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Nucleic Acids Res. 2010 Jan;38(Database issue):D640-51. doi: 10.1093/nar/gkp926. Epub 2009 Nov 11.

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

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  • 1Unit of Animal Genomics, GIGA-RSystems and Modeling, Montefiore Institute, University of Liège, Belgium.

Abstract

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate 'Patrocles DSPs', including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on 'Patrocles single nucleotide polymorphisms (pSNPs)' in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep.

PMID:
19906729
PMCID:
PMC2808989
DOI:
10.1093/nar/gkp926
[PubMed - indexed for MEDLINE]
Free PMC Article
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