将基因与功能相关联：使用 ENCODE ChIP-Seq 显著工具识别富集的转录因子。
Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.
机构信息
Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.
出版信息
Bioinformatics. 2013 Aug 1;29(15):1922-4. doi: 10.1093/bioinformatics/btt316. Epub 2013 Jun 3.
MOTIVATION
Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.
IMPLEMENTATION
The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary material is available at Bioinformatics online.
动机
生物分析已从识别基因和转录本转变为将这些基因和转录本映射到生物功能。ENCODE 项目已经生成了数百个跨越多个转录因子和细胞系的 ChIP-Seq 实验，供公众使用，但生物医学科学家分析这些数据的工具要么不存在，要么针对狭隘的生物学问题进行了定制。我们提出了 ENCODE ChIP-Seq 显著性工具，这是一个灵活的 Web 应用程序，利用公共的 ENCODE 数据来识别基因或转录本列表中富集的转录因子，以便进行比较分析。
实现
ENCODE ChIP-Seq 显著性工具在客户端使用 JavaScript 编写，并在 Google Chrome、Apple Safari 和 Mozilla Firefox 浏览器上进行了测试。服务器端脚本使用 PHP 编写，并利用 R 和 MySQL 数据库。该工具可在 http://encodeqt.stanford.edu 获得。
联系人
补充信息
补充材料可在 Bioinformatics 在线获得。
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