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. 2008 Jun;14(6):1012-7.
doi: 10.1261/rna.965408. Epub 2008 Apr 21.

miRDB: a microRNA target prediction and functional annotation database with a wiki interface

Xiaowei Wang  1
Affiliations

miRDB: a microRNA target prediction and functional annotation database with a wiki interface

Xiaowei Wang. RNA. 2008 Jun.

Abstract

MicroRNAs (miRNAs) are short noncoding RNAs that are involved in the regulation of thousands of gene targets. Recent studies indicate that miRNAs are likely to be master regulators of many important biological processes. Due to their functional importance, miRNAs are under intense study at present, and many studies have been published in recent years on miRNA functional characterization. The rapid accumulation of miRNA knowledge makes it challenging to properly organize and present miRNA function data. Although several miRNA functional databases have been developed recently, this remains a major bioinformatics challenge to miRNA research community. Here, we describe a new online database system, miRDB, on miRNA target prediction and functional annotation. Flexible web search interface was developed for the retrieval of target prediction results, which were generated with a new bioinformatics algorithm we developed recently. Unlike most other miRNA databases, miRNA functional annotations in miRDB are presented with a primary focus on mature miRNAs, which are the functional carriers of miRNA-mediated gene expression regulation. In addition, a wiki editing interface was established to allow anyone with Internet access to make contributions on miRNA functional annotation. This is a new attempt to develop an interactive community-annotated miRNA functional catalog. All data stored in miRDB are freely accessible at http://mirdb.org.

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Figures

FIGURE 1.
FIGURE 1.
miRNA target search with the standard query interface in miRDB. (A) A screen shot of the web search page. There are two search options for either miRNA or the gene target. (B) A screen shot of one detailed result page.
FIGURE 2.
FIGURE 2.
Advanced target search for multiple miRNAs or genes. (A) A screen shot of the advance web search page. Target search may be performed using either miRNA names or target gene IDs. Search filters were also available to further exclude less relevant miRNAs or gene targets. (B) A screen shot of one pathway target search result. The pathway information was imported from PANTHER database.
FIGURE 3.
FIGURE 3.
A screen shot of one miRNA functional annotation page. hsa-let-7f is presented here as an example.
See this image and copyright information in PMC

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