DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.
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DOI：
10.1093/nar/gkw211
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Lengauer T
中科院分区：
文献类型：
--
作者：
Albrecht F;List M;Bock C;Lengauer T
大量表观基因组数据在国际人类表观基因组联盟的保护下产生，该联盟的目标是在未来几年内建立 1000 个参考表观基因组。这些数据有可能揭示表观基因组调控的复杂性。然而，由于缺乏灵活且易于使用的数据检索方法，它们的有效使用受到阻碍。提取感兴趣的区域集是一项繁琐的任务，涉及几个手动步骤：识别相关实验、下载相应的数据文件以及过滤感兴趣的区域集。在这里，我们介绍 DeepBlue 表观基因组数据服务器，它简化了表观基因组数据分析和软件开发。 DeepBlue 提供了一个全面的编程接口，用于查找、选择、过滤、总结和下载区域集。它包含来自四个主要表观基因组项目的数据，即 ENCODE、ROADMAP、BLUEPRINT 和 DEEP。 DeepBlue 附带用户手册、示例和记录良好的应用程序编程接口 (API)。后者通过许多编程语言支持的 XML-RPC 协议进行访问。为了演示 API 的用法并为非程序员提供方便的数据检索，我们提供了一个可选的 Web 界面。 DeepBlue 可以通过 http://deepblue.mpi-inf.mpg.de 公开访问。
Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de.