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

Abstract

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.

Figure 1.

DeepBlue Data Model: the experiments and annotation metadata are constituted by their names, controlled vocabulary terms and extra metadata. The experiments and annotations data form a set of regions. Each region is linked to the corresponding metadata and contains its start and end, as well as additional attributes found in the data files. The regions are stored in their respective genome and chromosome collections.

Figure 2.

Workflow diagram and source code for the identification of H3K27ac peaks that overlap with promoters in any of the BLUEPRINT datasets and subsequent identification of transcription factor peaks that overlap with these promoters in any of the ENCODE datasets. The different colors represent different types of commands, e.g. green for data selection, red for operations, purple for requests and gray for download.