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This article is part of the supplement: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2011: Genomics

Open Access Proceedings

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach

Jiandong Ding12, Danqing Li12, Uwe Ohler34, Jihong Guan5 and Shuigeng Zhou12*

Author Affiliations

1 Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China

2 School of Computer Science, Fudan University, Shanghai, China

3 Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, USA

4 Department of Biostatistics & Bioinformatics, Duke University, Durham, North Carolina, USA

5 Department of Computer Science & Technology, Tongji University, Shanghai, China

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BMC Genomics 2012, 13(Suppl 3):S3  doi:10.1186/1471-2164-13-S3-S3

Published: 11 June 2012

Abstract

Background

MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to understand their function. Currently, several integrated computational programs and databases are available for animal miRNAs, the mechanisms of which are significantly different from plant miRNAs.

Methods

Here we present an integrated MTI prediction and analysis toolkit (imiRTP) for Arabidopsis thaliana. It features two important functions: (i) combination of several effective plant miRNA target prediction methods provides a sufficiently large MTI candidate set, and (ii) different filters allow for an efficient selection of potential targets. The modularity of imiRTP enables the prediction of high quality targets on genome-wide scale. Moreover, predicted MTIs can be presented in various ways, which allows for browsing through the putative target sites as well as conducting simple and advanced analyses.

Results

Results show that imiRTP could always find high quality candidates compared with single method by choosing appropriate filter and parameter. And we also reveal that a portion of plant miRNA could bind target genes out of coding region. Based on our results, imiRTP could facilitate the further study of Arabidopsis miRNAs in real use. All materials of imiRTP are freely available under a GNU license at (http://admis.fudan.edu.cn/projects/imiRTP.htm webcite).