MicroSNiPer: A Web Tool for Prediction of SNP Effects on Putative microRNA Targets

被引:119
作者
Barenboim, Maxim [1 ]
Zoltick, Brad J. [1 ]
Guo, Yongjian [2 ]
Weinberger, Daniel R. [1 ]
机构
[1] NIMH, Genes Cognit & Psychosis Program, Clin Brain Disorders Branch, NIH, Bethesda, MD 20892 USA
[2] NIAID, Bioinformat & Computat Biosci Branch, OCICB OSMO OD, NIH, Bethesda, MD 20892 USA
关键词
microRNA; SNP; FASTA program; 3 ' UTR; gene expression; computational prediction; BINDING-SITES; MESSENGER-RNAS; GENE; POLYMORPHISMS; DATABASE; IDENTIFICATION; COMPLEMENTARY; EXPRESSION; ALPHA; RISK;
D O I
10.1002/humu.21349
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
MicroRNAs are short, approximately 22 nucleotide noncoding RNAs binding to partially complementary sites in the 3'UTR of target mRNAs. This process generally results in repression of multiple targets by a particular microRNA. There is substantial interest in methods designed to predict the microRNA targets and effect of single nucleotide polymorphisms (SNPs) on microRNA binding, given the impact of microRNA on posttranscriptional regulation and its potential relation to complex diseases. We developed a web-based application, MicroSNiPer, which predicts the impact of a SNP on putative microRNA targets. This application interrogates the 30-untranslated region and predicts if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. MicroSNiPer computes these sites and examines the effects of SNPs in real time. MicroSNiPer is a user-friendly Web-based tool. Its advantages include ease of use, flexibility, and straightforward graphical representation of the results. It is freely accessible at http://cbdb.nimh.nih.gov/microsniper. Hum Mutat 31: 1223-1232, 2010. (C) 2010 Wiley-Liss, Inc.
引用
收藏
页码:1223 / 1232
页数:10
相关论文
共 52 条
[1]   Sequence variants in SLITRK1 are associated with Tourette's syndrome [J].
Abelson, JF ;
Kwan, KY ;
O'Roak, BJ ;
Baek, DY ;
Stillman, AA ;
Morgan, TM ;
Mathews, CA ;
Pauls, DA ;
Rasin, MR ;
Gunel, M ;
Davis, NR ;
Ercan-Sencicek, AG ;
Guez, DH ;
Spertus, JA ;
Leckman, JF ;
Dure, LS ;
Kurlan, R ;
Singer, HS ;
Gilbert, DL ;
Farhi, A ;
Louvi, A ;
Lifton, RP ;
Sestan, N ;
State, MW .
SCIENCE, 2005, 310 (5746) :317-320
[2]   The micro-ribonucleic acid (miRNA) miR-206 targets the human estrogen receptor-α (ERα) and represses ERα messenger RNA and protein expression in breast cancer cell lines [J].
Adams, Brian D. ;
Furneaux, Henry ;
White, Bruce A. .
MOLECULAR ENDOCRINOLOGY, 2007, 21 (05) :1132-1147
[3]   PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits [J].
Bao, Lei ;
Zhou, Mi ;
Wu, Ligang ;
Lu, Lu ;
Goldowitz, Dan ;
Williams, Robert W. ;
Cui, Yan .
NUCLEIC ACIDS RESEARCH, 2007, 35 :D51-D54
[4]  
Barenboim M., 2003, Biophysics, V48, pS90
[5]   MicroRNAs: Target Recognition and Regulatory Functions [J].
Bartel, David P. .
CELL, 2009, 136 (02) :215-233
[6]   The microRNA.org resource: targets and expression [J].
Betel, Doron ;
Wilson, Manda ;
Gabow, Aaron ;
Marks, Debora S. ;
Sander, Chris .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D149-D153
[7]   Principles of MicroRNA-target recognition [J].
Brennecke, J ;
Stark, A ;
Russell, RB ;
Cohen, SM .
PLOS BIOLOGY, 2005, 3 (03) :404-418
[8]   Natural selection on human microRNA binding sites inferred from SNP data [J].
Chen, Kevin ;
Rajewsky, Nikolaus .
NATURE GENETICS, 2006, 38 (12) :1452-1456
[9]   Inferring MicroRNA Activities by Combining Gene Expression with MicroRNA Target Prediction [J].
Cheng, Chao ;
Li, Lei M. .
PLOS ONE, 2008, 3 (04)
[10]   A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep [J].
Clop, Alex ;
Marcq, Fabienne ;
Takeda, Haruko ;
Pirottin, Dimitri ;
Tordoir, Xavier ;
Bibe, Bernard ;
Bouix, Jacques ;
Caiment, Florian ;
Elsen, Jean-Michel ;
Eychenne, Francis ;
Larzul, Catherine ;
Laville, Elisabeth ;
Meish, Francoise ;
Milenkovic, Dragan ;
Tobin, James ;
Charlier, Carole ;
Georges, Michel .
NATURE GENETICS, 2006, 38 (07) :813-818