DevMouse, the Mouse Developmental Methylome Database and Analysis Tools

Overview

Journal Database (Oxford)

Specialty Biology

Date 2014 Jan 11

PMID 24408217

Citations 4

Authors

Hongbo Liu

Rangfei Zhu

Jie Lv

Hongjuan He

Lin Yang

Zhijun Huang

Jianzhong Su

Yan Zhang

Shihuan Yu

Qiong Wu

Affiliations

Soon will be listed here.

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/

Citing Articles

EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis.

Zheng L, Liang P, Long C, Li H, Li H, Liang Y Nucleic Acids Res. 2022; 51(D1):D924-D932.

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EmExplorer: a database for exploring time activation of gene expression in mammalian embryos.

Hu B, Zheng L, Long C, Song M, Li T, Yang L Open Biol. 2019; 9(6):190054.

PMID: 31164042 PMC: 6597754. DOI: 10.1098/rsob.190054.

Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development.

Lv J, Liu H, Yu S, Liu H, Cui W, Gao Y Mol Genet Genomics. 2014; 290(2):685-97.

PMID: 25428585 DOI: 10.1007/s00438-014-0952-z.

Identification and characterization of long intergenic non-coding RNAs related to mouse liver development.

Lv J, Huang Z, Liu H, Liu H, Cui W, Li B Mol Genet Genomics. 2014; 289(6):1225-35.

PMID: 25012394 DOI: 10.1007/s00438-014-0882-9.

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