MethBank


36318250	MethBank 4.0: an updated database of DNA methylation across a variety of species. [PMID: 36318250] Zhang M, Zong W, Zou D, Wang G, Zhao W, Yang F, Wu S, Zhang X, Guo X, Ma Y, Xiong Z, Zhang Z, Bao Y, Li R. Abstract DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, integrating, archiving, analyzing, and visualizing those data becomes critical. Since its first publication in 2015, MethBank has been continuously updated to include more DNA methylomes across more diverse species. Here, we present MethBank 4.0 (https://ngdc.cncb.ac.cn/methbank/), which reports an increase of 309% in data volume, with 1449 single-base resolution methylomes of 23 species, covering 236 tissues/cell lines and 15 biological contexts. Value-added information, such as more rigorous quality evaluation, more standardized metadata, and comprehensive downstream annotations have been integrated in the new version. Moreover, expert-curated knowledge modules of featured differentially methylated genes associated with biological contexts and methylation analysis tools have been incorporated as new components of MethBank. In addition, MethBank 4.0 is equipped with a series of new web interfaces to browse, search, and visualize DNA methylation profiles and related information. With all these improvements, we believe the updated MethBank 4.0 will serve as a fundamental resource to provide a wide range of data services for the global research community. Nucleic Acids Res. 2023:51(D1) \| 8 Citations (from Europe PMC, 2025-03-01)
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. Abstract 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) \| 32 Citations (from Europe PMC, 2025-03-01)
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. 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. Nucleic Acids Res. 2015:43(Database issue) \| 20 Citations (from Europe PMC, 2025-03-01)

MethBank 4.0: an updated database of DNA methylation across a variety of species. [PMID: 36318250]

Zhang M, Zong W, Zou D, Wang G, Zhao W, Yang F, Wu S, Zhang X, Guo X, Ma Y, Xiong Z, Zhang Z, Bao Y, Li R.

DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, integrating, archiving, analyzing, and visualizing those data becomes critical. Since its first publication in 2015, MethBank has been continuously updated to include more DNA methylomes across more diverse species. Here, we present MethBank 4.0 (https://ngdc.cncb.ac.cn/methbank/), which reports an increase of 309% in data volume, with 1449 single-base resolution methylomes of 23 species, covering 236 tissues/cell lines and 15 biological contexts. Value-added information, such as more rigorous quality evaluation, more standardized metadata, and comprehensive downstream annotations have been integrated in the new version. Moreover, expert-curated knowledge modules of featured differentially methylated genes associated with biological contexts and methylation analysis tools have been incorporated as new components of MethBank. In addition, MethBank 4.0 is equipped with a series of new web interfaces to browse, search, and visualize DNA methylation profiles and related information. With all these improvements, we believe the updated MethBank 4.0 will serve as a fundamental resource to provide a wide range of data services for the global research community.

Nucleic Acids Res. 2023:51(D1) | 8 Citations (from Europe PMC, 2025-03-01)

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.

Abstract

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) | 32 Citations (from Europe PMC, 2025-03-01)

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.

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.

Nucleic Acids Res. 2015:43(Database issue) | 20 Citations (from Europe PMC, 2025-03-01)

URL:	https://ngdc.cncb.ac.cn/methbank
Full name:	Methylation Bank
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:	2022-09-25
Version:	v4.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA RNA
Data object:	Animal Plant
Database category:	Expression Gene genome and annotation Modification
Major species:	Danio rerio Mus musculus Oryza sativa Homo sapiens Glycine max Phaseolus vulgaris
Keywords:	DNA methylation embryo visualization

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:	Beijing
Country/Region:	China
Contact name (PI/Team):	Rujiaoa Li
Contact email (PI/Helpdesk):	lirj@big.ac.cn

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Database Commons a catalog of worldwide biological databases