NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• Next-generation sequencing (NGS) combined with bisulphite conversion enables high-resolution genome-wide DNA methylation mapping.
• Existing resources lack comprehensive databases for storing and analyzing diverse methylation data from various tissues and conditions.

Purpose of the Study:

• To introduce NGSmethDB, a novel database for storing and retrieving DNA methylation data generated by NGS.
• To provide tools for analyzing methylation states, differential tissue methylation, and methylation changes in pathological conditions.

Main Methods:

• Development of a database system using a MySQL backend and a browser interface.
• Incorporation of data mining tools for querying methylation states and values.
• Consideration of CpG and CAG/CTG methylation contexts.

Main Results:

• NGSmethDB provides a platform for accessing methylation data for human, mouse, and Arabidopsis.
• Users can search for methylation states across tissues, retrieve methylation values for specific regions, and visualize promoter methylation.
• Data downloads are available at different coverage levels (1, 5, or 10 reads).

Conclusions:

• NGSmethDB addresses the need for a centralized repository of NGS-derived methylation data.
• The database facilitates research for both experimental scientists and bioinformaticians.
• It supports the exploration of epigenomic variations across different biological contexts.