miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes

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, mou...

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Published inNucleic acids research Vol. 36; no. suppl-1; pp. D165 - D169
Main Authors Hsu, Sheng-Da, Chu, Chia-Huei, Tsou, Ann-Ping, Chen, Shu-Jen, Chen, Hua-Chien, Hsu, Paul Wei-Che, Wong, Yung-Hao, Chen, Yi-Hsuan, Chen, Gian-Hung, Huang, Hsien-Da
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.01.2008
Oxford Publishing Limited (England)
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Summary: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/.
Bibliography:http://www.nar.oupjournals.org/
ark:/67375/HXZ-PX7RSGC0-T
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
istex:8D6E9416F1119DE756783FED2D9970C461E85614
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkm1012