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. 2007 Jan;35(Database issue):D149-55.
doi: 10.1093/nar/gkl904. Epub 2006 Nov 15.

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

Molly Megraw  1 , Praveen Sethupathy, Benoit Corda, Artemis G Hatzigeorgiou
Affiliations

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

Molly Megraw et al. Nucleic Acids Res. 2007 Jan.

Abstract

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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Figures

Figure 1
Figure 1
miRGen Genomics interface links to the UCSC genome browser and to the miRGen Targets interface Links to the UCSC genome browser for each miRNA and gene provide graphical views. Links to the miRGen Targets interface provide tabular views of predicted or experimentally supported targets.
Figure 2
Figure 2
miRGen Clusters Interface Users can choose which interface that the clusters should link to. The figure above shows links to the ‘Predicted Targets Optimized Intersection (PicTar, TargetScanS)’ target set and to the UCSC view for a particular cluster.
Figure 3
Figure 3
Growth in Number of miRNAs and Experimentally Supported Targets This chart tracks the number of Human miRNAs in miRBase and the number of experimentally supported target instances, published through recent years.
See this image and copyright information in PMC

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References

    1. Lee R.C., Feinbaum R.L., Ambros V. The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75:843–854. - PubMed
    1. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Identification of novel genes coding for small expressed RNAs. Science. 2001;294:853–858. - PubMed
    1. Mourelatos Z., Dostie J., Paushkin S., Sharma A., Charroux B., Abel L., Rappsilber J., Mann M., Dreyfuss G. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 2002;16:720–728. - PMC - PubMed
    1. Lee R.C., Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science. 2001;294:862–864. - PubMed
    1. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 2001;294:858–862. - PubMed

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