title: miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
abstract: 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/.
authors.affiliation: Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan.
authors.forename: Sheng-Da
authors.initials: SD
authors.lastname: Hsu
authors.forename: Chia-Huei
authors.initials: CH
authors.lastname: Chu
authors.forename: Ann-Ping
authors.initials: AP
authors.lastname: Tsou
authors.forename: Shu-Jen
authors.initials: SJ
authors.lastname: Chen
authors.forename: Hua-Chien
authors.initials: HC
authors.lastname: Chen
authors.forename: Paul Wei-Che
authors.initials: PW
authors.lastname: Hsu
authors.forename: Yung-Hao
authors.initials: YH
authors.lastname: Wong
authors.forename: Yi-Hsuan
authors.initials: YH
authors.lastname: Chen
authors.forename: Gian-Hung
authors.initials: GH
authors.lastname: Chen
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D000818:Animals; D001665:Binding Sites; D002874:Chromosome Mapping; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D020868:Gene Silencing; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D051381:Rats; D012984:Software; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs