NGSmethDB

NGSmethDB stores genome-wide DNA methylation measurements derived from next-generation sequencing and bisulphite-conversion experiments at single-cytosine resolution for comparative epigenetic analysis.

Key Features:

• Methylation contexts: Reports cytosine methylation in CpG and CAG/CTG contexts at single-cytosine resolution.
• Sequencing provenance: Data are derived from next-generation sequencing (NGS) experiments employing bisulphite conversion.
• Multi-species integration: Includes methylomes from human, mouse, and Arabidopsis for cross-species comparisons.
• Coverage thresholds: Provides methylation calls at coverage levels of 1, 5, and 10 reads.
• Automatic incorporation pipeline: Incorporates new methylomes automatically as they become available.
• Storage backend: Stores methylation data in a MySQL relational database.
• Query capabilities: Supports queries for methylation states across tissues, retrieval of values within specified chromosomal regions, and promoter methylation comparisons among tissues.

Scientific Applications:

• Differential tissue methylation: Comparative analysis of methylation differences between tissues.
• Identification of unmethylated regions: Detection of absence of methylation in specific genomic regions across tissues.
• Disease-associated methylation changes: Analysis of methylation pattern alterations associated with pathological conditions.
• Gene expression and epigenetic inheritance studies: Investigation of relationships between DNA methylation, gene regulation, and epigenetic transmission.
• Molecular mechanism exploration: Support for studies on molecular mechanisms underlying disease-related epigenetic changes.

Methodology:

Data are stored in a MySQL backend and incorporated via an automatic data incorporation pipeline; methylation values are provided at coverage thresholds of 1, 5, and 10 reads.