Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, China.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W430-6. doi: 10.1093/nar/gkr332. Epub 2011 May 17.
Chromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-Array, with free access to academic users.
染色质免疫沉淀（ChIP）与高通量技术（ChIP-X）相结合，如下一代测序（ChIP-Seq）和微阵列（ChIP-chip），已成功用于绘制转录因子（TF）的活性转录因子结合位点（TFBS）。该 TF 可以激活或抑制靶向基因，或者对 TF 无反应。微阵列技术已被用于测量在 TF 干扰下数千个基因的实际表达变化，但无法确定受影响的基因是 TF 的直接还是间接靶标。此外，ChIP-X 和微阵列方法都会产生大量的假阳性。将微阵列表达谱分析和 ChIP-X 数据相结合，可更有效地分析 TFBS，从而研究 TF 的功能。然而，目前的网络服务器仅提供用于分析 ChIP-X 或表达数据的工具，但不能同时分析两者。在这里，我们介绍了 ChIP-Array，这是一个整合了来自人类、小鼠、酵母、果蝇和拟南芥的 ChIP-X 和表达数据的网络服务器。该服务器将帮助生物学家检测由感兴趣的 TF 调节的直接和间接靶基因，并有助于 TF 的功能特征分析。ChIP-Array 可在 http://jjwanglab.hku.hk/ChIP-Array 上免费获取，供学术用户使用。
