miRTar: an integrated system for identifying miRNA-target interactions in human

BMC Bioinformatics

Software

Wei-Yun Huang¹  Tzong-Yi Lee²  Sheng-Da Hsu³  Justin Bo-Kai Hsu³  Chih-Min Chiu³  Chia-Hung Chien³  Hsien-Da Huang⁴ 

[1] Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan;Department of Computer Science and Engineering, Yuan Ze University, 320, Chungli, Taiwan;Institute of Bioinformatics and Systems Biology, National Chiao Tung University, 300, Hsin-Chu, Taiwan;Institute of Bioinformatics and Systems Biology, National Chiao Tung University, 300, Hsin-Chu, Taiwan;Department of Biological Science and Technology, National Chiao Tung University, 300, Hsin-Chu, Taiwan;

关键词: Alternative Splice;    miRNA Target;    Regulatory Relationship;    miRNA Target Gene;    miRNA Target Site;   

DOI  :  10.1186/1471-2105-12-300

 received in 2010-11-09, accepted in 2011-07-26,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (miRNAs) are small non-coding RNA molecules that are ~22-nt-long sequences capable of suppressing protein synthesis. Previous research has suggested that miRNAs regulate 30% or more of the human protein-coding genes. The aim of this work is to consider various analyzing scenarios in the identification of miRNA-target interactions, as well as to provide an integrated system that will aid in facilitating investigation on the influence of miRNA targets by alternative splicing and the biological function of miRNAs in biological pathways.ResultsThis work presents an integrated system, miRTar, which adopts various analyzing scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in biological pathways. The system has three major features. First, the prediction system is able to consider various analyzing scenarios (1 miRNA:1 gene, 1:N, N:1, N:M, all miRNAs:N genes, and N miRNAs: genes involved in a pathway) to easily identify the regulatory relationships between interesting miRNAs and their targets, in 3'UTR, 5'UTR and coding regions. Second, miRTar can analyze and highlight a group of miRNA-regulated genes that participate in particular KEGG pathways to elucidate the biological roles of miRNAs in biological pathways. Third, miRTar can provide further information for elucidating the miRNA regulation, i.e., miRNA-target interactions, affected by alternative splicing.ConclusionsIn this work, we developed an integrated resource, miRTar, to enable biologists to easily identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. miRTar is now available at http://miRTar.mbc.nctu.edu.tw/.

【 授权许可】

Unknown   
© Hsu et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.