title: DevMouse, the mouse developmental methylome database and analysis tools.
abstract: DNA methylation undergoes dynamic changes during mouse 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 developed DevMouse, which focuses on the efficient storage of DNA methylomes in temporal order and quantitative analysis of methylation dynamics during mouse development. The latest release of DevMouse incorporates 32 normalized and temporally ordered methylomes across 15 developmental stages and related genome information. 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/
authors.affiliation: Department of Developmental Biology, School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China, Department of Computational Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China, Department of Food Science, School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150001, China and Department of Respiratory Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Liu
authors.forename: Rangfei
authors.initials: R
authors.lastname: Zhu
authors.forename: Jie
authors.initials: J
authors.lastname: Lv
authors.forename: Hongjuan
authors.initials: H
authors.lastname: He
authors.forename: Lin
authors.initials: L
authors.lastname: Yang
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Huang
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Su
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Shihuan
authors.initials: S
authors.lastname: Yu
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
mesh_terms: D000818:Animals; D019175:DNA Methylation / Q000235:genetics*; D030541:Databases, Genetic; D050437:Genes, Developmental; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D057386:Search Engine; D012984:Software