ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.
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ChIPBase v2.0：从 ChIP-seq 数据中解码非编码 RNA 和蛋白质编码基因的转录调控网络
DOI：
10.1093/nar/gkw965
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发表时间：
2017-01-04
影响因子：
14.9
通讯作者：
Qu LH
中科院分区：
文献类型：
--
作者：
Zhou KR;Liu S;Sun WJ;Zheng LL;Zhou H;Yang JH;Qu LH
非编码RNA（ncRNA）和蛋白质编码基因（PCG）的异常转录调控导致了多种生物过程并与人类疾病相关，但其潜在机制仍然难以捉摸。在本研究中，我们开发了ChIPBase v2.0（http://rna.sysu.edu.cn/chipbase/）来探索ncRNA和PCG的转录调控网络。 ChIPBase v2.0 已扩展了约 10 200 个精选的 ChIP-seq 数据集，与之前发布的版本相比，扩展了约 20 倍。我们从 DNA 结合蛋白的 ChIP-seq 数据中识别出数千个结合基序矩阵及其结合位点，并预测了转录因子 (TF) 和基因之间的数百万个转录调控关系。我们构建了“调节器”模块来预测数百个参与或影响 ncRNA 和 PCG 转录的 TF 和组蛋白修饰。此外，我们构建了一个基于网络的工具 Co-Expression，通过整合约 10 000 个肿瘤样本和约 9100 个正常组织和细胞系的基因表达谱来探索 DNA 结合蛋白和各种类型基因之间的共表达模式。 ChIPBase 还提供 ChIP-Function 工具和基因组浏览器来预测不同基因的功能并可视化各种 ChIP-seq 数据。这项研究将极大地扩展我们对 ncRNA 和 PCG 转录调控的理解。
The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version. We identified thousands of binding motif matrices and their binding sites from ChIP-seq data of DNA-binding proteins and predicted millions of transcriptional regulatory relationships between transcription factors (TFs) and genes. We constructed ‘Regulator’ module to predict hundreds of TFs and histone modifications that were involved in or affected transcription of ncRNAs and PCGs. Moreover, we built a web-based tool, Co-Expression, to explore the co-expression patterns between DNA-binding proteins and various types of genes by integrating the gene expression profiles of ∼10 000 tumor samples and ∼9100 normal tissues and cell lines. ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and PCGs.
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影响因子：
9.8
作者：
ENCODE Project Consortium
通讯作者：
ENCODE Project Consortium
影响因子：
14.9
作者：
Moseley SC;Rizkallah R;Tremblay DC;Anderson BR;Hurt MM;Chadwick BP
通讯作者：
Chadwick BP
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
64.5
作者：
Marson A;Levine SS;Cole MF;Frampton GM;Brambrink T;Johnstone S;Guenther MG;Johnston WK;Wernig M;Newman J;Calabrese JM;Dennis LM;Volkert TL;Gupta S;Love J;Hannett N;Sharp PA;Bartel DP;Jaenisch R;Young RA
通讯作者：
Young RA