The MethDB DAS server: adding an epigenetic information layer to the human genome.

Area of Science:

• Epigenetics and Genomics
• Bioinformatics and Database Development

Background:

• Dispersed data on DNA methylation, an epigenetic phenomenon, necessitates standardization and centralization.
• Previous versions of MethDB facilitated data querying but lacked public submission and network integration.

Purpose of the Study:

• To present the Distributed Annotation System (DAS) annotation server for MethDB, enabling integration into the biological database network.
• To represent DNA methylation data as an epigenetic information layer for the human genome.
• To validate the MethDB system by incorporating large-scale human genome methylation analysis data.

Main Methods:

• Development of an online data submission system for public access to MethDB.
• Implementation of a DAS annotation server for MethDB.
• Assembly of 31,312 human CpG island tagging project sequences into 13,786 CpG islands for import.
• Importation of assembled CpG islands and associated methylation data into MethDB.

Main Results:

• MethDB now integrates with other biological databases via DAS, serving as an epigenetic information layer for the human genome.
• The database houses 19,905 methylation content data and 5,382 methylation patterns/profiles.
• Data spans 48 species, 1,511 individuals, 198 tissues/cell lines, and 79 phenotypes, including data from the first large-scale human genome methylation analysis.

Conclusions:

• The MethDB DAS annotation server enhances the integration and accessibility of DNA methylation data within the broader biological research community.
• MethDB serves as a valuable, standardized resource for studying epigenetic variations across diverse biological contexts and species.