ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.
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ChIPBase：用于从 ChIP-Seq 数据中解码长非编码 RNA 和 microRNA 基因转录调控的数据库
DOI：
10.1093/nar/gks1060
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发表时间：
2013-01
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;Jiang S;Zhou H;Qu LH
长链非编码RNA（lncRNA）和微小RNA（miRNAs）代表了真核生物中两类重要的非编码RNA。尽管这些非编码RNA与生物体发育和各种人类疾病有关，但令人惊讶的是，人们对它们的转录调控知之甚少。染色质免疫沉淀与下一代DNA测序（ChIP-Seq）的最新进展提供了具有前所未有的灵敏度的检测转录因子结合位点（TFBS）的方法。在这项研究中，我们描述了ChIPBase（http：//deepbase.sysu.edu.cn/chipbase/），我们开发了一个新的数据库，以促进从ChIP-Seq数据中全面注释和发现转录因子结合图谱以及lncRNA和miRNAs的转录调控关系。目前发布的ChIPBase包括来自六种生物体的不同组织和细胞系中的543个ChIP-Seq实验产生的高通量测序数据。通过分析数以百万计的TFBS，我们确定了数以万计的TF-lncRNA和TF-miRNA调控关系。此外，开发了两个基于Web的服务器来注释和发现来自ChIP-Seq数据的lncRNA和miRNAs的转录调控关系。此外，我们开发了两个基因组浏览器，deepView和genomeView，以提供多维数据的集成视图。此外，我们的Web实现支持不同的查询类型和TF，lncRNA，miRNA，基因本体和途径的探索。
Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity. In this study, we describe ChIPBase (http://deepbase.sysu.edu.cn/chipbase/), a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. The current release of ChIPBase includes high-throughput sequencing data that were generated by 543 ChIP-Seq experiments in diverse tissues and cell lines from six organisms. By analysing millions of TFBSs, we identified tens of thousands of TF-lncRNA and TF-miRNA regulatory relationships. Furthermore, two web-based servers were developed to annotate and discover transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. In addition, we developed two genome browsers, deepView and genomeView, to provide integrated views of multidimensional data. Moreover, our web implementation supports diverse query types and the exploration of TFs, lncRNAs, miRNAs, gene ontologies and pathways.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
DOI：
10.1073/pnas.1016959108
发表时间：
2011-04-05
影响因子：
11.1
作者：
He, Aibin;Kong, Sek Won;Pu, William T.
通讯作者：
Pu, William T.
影响因子：
16
作者：
Fujiwara T;O'Geen H;Keles S;Blahnik K;Linnemann AK;Kang YA;Choi K;Farnham PJ;Bresnick EH
通讯作者：
Bresnick EH
影响因子：
14.9
作者：
Dreszer TR;Karolchik D;Zweig AS;Hinrichs AS;Raney BJ;Kuhn RM;Meyer LR;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Pohl A;Malladi VS;Li CH;Learned K;Kirkup V;Hsu F;Harte RA;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;James Kent W
通讯作者：
James Kent W
影响因子：
23.9
作者：
Heng, Jian-Chien Dominic;Feng, Bo;Ng, Huck-Hui
通讯作者：
Ng, Huck-Hui