DevMouse, the mouse developmental methylome database and analysis tools

Abstract

DNAmethylation undergoes dynamic changes duringmouse development and plays crucial roles in embryogenesis, cell-lineage determination and genomic imprinting. Bisulfite sequencing enables profiling of mouse developmental methylomes on an unprecedented scale; however, integrating and mining these data are challenges for experimental biologists. Therefore, we developedDevMouse, which focuses on the efficient storage ofDNAmethylomes in temporal order and quantitative analysis of methylation dynamics during mouse development. The latest release of DevMouse incorporates 32 normalized and temporally orderedmethylomes across 15 developmental stages and related genomeinformation.A flexible query engine is developed for acquisition of methylation profiles for genes, microRNAs, long non-coding RNAs and genomic intervals of interest across selected developmental stages. To facilitate in-depth mining of these profiles, DevMouse offers online analysis tools for the quantification of methylation variation, identification of differentially methylated genes, hierarchical clustering, gene function annotation and enrichment. Moreover, a configurable MethyBrowser is provided to view the base-resolution methylomes under a genomic context. In brief, DevMouse hosts comprehensive mouse developmental methylome data and provides online tools to explore the relationships of DNA methylation and development. Database URL: http://www.devmouse.org/ © The Author(s) 2014. Published by Oxford University Press.