MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs.
MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs.
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DOI：
10.1186/1471-2164-13-661
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发表时间：
2012-11-23
期刊：
影响因子：
4.4
通讯作者：
Zhang D
中科院分区：
文献类型：
--
作者：
Liu C;Zhang F;Li T;Lu M;Wang L;Yue W;Zhang D
全基因组关联研究（GWAS）和表达数量性状基因座（eQTL）研究发现了许多与复杂疾病相关的单核苷酸多态性（SNPs）。然而，这些SNP中很少有明确的生物学功能。近年来的研究表明，易感基因3 'UTR区域内的SNPs可以通过影响miRNAs的功能而影响复杂的性状/疾病。这些3 'UTR SNPs是功能候选者，因此对GWAS和eQTL研究人员感兴趣。我们开发了一个公开可用的在线数据库MirSNP（http：//cmbi.bjmu.edu.cn/mirsnp），其是预测的miRNA-mRNA结合位点中的人类SNP的集合。我们鉴定了414，510个可能影响miRNA-mRNA结合的SNP。将注释添加到这些SNP中以预测靶位点内的SNP是否会减少/破坏或增强/产生miRNA-mRNA结合位点。通过将MirSNP数据库应用于三个脑eQTL数据集，我们发现了四个未报道的SNP（rs3087822，rs 13042，rs 1058381和rs 1058398），它们可能影响miRNA结合，从而影响其宿主基因在脑中的表达。我们还将MirSNP数据库应用于我们的精神分裂症GWAS：在精神分裂症GWAS中发现了7个预测的miRNA相关SNP（p < 0.0001）。我们的研究结果确定了这些SNP位点的可能功能，并为后续的功能研究提供了基础。MirSNP可以从GWAS和eQTL研究中识别出可能与miRNA相关的SNPs，为后续的功能研究提供方向。
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. 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. MirSNP could identify the putative miRNA-related SNPs from GWAS and eQTLs researches and provide the direction for subsequent functional researches.