NAR Molecular Biology Database Collection entry number 994
Megraw M.1,2, Sethupathy P.1,2, Corda B.1,2 and Hatzigeorgiou A.G.1,2,3
1Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
2Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
3Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, USA

Database Description

miRGen is an integrated database of (1) positional relationships between animal miRNAs and genomic annotation sets, and (2) mammalian 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.


We thank the reviewers and Shane Jensen for helpful commentary on this work. We also thank Julien Hirel for his contribution to the web interface style sheets. The development of miRGen was supported by the National Science Foundation under Grant No. 0238295. P.S. is supported by a predoctoral NIH training grant (5T32GM008216).

Go to the abstract in the NAR 2007 Database Issue.
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