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
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.
The Targets interface provides access to unions and intersections of four widely used target prediction programs, and experimentally supported targets from TarBase.
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)?
- 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
ReferencesIf you use miRGen for any research that results in a publication, please cite :