EpiExplorer: live exploration and global analysis of large epigenomic datasets

Understanding gene regulation is an important goal in biomedical research. Historically, much of what we know about regulatory mechanisms has been discovered by mechanism-focused studies on a small set of model genes [1,2]. High-throughput genomic mapping technologies have recently emerged as a complementary approach [3]; and large-scale community projects are now generating comprehensive maps of genetic and epigenetic regulation for the human and mouse genomes [4-7]. Substantial potential for discovery lies in better connecting mechanism-focused studies to the wealth of functional genomics and epigenomics data that are being generated. A handful of pilot studies highlight the value of combining high-throughput and mechanism-focused research (for example, in [8-10]), but few research groups are equally proficient in bioinformatics, large-scale genomics and in-depth functional analysis to conduct highly integrated studies of gene regulation. A new generation of software tools could bridge this gap by enabling user-friendly navigation and analysis of large genomic databases.Genome browsers are currently the only software tools for navigating through genome data that are widely used, not only by bioinformaticians but also by biomedical researchers with little computational background. The strength of web tools such as the UCSC Genome Browser [11], Ensembl [12] and the WashU Human Epigenome Browser [13] lies in their intuitive interface, which allows users to browse through the genome by representing it as a one-dimensional map with various annotation tracks. This approach is powerful for visualizing individual gene loci, but the key concept of genomics - investigating many genomic regions in concert - tends to get lost when working with genome browsers only. Therefore, complementary tools are needed that handle the complexity of large genomic datasets while maintaining the interactive and user-friendly character of genome browsers.Existing tools do not fully address th