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MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs
Liu, Chenxing1,2; Zhang, Fuquan1,2; Li, Tingting4,5; Lu, Ming4; Wang, Lifang1,2; Yue, Weihua1,2; Zhang, Dai1,2,3
关键词microRNA Single nucleotide polymorphism (SNP) Genome-wide association study (GWAS) Expression quantitative trait loci (eQTLs) MirSNP
刊名BMC GENOMICS
2012-11-23
DOI10.1186/1471-2164-13-661
13
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Biotechnology & Applied Microbiology ; Genetics & Heredity
资助者National Natural Science Foundation of China ; International Science &amp ; Technology Cooperation Program of China ; National High Technology Research and Development Program of China ; National Natural Science Foundation of China ; International Science &amp ; Technology Cooperation Program of China ; National High Technology Research and Development Program of China
研究领域[WOS]Biotechnology & Applied Microbiology ; Genetics & Heredity
关键词[WOS]MICRORNA TARGETS ; GENETIC-VARIATION ; GENOME ; BIOGENESIS ; CANCER ; EXPRESSION ; SUSCEPTIBILITY ; ASSOCIATION ; POPULATION ; EVOLUTION
英文摘要

Background: Numerous single nucleotide polymorphisms (SNPs) associated with complex diseases have been identified by genome-wide association studies (GWAS) and expression quantitative trait loci (eQTLs) studies. However, few of these SNPs have explicit biological functions. Recent studies indicated that the SNPs within the 3′UTR regions of susceptibility genes could affect complex traits/diseases by affecting the function of miRNAs. These 3′UTR SNPs are functional candidates and therefore of interest to GWAS and eQTL researchers.

Description: We developed a publicly available online database, MirSNP (http://cmbi.bjmu.edu.cn/mirsnp), which is a collection of human SNPs in predicted miRNA-mRNA binding sites. We identified 414,510 SNPs that might affect miRNA-mRNA binding. Annotations were added to these SNPs to predict whether a SNP within the target site would decrease/break or enhance/create an miRNA-mRNA binding site. By applying MirSNP database to three brain eQTL data sets, we identified four unreported SNPs (rs3087822, rs13042, rs1058381, and rs1058398), which might affect miRNA binding and thus affect the expression of their host genes in the brain. We also applied the MirSNP database to our GWAS for schizophrenia: seven predicted miRNA-related SNPs (p < 0.0001) were found in the schizophrenia GWAS. Our findings identified the possible functions of these SNP loci, and provide the basis for subsequent functional research.

Conclusion: MirSNP could identify the putative miRNA-related SNPs from GWAS and eQTLs researches and provide the direction for subsequent functional researches.

语种英语
所属项目编号81071087 ; 81071088 ; 2010DFB30820 ; 2009AA022702
资助者National Natural Science Foundation of China ; International Science &amp ; Technology Cooperation Program of China ; National High Technology Research and Development Program of China ; National Natural Science Foundation of China ; International Science &amp ; Technology Cooperation Program of China ; National High Technology Research and Development Program of China
WOS记录号WOS:000315743500001
引用统计
被引频次:94[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/62582
专题北京大学精神卫生研究所
作者单位1.Peking Univ, Inst Mental Hlth, Beijing 100191, Peoples R China
2.Peking Univ, Minist Hlth, Key Lab Mental Hlth, Beijing 100191, Peoples R China
3.Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China
4.Peking Univ, Hlth Sci Ctr, Sch Basic Med Sci, Dept Biomed Informat, Beijing 100191, Peoples R China
5.Peking Univ, Hlth Sci Ctr, Sch Basic Med Sci, Inst Syst Biomed, Beijing 100191, Peoples R China
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GB/T 7714
Liu, Chenxing,Zhang, Fuquan,Li, Tingting,et al. MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs[J]. BMC GENOMICS,2012,13.
APA Liu, Chenxing.,Zhang, Fuquan.,Li, Tingting.,Lu, Ming.,Wang, Lifang.,...&Zhang, Dai.(2012).MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs.BMC GENOMICS,13.
MLA Liu, Chenxing,et al."MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs".BMC GENOMICS 13(2012).
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