Backes Christina, Kehl Tim, Stöckel Daniel, Fehlmann Tobias, Schneider Lara, Meese Eckart, Lenhof Hans-Peter, Keller Andreas
Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany.
Chair for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany.
Nucleic Acids Res. 2017 Jan 4;45(D1):D90-D96. doi: 10.1093/nar/gkw926. Epub 2016 Oct 13.
In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/ With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways.
在过去十年中，人们对微小RNA（miRNA）及其调控机制进行了深入研究，并开发了许多用于分析miRNA及其靶标的工具。我们之前曾推出过一本关于单个miRNA及其假定靶标途径的词典。从那时起，miRNA的数量增加了两倍，关于miRNA及其靶标的知识也大幅增长。这与诸如京都基因与基因组百科全书（KEGG）等途径资源的变化一起，使得人们对miRNA、其靶基因及相关途径有了更深入的了解。在此，我们介绍miRNA途径词典数据库（miRPathDB），可通过https://mpd.bioinf.uni-sb.de/免费访问。通过该数据库，我们旨在为研究人员提供便捷途径，使其能够获取关于哪些途径受miRNA调控、哪些miRNA靶向某一途径以及这些调控的特异性如何等信息，从而补充现有的靶标途径网络服务器。该数据库包含大量miRNA（2595个人类miRNA）、不同的miRNA靶标集（14773个经实验验证的靶基因以及19281个预测靶基因），以及广泛的功能生化类别选择（KEGG途径、维基途径、生物卡塔途径、SMPDB途径、PID途径、Reactome途径、来自基因本体论（GO）的功能类别、来自Pfam的蛋白质家族以及染色体位置，共计12875个类别）。除了智人，小家鼠的数据也被存储下来，并可与人类靶标途径进行比较。
