CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.
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DOI：
10.1093/nar/gkq940
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Zavolan M
中科院分区：
文献类型：
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作者：
Khorshid M;Rodak C;Zavolan M
mRNA的稳定性、定位和翻译速率由大量的RNA结合蛋白（RBP）调节，这些RNA结合蛋白直接或在向导RNA的帮助下找到它们的靶点。在绘制RBP结合位点的实验方法中，交联和免疫沉淀（CLIP）结合深度测序提供了全转录组覆盖以及高分辨率。然而，部分由于其庞大的体积，迄今为止在CLIP实验中产生的数据还没有以能够快速和交互式探索结合位点的形式呈现。为了满足这一需求，我们开发了CLIPZ数据库和分析环境。RBP如Argonaute 1-4、胰岛素样生长因子II mRNA结合蛋白1-3、TNRC 6蛋白A-C、Pumilio 2、Quaking和聚嘧啶束结合蛋白的结合位点数据可以在基因组和单个转录物的水平上可视化。个人用户可以上传他们自己的序列数据集，同时能够限制特定用户对这些数据的访问，并且可以交互地执行公共和私有数据集的分析。CLIPZ，可在http://www.clipz.unibas.ch上获得，旨在为转录后调控元件提供一个开放获取的信息库。
The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements.
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影响因子：
3
作者：
Gaidatzis D;van Nimwegen E;Hausser J;Zavolan M
通讯作者：
Zavolan M
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
4.8
作者：
Izquierdo, Jose M.;Valcarcel, Juan
通讯作者：
Valcarcel, Juan
影响因子：
1.7
作者：
Holmes, I;Durbin, R
通讯作者：
Durbin, R
影响因子：
16.8
作者：
通讯作者：
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