Abstract
Summary: We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons.Availability: CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.Contact: szhong@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Epigenomes play pivotal roles in cell identity, organismal development and disease processes (Bernstein et al, 2007; Maunakea et al, 2010), contribute to regulating cognition and behavior (Zhang and Meaney, 2010) and reflect personal variation (McDaniell et al, 2010)
Supplementary information: Supplementary data are available at Bioinformatics online
By integrating environmental signals with genomic instructions, epigenomes are instrumental in bridging genotypic variation and phenotypic diversity
Summary
Epigenomes play pivotal roles in cell identity, organismal development and disease processes (Bernstein et al, 2007; Maunakea et al, 2010), contribute to regulating cognition and behavior (Zhang and Meaney, 2010) and reflect personal variation (McDaniell et al, 2010). Leveraging a number of high-throughput sequencing enabled technologies, large international consortia are aiming to generate 41000 epigenomes from normal tissues and associated disease conditions (Abbott, 2011; Bernstein et al, 2010; The ENCODE Project Consortium, 2004) [ see Box 1 in Satterlee et al (2010)]. The concept of using cross-species comparison to annotate epigenomic functions may revolutionize epigenomic analysis (Feng et al, 2010; Mikkelsen et al, 2010; Milosavljevic, 2010; Xiao et al, 2012). We have developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser extends the concepts of the UCSC and Ensembl Genome Browsers. (Flicek et al, 2011; Kent et al, 2002; Zhu et al, 2009) to integrate, manage and visualize large sequencing-based datasets for cross-species comparisons
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