DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets

被引：41

作者：

Albrecht, Felipe ^{[1
,2
]}

List, Markus ^{[1
]}

Bock, Christoph ^{[1
,3
,4
]}

Lengauer, Thomas ^{[1
]}

机构：

[1] Max Planck Inst Informat, D-66123 Saarbrucken, Germany

[2] Univ Saarland, Grad Sch Comp Sci, D-66123 Saarbrucken, Germany

[3] Austrian Acad Sci, CeMM Res Ctr Mol Med, A-1090 Vienna, Austria

[4] Med Univ Vienna, Dept Lab Med, A-1090 Vienna, Austria

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / W1期

关键词：

D O I：

10.1093/nar/gkw211

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 fewyears. 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.

引用

页码：W581 / W586

页数：6

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