MethBank 4.0: An Updated Database of DNA Methylation Across A Variety of Species

NGDC  Nov 30, 2022

As a comprehensive DNA methylation database, MethBank has been dedicated to integrating high-quality whole-genome DNA methylation data of multiple species since its launch in 2014. For its high-quality data resources, intuitive visual presentation, and user-friendly operation pages, MethBank has been widely used by researchers in the related field.

Recently, the research group from the National Genomics Data Center, Beijing Institute of Genomics, and Chinese Academy of Sciences (China National Center for Bioinformation) developed the updated MethBank 4.0. This work was published online in the journal Nucleic Acids Research under the title "MethBank 4.0: an updated database of DNA methylation across a variety of species".

In the current version, based on unified data processing pipelines, MethBank 4.0 houses whole-genome single-base resolution methylomes in CG, CHG, and CHH (H=A, T or C) sequence contexts from 1,449 high-quality WGBS data, covering 23 species, 236 tissues/cell lines, and 15 biological contexts. Taking advantage of both massive high-quality data and standardized metadata, MethBank 4.0 provides comprehensive downstream annotations of differentially methylated regions (DMRs), gene methylation profiles, and methylated CpG islands (mCpGIs), helping users obtain a systematic, comprehensive, and intuitive landscape of DNA methylation signatures across multiple biological contexts. 

To increase the potential availability of retrieving epigenetic marker genes and shared properties for various biological contexts, MethBank 4.0 summarizes featured DMGs associated with biological contexts, involving 77 tissues/cell lines, 128 diseases, and 11 biological contexts in two species (human and mouse), which are completely based on manual curation from 1,039 publications since 2010. Meanwhile, MethBank 4.0 summarizes 501 methylation tools for researchers to quickly and accurately locate the tools they need. 

In addition, with the original analysis tool for differentially methylated promoters called IDMP and the online service for human methylation age estimation called Age Predictor, MethBank 4.0 is additionally equipped with DMR Toolkit to support the identification and analysis of DMRs.

Equipped with user-friendly interfaces for browsing, searching, and visualization, MethBank 4.0 provides a comprehensive system for DNA methylation data resources, knowledge collection, and analysis tools. To sum up, MethBank 4.0 serves as an essential resource for researchers to explore the regulatory mechanisms of DNA methylation in multiple biological contexts.


Dr. ZHANG Zhang 


Dr. BAO Yiming


Dr. LI Rujiao