Paper Info
Title
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Abstract
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 oncomparative 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/.
Year
DOI
Venue
2006
10.1093/nar/gkj135
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
nucleic,machine learning,microrna,genome mapping,biological database,non coding rna,web interface
Genome,Untranslated region,Gene,Biology,Genomics,Regulation of gene expression,MiRBase,Genetics,Molecular biology,Gene Annotation,Sequence analysis
Journal
Volume
Issue
ISSN
34
Database-Issue
0305-1048
Citations 
PageRank 
References 
26
5.75
6
Authors
9
Name
Order
Citations
PageRank
Paul Wei-Che Hsu15810.51
Hsien-Da Huang283563.83
Sheng-Da Hsu331524.16
Li-Zen Lin4296.33
Ann-Ping Tsou519219.67
Ching-Ping Tseng6366.80
Peter F. Stadler71839152.96
Stefan Washietl829219.82
Ivo L. Hofacker91669131.57