miRGen is an integrated database of:

positional relationships between animal miRNAs and genomic annotation sets
animal miRNA targets according to combinations of widely used target prediction programs

miRGen has three connected interfaces which query this data.

Right Arrow 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.

Right Arrow The Targets interface provides access to unions and intersections of four widely used target prediction programs, and experimentally supported targets from TarBase.

Right Arrow 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.

For optimal use of the UCSC links from this site, please turn on the miRNA track in your UCSC browser.

How is miRGen different from other resources (miRBase, Argonaute, miRNAMap, MicroRNAdb)?

miRGen provides:

UCSC data integration
Direct queries for miRNAs located in introns, exons, and UTRs of protein-coding genes
Queries for miRNAs located in other genomic entities such as pseudogenes and CpG Islands
miRNA clusters at any user-defined inter-miRNA distance
Cluster-target data integration for the study of functional similarity of miRNAs within clusters
Integration with Tarbase, a comprehensive literature-curated database of experimentally supported targets
Intersections and unions of several widely used target prediction programs
Gene ID integration for predicted target genes, so that targets can be compared across multiple programs
Interface with 11 animal genomes (A. gambiae, C. elegans, C. familiaris, D. melanogaster, D. rerio, G. gallus, H. sapiens, M. musculus, R. norvegicus, T. nigroviridis, and P. troglodytes)
Open access to underlying software under GNU Public License
Full access to previous versions

References

If you use miRGen for any research that results in a publication, please cite :

M. Megraw, P. Sethupathy, B. Corda, and A.G. Hatzigeorgiou (2006). miRGen: A database for the study of animal microRNA genomic organization and function. Nucleic Acids Research, 35: D149-D155.

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How is miRGen different from other resources (miRBase, Argonaute, miRNAMap, MicroRNAdb)?

References