miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
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DOI：
10.1371/journal.pone.0042390
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Chuang EY
中科院分区：
文献类型：
--
作者：
Lu TP;Lee CY;Tsai MH;Chiu YC;Hsiao CK;Lai LC;Chuang EY
许多针对微小RNA（miRNA）靶点的预测工具已经被开发出来，但在多种算法之间观察到不一致的预测结果，这可能会使进一步的分析变得困难。此外，人类miRNA的命名变化迅速。为了解决这些问题，我们开发了一个基于网络的系统——miRSystem，它通过整合miRNA靶点基因预测以及功能/通路分析，将查询的miRNAs转换为最新的注释并预测miRNA的功能。
首先，将查询的miRNA标识符转换为最新的注释版本，以防止由多个别名导致的潜在冲突。接下来，通过结合七种算法和两个经过验证的数据库，基于独立算法之间的一致性以及观察值/预期值比率，预测miRNAs的潜在基因靶点及其功能。最后，纳入五个通路数据库，通过自助法（bootstrap approaches）描述靶点基因的富集通路。基于靶点基因的富集通路，可以预测查询的miRNAs的功能。
miRSystem是一种用户友好型工具，可同时针对许多miRNAs预测其靶点基因及其相关通路。该网络服务器及相关文档可在http://mirsystem.cgm.ntu.edu.tw/免费获取。
Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses. First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted. MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.
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