title: PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits.
abstract: The polymorphism in microRNA target site (PolymiRTS) database aims to identify single-nucleotide polymorphisms (SNPs) that affect miRNA targeting in human and mouse. These polymorphisms can disrupt the regulation of gene expression by miRNAs and are candidate genetic variants responsible for transcriptional and phenotypic variation. The database is therefore organized to provide links between SNPs in miRNA target sites, cis-acting expression quantitative trait loci (eQTLs), and the results of genome-wide association studies (GWAS) of human diseases. Here, we describe new features that have been integrated in the PolymiRTS database, including: (i) polymiRTSs in genes associated with human diseases and traits in GWAS, (ii) polymorphisms in target sites that have been supported by a variety of experimental methods and (iii) polymorphisms in miRNA seed regions. A large number of newly identified microRNAs and SNPs, recently published mouse phenotypes, and human and mouse eQTLs have also been integrated into the database. The PolymiRTS database is available at http://compbio.uthsc.edu/miRSNP/.
authors.affiliation: Department of Microbiology, Immunology and Biochemistry, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
authors.forename: Jesse D
authors.initials: JD
authors.lastname: Ziebarth
authors.forename: Anindya
authors.initials: A
authors.lastname: Bhattacharya
authors.forename: Anlong
authors.initials: A
authors.lastname: Chen
authors.forename: Yan
authors.initials: Y
authors.lastname: Cui
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D004194:Disease / Q000235:genetics*; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
chemical_list: D035683:MicroRNAs
references.citation: Nature. 2010 Apr 1;464(7289):768-72
references.pmid: 20220758
references.citation: Nature. 2009 Jul 23;460(7254):479-86
references.pmid: 19536157
references.citation: Am J Hum Genet. 2010 Dec 10;87(6):779-89
references.pmid: 21129726
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7
references.pmid: 19474294
references.citation: Carcinogenesis. 2008 Jul;29(7):1306-11
references.pmid: 18477647
references.citation: Genome Res. 2005 Oct;15(10):1451-5
references.pmid: 16169926
references.citation: Nat Biotechnol. 2009 May;27(5):472-7
references.pmid: 19396161
references.citation: Clin Genet. 2010 Apr;77(4):306-13
references.pmid: 20132241
references.citation: Semin Cell Dev Biol. 2010 Sep;21(7):738-44
references.pmid: 20079866
references.citation: Mamm Genome. 2010 Feb;21(1-2):1-12
references.pmid: 20012966
references.citation: Cell. 2010 Apr 2;141(1):129-41
references.pmid: 20371350
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D163-9
references.pmid: 21071411
references.citation: Nucleic Acids Res. 2009 May;37(8):2419-33
references.pmid: 19295136
references.citation: Am J Hum Genet. 2008 Feb;82(2):283-9
references.pmid: 18252210
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references.pmid: 21037258
references.citation: Trends Genet. 2008 Oct;24(10):489-97
references.pmid: 18778868
references.citation: Nat Genet. 2007 Oct;39(10):1181-6
references.pmid: 17898773
references.citation: Genome Res. 2009 Jan;19(1):92-105
references.pmid: 18955434
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):308-11
references.pmid: 11125122
references.citation: Nat Genet. 2009 May;41(5):614-8
references.pmid: 19363478
references.citation: Genome Biol. 2010;11(8):R86
references.pmid: 20738864
references.citation: RNA. 2006 Feb;12(2):192-7
references.pmid: 16373484
references.citation: PLoS One. 2010 May 18;5(5):e10693
references.pmid: 20502693
references.citation: Physiol Rev. 2011 Jul;91(3):827-87
references.pmid: 21742789
references.citation: Biochem Biophys Res Commun. 2008 Sep 12;374(1):101-5
references.pmid: 18602895
references.citation: Clin Cancer Res. 2011 Feb 15;17(4):928-36
references.pmid: 21149617
references.citation: J Bone Miner Res. 2011 Jan;26(1):72-8
references.pmid: 20641033
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51
references.pmid: 21097890
references.citation: Nat Rev Cancer. 2010 Jun;10(6):389-402
references.pmid: 20495573
references.citation: J Biol Chem. 2007 Aug 17;282(33):24262-9
references.pmid: 17588946
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D105-10
references.pmid: 18996891
references.citation: Nature. 2008 Sep 4;455(7209):64-71
references.pmid: 18668037
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D51-4
references.pmid: 17099235
references.citation: Nat Methods. 2006 Nov;3(11):881-6
references.pmid: 17060911
references.citation: Nat Genet. 2009 May;41(5):609-13
references.pmid: 19363479
references.citation: Nat Genet. 2007 Dec;39(12):1494-9
references.pmid: 17982457
references.citation: Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21
references.pmid: 20069535
references.citation: Database (Oxford). 2011 Jul 23;2011:bar030
references.pmid: 21785142