mrSNP: software to detect SNP effects on microRNA binding.
mrSNP: software to detect SNP effects on microRNA binding.
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DOI：
10.1186/1471-2105-15-73
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发表时间：
2014-03-15
影响因子：
3
通讯作者：
Toland AE
中科院分区：
文献类型：
--
作者：
Deveci M;Catalyürek UV;Toland AE
MicroRNA (miRNA) 是短的（19-23 个核苷酸）非编码 RNA，可与目标信使 RNA (mRNA) 的 3' 非翻译区 (3'UTR) 中的位点结合。结合导致转录物降解或翻译受阻，从而导致目标基因的表达减少。在 3’UTR 中发现了单核苷酸多态性 (SNP)，它们会破坏正常的 miRNA 结合或引入新的结合位点，其中一些与疾病发病机制有关。这提高了检测 miRNA 靶点和预测 SNP 对结合位点可能产生的影响的重要性。在过去的十年中，已经进行了大量研究来预测 miRNA 结合位点的位置。然而，用于分析 SNP 对 miRNA 结合影响的算法较少。此外，现有软件存在一些缺点，包括在处理大量 SNP 列表时需要大量的体力劳动，并且算法仅适用于 dbSNP 等数据库中存在的 SNP。随着下一代测序导致 3’UTR 中出现大量新变异，这些限制成为问题。为了克服这些问题，我们开发了一个名为 mrSNP 的网络服务器，它可以预测 3'UTR 中的 SNP 对 miRNA 结合的影响。所提出的工具减少了体力劳动需求，并允许用户输入任何 SNP 调用程序已识别的任何 SNP。在测试 mrSNP 对经实验验证可影响 miRNA 结合的 SNP 的性能时，mrSNP 正确识别了 69% (11/16) 的破坏结合的 SNP。 mrSNP 是一种适应性强、执行力强的工具，用于预测 3'UTR SNP 对 miRNA 结合的影响。该工具比现有算法具有优势，因为它可以评估新型 SNP 对 miRNA 结合的影响，而无需花费大量时间。
MicroRNAs (miRNAs) are short (19-23 nucleotides) non-coding RNAs that bind to sites in the 3’untranslated regions (3’UTR) of a targeted messenger RNA (mRNA). Binding leads to degradation of the transcript or blocked translation resulting in decreased expression of the targeted gene. Single nucleotide polymorphisms (SNPs) have been found in 3’UTRs that disrupt normal miRNA binding or introduce new binding sites and some of these have been associated with disease pathogenesis. This raises the importance of detecting miRNA targets and predicting the possible effects of SNPs on binding sites. In the last decade a number of studies have been conducted to predict the location of miRNA binding sites. However, there have been fewer algorithms published to analyze the effects of SNPs on miRNA binding. Moreover, the existing software has some shortcomings including the requirement for significant manual labor when working with huge lists of SNPs and that algorithms work only for SNPs present in databases such as dbSNP. These limitations become problematic as next-generation sequencing is leading to large numbers of novel variants in 3’UTRs. In order to overcome these issues, we developed a web-server named mrSNP which predicts the impact of a SNP in a 3’UTR on miRNA binding. The proposed tool reduces the manual labor requirements and allows users to input any SNP that has been identified by any SNP-calling program. In testing the performance of mrSNP on SNPs experimentally validated to affect miRNA binding, mrSNP correctly identified 69% (11/16) of the SNPs disrupting binding. mrSNP is a highly adaptable and performing tool for predicting the effect a 3’UTR SNP will have on miRNA binding. This tool has advantages over existing algorithms because it can assess the effect of novel SNPs on miRNA binding without requiring significant hands on time.
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DOI：
10.1093/bioinformatics/bts180
发表时间：
2012-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Shah TS;Liu JZ;Floyd JA;Morris JA;Wirth N;Barrett JC;Anderson CA
通讯作者：
Anderson CA
影响因子：
64.8
作者：
Mullighan, Charles G.;Goorha, Salil;Downing, James R.
通讯作者：
Downing, James R.
影响因子：
5.8
作者：
Yang, Shengping;Pounds, Stanley;Fang, Zhide
通讯作者：
Fang, Zhide
影响因子：
2.1
作者：
Olshen, AB;Venkatraman, ES;Wigler, M
通讯作者：
Wigler, M
影响因子：
2.1
作者：
Carvalho, Benilton;Bengtsson, Henrik;Irizarry, Rafael A.
通讯作者：
Irizarry, Rafael A.