W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
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DOI：
10.1093/bioinformatics/btq669
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发表时间：
2011-02-01
期刊：
影响因子：
--
通讯作者：
Jin VX
中科院分区：
文献类型：
--
作者：
Lan X;Bonneville R;Apostolos J;Wu W;Jin VX
摘要：基于染色质免疫沉淀（ChIP）的技术正在成为在活细胞中全面分析数千种转录因子并阐明转录调控机制的领先技术。近年来它发展迅速，从与斑点或拼接微阵列杂交（ChIP - chip），到双端标签测序（ChIP - PET），再到当前的大规模平行测序（ChIP - seq）。尽管有许多工具可用于识别ChIP - chip和ChIP - seq的结合位点（峰），但很少有工具能作为易于使用的在线网络工具，供基于ChIP的用户群体处理ChIP - chip和ChIP - seq数据。因此，我们开发了一种用于处理ChIP - chip和ChIP - seq数据的综合网络应用工具。我们的网络工具W - ChIPeaks采用基于探针（或基于区间）的富集阈值来定义峰，并应用统计方法来控制所识别峰的错误发现率。该网络工具包括两个不同的网络界面：用于ChIP - chip的PELT和用于ChIP - seq的BELT，两者都在先前发表的实验数据上进行了测试。我们工具的新特性包括以GFF、BED、bedGraph和.wig格式对所识别峰的全面输出，这些峰相关的注释基因，以及通过用户友好的网络界面对结果进行图形解释和可视化。
可用性：http://motif.bmi.ohio - state.edu/W - ChIPeaks/
联系人：victor.jin@osumc.edu
补充信息：补充数据可在Bioinformatics在线获取。
Summary: ChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Although there are many tools available for identifying binding sites (peaks) for ChIP-chip and ChIP-seq, few of them are available as easy-accessible online web tools for processing both ChIP-chip and ChIP-seq data for the ChIP-based user community. As such, we have developed a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Our web tool W-ChIPeaks employed a probe-based (or bin-based) enrichment threshold to define peaks and applied statistical methods to control false discovery rate for identified peaks. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on previously published experimental data. The novel features of our tool include a comprehensive output for identified peaks with GFF, BED, bedGraph and .wig formats, annotated genes to which these peaks are related, a graphical interpretation and visualization of the results via a user-friendly web interface. Availability: http://motif.bmi.ohio-state.edu/W-ChIPeaks/. Contact: victor.jin@osumc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
46.9
作者：
Ji, Hongkai;Jiang, Hui;Ma, Wenxiu;Johnson, David S.;Myers, Richard M.;Wong, Wing H.
通讯作者：
Wong, Wing H.
影响因子：
7
作者：
Jin, Victor X.;Rabinovich, Alina;Farnham, Peggy J.
通讯作者：
Farnham, Peggy J.
影响因子：
7
作者：
Johnson, David S.;Li, Wei;Liu, X. Shirley
通讯作者：
Liu, X. Shirley
DOI：
10.1038/nrg2636
发表时间：
2009-09
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
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影响因子：
12.3
作者：
Zhang, Yong;Liu, Tao;Meyer, Clifford A.;Eeckhoute, Jerome;Johnson, David S.;Bernstein, Bradley E.;Nussbaum, Chad;Myers, Richard M.;Brown, Myles;Li, Wei;Liu, X. Shirley
通讯作者：
Liu, X. Shirley