and KEGG pathways. For the KEGG pathway, genes with enriched miRNA sets are highlighted according to various rules. We confirmed the usefulness of miR2Gene through case studies.
miR2Gene represents a novel and useful tool that integrates miRNA knowledge for protein-coding gene analysis. miR2Gene is freely available at http://cmbi.hsc.pku.edu.cn/mir2gene.
近年来，已经开发了许多工具通过分析其靶基因来探索微小RNA（miRNA）。然而，一个相反的问题，即通过其miRNA调节因子推断蛋白质编码基因的模式，尚未得到探索。随着各种miRNA注释数据的可得，通过分析其miRNA调节因子的先验知识来探索基因模式变得更加可行。
在本研究中，我们为此目的开发了一种工具miR2Gene。根据功能、相关疾病、组织特异性、家族和簇等先验规则，将各种miRNA集与miR2Gene整合。对于给定的基因，miR2Gene评估在每个miRNA集中调节它们的预测miRNA的富集情况。该工具可用于单个基因、多个基因和KEGG通路。对于KEGG通路，根据各种规则突出显示具有富集miRNA集的基因。我们通过案例研究证实了miR2Gene的有用性。
miR2Gene是一种新颖且有用的工具，可整合miRNA知识用于蛋白质编码基因分析。miR2Gene可在http://cmbi.hsc.pku.edu.cn/mir2gene免费获取。
