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Nucleic Acids Research Advance Access published online on November 19, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm1012
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes

Sheng-Da Hsu1, Chia-Huei Chu1, Ann-Ping Tsou2, Shu-Jen Chen3, Hua-Chien Chen3, Paul Wei-Che Hsu1, Yung-Hao Wong1, Yi-Hsuan Chen3, Gian-Hung Chen3 and Hsien-Da Huang1,4,5,*

1Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, 2Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, 3Molecular Medicine Research Center, Chang Gung University, Tao-Yuan 333, 4Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300 and 5Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan

*To whom correspondence should be addressed: Tel: +886 3 5712121, Ext. 56952; Fax: 886 3 5729288; Email: bryan{at}mail.nctu.edu.tw

Received September 23, 2007. Revised October 22, 2007. Accepted October 24, 2007.

MicroRNAs (miRNAs) are small non-coding RNA molecules that can negatively regulate gene expression and thus control numerous cellular mechanisms. This work develops a resource, miRNAMap 2.0, for collecting experimentally verified microRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes. Three computational tools, miRanda, RNAhybrid and TargetScan, were employed to identify miRNA targets in 3'-UTR of genes as well as the known miRNA targets. Various criteria for filtering the putative miRNA targets are applied to reduce the false positive prediction rate of miRNA target sites. Additionally, miRNA expression profiles can provide valuable clues on the characteristics of miRNAs, including tissue specificity and differential expression in cancer/normal cell. Therefore, quantitative polymerase chain reaction experiments were performed to monitor the expression profiles of 224 human miRNAs in 18 major normal tissues in human. The negative correlation between the miRNA expression profile and the expression profiles of its target genes typically helps to elucidate the regulatory functions of the miRNA. The interface is also redesigned and enhanced. The miRNAMap 2.0 is now available at http://miRNAMap.mbc.nctu.edu.tw/.

Present address: Hsien-Da, Huang, Ph.D. Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan, ROC


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