sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria.
sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria.
复制标题
sRNATarBase 3.0：细菌中 sRNA 靶标相互作用的更新数据库。
DOI：
10.1093/nar/gkv1127
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Li W
中科院分区：
文献类型：
--
作者：
Wang J;Liu T;Zhao B;Lu Q;Wang Z;Cao Y;Li W
细菌sRNAs是一类长度约为40-500个核苷酸的小分子调控RNA，它们通过与靶基因或蛋白质结合而发挥多种生物学作用。因此，阐明sRNA靶标是非常重要的。然而，只有少数sRNA的靶标已被描述。为了促进sRNA功能研究，如开发sRNA靶标预测模型，我们更新了sRNatarBase数据库，该数据库最初开发于2010年。新版本(最近转移到http://ccb1.bmi.ac.cn/srnatarbase/))包含从213篇论文中手动收集的771个sRNA目标条目，以及分别来自sRNatarget和sTarPicker的23290个和11750个预测目标。在771个条目中，475个和17个分别参与了验证的sRNA-mRNA和sRNA-蛋白质的相互作用，而279个没有报道的相互作用。我们还介绍了sRNA-靶mRNA相互作用的316个结合区的详细信息和相关的突变实验，以及新功能，包括NCBI序列查看器、sRNA调控网络、基于靶预测的GO和途径注释以及错误报告系统。新版本提供了有效的sRNA-目标相互作用的全面注释，并将成为细菌sRNA研究的有用资源。
Bacterial sRNAs are a class of small regulatory RNAs of about 40–500 nt in length; they play multiple biological roles through binding to their target mRNAs or proteins. Therefore, elucidating sRNA targets is very important. However, only targets of a few sRNAs have been described. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA–mRNA and sRNA–protein interactions, respectively, while 279 had no reported interactions. We also presented detailed information for 316 binding regions of sRNA-target mRNA interactions and related mutation experiments, as well as new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. The new version provides a comprehensive annotation of validated sRNA-target interactions, and will be a useful resource for bacterial sRNA studies.