Nucleic Acids Research Advance Access originally published online on November 15, 2006
Nucleic Acids Research 2007 35(Database issue):D149-D155; doi:10.1093/nar/gkl904
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Nucleic Acids Research, 2007, Vol. 35, Database issue D149-D155
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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miRGen: a database for the study of animal microRNA genomic organization and function
1 Center for Bioinformatics University of Pennsylvania, Philadelphia, PA, USA 2 Department of Genetics, School of Medicine University of Pennsylvania, Philadelphia, PA, USA 3 Department of Computer and Information Science, School of Engineering University of Pennsylvania, Philadelphia, PA, USA
*To whom correspondence should be addressed. Tel: +1 215 479 6894; Fax: +1 215 573 3111; Email: megraw{at}mail.med.upenn.edu
Received August 15, 2006. Revised October 11, 2006. Accepted October 12, 2006.
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.
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