Journal Article

DevMouse, the mouse developmental methylome database and analysis tools

Hongbo Liu, Rangfei Zhu, Jie Lv, Hongjuan He, Lin Yang, Zhijun Huang, Jianzhong Su, Yan Zhang, Shihuan Yu and Qiong Wu

in Database

Volume 2014, issue ISSN: 0000-0000
Published online January 2014 | e-ISSN: 1758-0463 | DOI: https://dx.doi.org/10.1093/database/bat084

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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/

Journal Article.  3054 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Ecology and Conservation ; Evolutionary Biology

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