Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

MethBank (Methylation Bank)

General information

Description: MethBank is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of large-scale methylation data.
Year founded: 2014
Last update: 2019-09-25
Version: v4.0
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
City: Beijing
Province/State:
Country/Region: China
Contact name (PI/Team): Zhang Zhang
Contact email (PI/Helpdesk): zhangzhang@big.ac.cn

Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2019-11-12]
Dong Zou [2019-11-06]
Dong Zou [2019-03-23]
Zhang Zhang [2018-11-27]
Dong Zou [2018-11-26]
Dong Zou [2018-11-23]
Dong Zou [2018-11-22]
Dong Zou [2018-11-21]
Dong Zou [2018-11-14]
Dong Zou [2017-12-05]
Zhang Zhang [2017-06-26]
Shixiang Sun [2017-03-06]
Zhang Zhang [2016-05-29]
Lin Liu [2016-03-29]
Lin Liu [2016-03-26]
Lina Ma [2015-11-18]
Zhang Zhang [2015-06-27]
Zhang Zhang [2015-06-26]
Li Yang [2015-06-26]
Zhang Zhang [2015-06-25]
Zhang Zhang [2015-06-23]
Zhang Zhang [2015-06-22]

Ranking

All databases:
1891/4549 (58.452%)
Expression:
361/800 (55%)
Modification:
94/185 (49.73%)
Gene genome and annotation:
577/1211 (52.436%)
1891
Total Rank
14
Citations
2.8
z-index

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Word cloud

Publications

29161430
MethBank 3.0: a database of DNA methylomes across a variety of species. [PMID: 29161430]
Li R, Liang F, Li M, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z.

MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals. Additionally, it is enhanced by improving the functionalities for data annotation, which accordingly enables systematic identification of methylation sites closely associated with age, sites with constant methylation levels across different ages, differentially methylated promoters, age-specific differentially methylated cytosines/regions, and methylated CpG islands. Moreover, MethBank provides tools to estimate human methylation age online and to identify differentially methylated promoters, respectively. Taken together, MethBank is upgraded with significant improvements and advances over the previous version, which is of great help for deciphering DNA methylation regulatory mechanisms for epigenetic studies.

Nucleic Acids Res. 2018:46(D1) | 2 Citations (from Europe PMC, 2020-03-28)
25294826
MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data. [PMID: 25294826]
Zou D, Sun S, Li R, Liu J, Zhang J, Zhang Z.

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.

Nucleic Acids Res. 2015:43(Database issue) | 12 Citations (from Europe PMC, 2020-03-28)