NCBI Epigenomics

NCBI Epigenomics provides a public repository of whole-genome epigenetic datasets to support access, visualization, and analysis of epigenetic modifications including histone post-translational modifications, DNA methylation, chromatin conformation changes, and non-coding RNAs.

Key Features:

• Curated data sources: Epigenetics-specific datasets are extracted from the Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA) and subjected to curation.
• Epigenetic data types: Contains whole-genome data for histone post-translational modifications, DNA methylation, chromatin conformation changes, and non-coding RNAs.
• Data processing and mapping: Raw data are processed and mapped onto genomic coordinates to generate genome-aligned data tracks.
• Data tracks: Over 1100 data tracks are provided for visualization and download, representing processed epigenomic signals.
• Scope and provenance: Aggregates data from 69 studies comprising 337 samples across five species.

Scientific Applications:

• Epigenetic mechanism analysis: Enables genome-wide investigation of histone modifications, DNA methylation patterns, chromatin conformation, and non-coding RNA distributions.
• Disease association studies: Supports comparison of epigenetic states to identify alterations associated with human disease and dysregulated gene expression.
• Comparative epigenomics: Facilitates cross-study and cross-species comparisons using standardized, mapped tracks.
• Locus-specific visualization: Allows visualization of epigenetic signals at specific genomic loci via genome-aligned tracks.

Methodology:

Epigenetics-specific records are extracted from GEO and SRA, undergo review, annotation, and reorganization, and raw data are processed and mapped to genomic coordinates to produce data tracks.