Article (Scientific journals)
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates
Hiard, Samuel; Charlier, Carole; Coppieters, Wouter et al.
2010In Nucleic Acids Research, 38 (Database), p. 640-D651
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Keywords :
Patrocles; miRNA; regulation; gene; polymorphic; database
Abstract :
[en] 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.
Research center :
SystMod
Disciplines :
Genetics & genetic processes
Author, co-author :
Hiard, Samuel ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et Modélisation
Charlier, Carole  ;  Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Coppieters, Wouter ;  Université de Liège - ULiège > Département de productions animales > Département de productions animales
Georges, Michel  ;  Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Baurain, Denis  ;  Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Language :
English
Title :
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates
Alternative titles :
[fr] Patrocles : Une base de données de régulation génétique par miARN polymorphiques chez les vertébrés
Publication date :
2010
Journal title :
Nucleic Acids Research
ISSN :
0305-1048
eISSN :
1362-4962
Publisher :
Oxford University Press, Oxford, United Kingdom
Volume :
38
Issue :
Database
Pages :
D640-D651
Peer reviewed :
Peer Reviewed verified by ORBi
Additional URL :
Funders :
ULiège - Université de Liège [BE]
Available on ORBi :
since 06 January 2010

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