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This article is part of the supplement: 22nd International Conference on Genome Informatics: Systems Biology

Open Access Proceedings

miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators

Chengxiang Qiu123, Juan Wang123 and Qinghua Cui123*

Author affiliations

1 Department of Biomedical Informatics, Peking University Health Science Center, Beijing, 100191, China

2 MOE Key Lab of Molecular Cardiovascular Science, Peking University, Beijing, 100191, China

3 Department of Chemical Defense, Institute of Chemical Defense, 1048 Mail Box, Beijing, 102205, China

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Citation and License

BMC Systems Biology 2011, 5(Suppl 2):S9  doi:10.1186/1752-0509-5-S2-S9

Published: 14 December 2011

Abstract

Background

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.

Results

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.

Conclusions

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 webcite.