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Nucleic Acids Research 2006 34(Database Issue):D135-D139; doi:10.1093/nar/gkj135
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Nucleic Acids Research, 2006, Vol. 34, Database issue D135-D139
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes

Paul W.C. Hsu1, Hsien-Da Huang1,2,*, Sheng-Da Hsu1, Li-Zen Lin1, Ann-Ping Tsou3, Ching-Ping Tseng2,4, Peter F. Stadler5, Stefan Washietl6 and Ivo L. Hofacker6

1Institute of Bioinformatics, National Chiao Tung University Hsin-Chu 300, Taiwan, ROC 2Department of Biological Science and Technology, National Chiao Tung University Hsin-Chu 300, Taiwan, ROC 3Institute of Biotechnology in Medicine, National Yang-Ming University Taipei 112, Taiwan, ROC 4Institute of Biochemical Engineering, National Chiao Tung University Hsin-Chu 300, Taiwan, ROC 5Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig Germany 6Institute of Theoretical Chemistry, University of Vienna Austria

*To whom correspondence should be addressed: Tel: +886-3-5712121 Ext. 56952; Email: bryan{at}mail.nctu.edu.tw

Received August 15, 2005. Revised October 17, 2005. Accepted October 27, 2005.

Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap, to store the known miRNA genes, the putative miRNA genes, the known miRNA targets and the putative miRNA targets. The known miRNA genes in four mammalian genomes such as human, mouse, rat and dog are obtained from miRBase, and experimentally validated miRNA targets are identified in a survey of the literature. Putative miRNA precursors were identified by RNAz, which is a non-coding RNA prediction tool based on comparative sequence analysis. The mature miRNA of the putative miRNA genes is accurately determined using a machine learning approach, mmiRNA. Then, miRanda was applied to predict the miRNA targets within the conserved regions in 3'-UTR of the genes in the four mammalian genomes. The miRNAMap also provides the expression profiles of the known miRNAs, cross-species comparisons, gene annotations and cross-links to other biological databases. Both textual and graphical web interface are provided to facilitate the retrieval of data from the miRNAMap. The database is freely available at http://mirnamap.mbc.nctu.edu.tw/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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