miRGen: a database for the study of animal microRNA genomic organization and function.

TitlemiRGen: a database for the study of animal microRNA genomic organization and function.
Publication TypeJournal Article
Year of Publication2007
AuthorsMegraw, M, Sethupathy, P, Corda, B, Hatzigeorgiou, AG
JournalNucleic Acids Res
IssueDatabase issue
Date Published2007 Jan
KeywordsAnimals, Data Interpretation, Statistical, Databases, Nucleic Acid, Genomics, Humans, Internet, Mice, MicroRNAs, Rats, User-Computer Interface

miRGen is an integrated database of (i) positional relationships between animal miRNAs and genomic annotation sets and (ii) animal miRNA targets according to combinations of widely used target prediction programs. A major goal of the database is the study of the relationship between miRNA genomic organization and miRNA function. This is made possible by three integrated and user friendly interfaces. The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands and pseudogenes. These miRNAs are connected through the Targets interface to their experimentally supported target genes from TarBase, as well as computationally predicted target genes from optimized intersections and unions of several widely used mammalian target prediction programs. Finally, the Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance and provides specific functional information on the targets of miRNAs within each cluster. All of these unique features of miRGen are designed to facilitate investigations into miRNA genomic organization, co-transcription and targeting. miRGen can be freely accessed at http://www.diana.pcbi.upenn.edu/miRGen.

Alternate JournalNucleic Acids Res.
PubMed ID17108354
PubMed Central IDPMC1669779
Grant List5T32GM008216 / GM / NIGMS NIH HHS / United States