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

By Molly Megraw, Praveen Sethupathy, Benoit Corda, Artemis G. Hatzigeorgiou. Nucleic Acids Res., 2006

310 citations recorded by the source corpus.

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 .

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cf49f5783b31e01ef8f3b83208f6c92fea3709bc

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Citations in the corpus

miR2Disease: a manually curated database for microRNA deregulation in human disease (2008, background): “miRBase (9), miRGator (10) and miRGen (11) aim at providing”
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. (2010, methodology): “sharing a genomic locus with no more than 500 bases between any two adjacent miRNAs, and were obtained via the Clusters interface of miRGen (Megraw et al. 2007).”
The microRNA.org resource: targets and expression (2007, background): “Additional information resources record experimentally validated microRNA targets [TarBase (8)], sequence annotation such as genomic organization, precursor sequences and literature citations [miRBase (9), miRGen (10), Argonaute (11), miRNAMap (12)], microRNA expression [smiRNAdb (13)] and miRNA tra”
Involvement of microRNA-451 in resistance of the MCF-7 breast cancer cells to chemotherapeutic drug doxorubicin (2008, unknown): “This prediction was further confirmed by the miRGen software (43).”
A novel and universal method for microRNA RT-qPCR data normalization (2009, methodology): “To avoid including miRNAs that are putatively co-regulated, we determined their genomic location and excluded those miRNAs that are located within 2 kb of each other using miRGen [42].”
miRecords: an integrated resource for microRNA–target interactions (2008, background): “The Predicted Targets component of miRecords integrates the miRNA targets predicted by 11 existing miRNA target prediction programs, outnumbering all other integrated resources of predicted miRNA targets, including miRGator (58), miRGen (31) and miRNAMap (59) (Table 2).”
The Diploid Genome Sequence of an Individual Human (2007, background): “These genomic datasets have also enabled the identification of additional functional sequence such as cis-regulatory DNA [24–29] as well as both noncoding and microRNA [30–34] .”