starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.
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starBase：用于探索 Argonaute CLIP-Seq 和 Degradome-Seq 数据中 microRNA 与 mRNA 相互作用图谱的数据库
DOI：
10.1093/nar/gkq1056
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Qu LH
中科院分区：
文献类型：
--
作者：
Yang JH;Li JH;Shao P;Zhou H;Chen YQ;Qu LH
MicroRNAs （miRNAs）是一类重要的小非编码rna (sRNAs)，通过靶向信使rna来调节基因表达。然而，将mirna分配到它们的调控靶基因在技术上仍然具有挑战性。近年来，高通量CLIP-Seq和降解组测序（degradation - seq）方法分别用于鉴定Argonaute相互作用位点和miRNA切割位点。在这项研究中，我们引入了一个新的数据库，starBase (sRNA target Base)，我们开发了这个数据库，以方便从CLIP-Seq和degradation - seq数据中全面探索miRNA-target相互作用图谱。目前的版本包括来自6种生物的21个CLIP-Seq和10个降解组- seq实验产生的高通量测序数据。通过分析数百万个绘制的CLIP-Seq和降解组- seq reads，我们分别在动物和植物中鉴定了约100万个ago结合簇和约200万个裂解靶簇。对这些集群和6个miRNA目标预测程序预测的靶点进行分析，我们分别从CLIP-Seq和降解组- seq数据中鉴定出大约40万个和大约66万个miRNA目标调控关系。此外，还提供了两个web服务器来从CLIP-Seq和degradation - seq数据中发现新的miRNA靶点。我们的web实现支持多种查询类型和共同目标，基因本体和途径的探索。starBase可在http://starbase.sysu.edu.cn/上获得。
MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed to facilitate the comprehensive exploration of miRNA–target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, we identified ∼1 million Ago-binding clusters and ∼2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in our identification of approximately 400 000 and approximately 66 000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways. The starBase is available at http://starbase.sysu.edu.cn/.
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影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
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64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
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作者：
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通讯作者：
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