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Nucleic acids research
Jan, 2015;43 (Database issue): D54-8.

MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.

Dong Zou, Shixiang Sun, Rujiao Li, Jiang Liu, Jing Zhang, Zhang Zhang
Author Information
  1. Dong Zou: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  2. Shixiang Sun: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China.
  3. Rujiao Li: Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  4. Jiang Liu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  5. Jing Zhang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China zhangj@big.ac.cn.
  6. Zhang Zhang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China zhangzhang@big.ac.cn.
PMID: 25294826 DOI: 10.1093/nar/gku920

Abstract

DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies.

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MeSH Term

Animals
CpG Islands
DNA Methylation
Databases, Nucleic Acid
Embryonic Development
Germ Cells
High-Throughput Nucleotide Sequencing
Internet
Mice
Polymorphism, Genetic
Sequence Analysis, DNA
Transcriptome
Zebrafish
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC000005 (MethBank)

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