EpiAnnotator

EpiAnnotator performs enrichment analysis of epigenomic regions using annotations from Blueprint, RoadMap, GENCODE, and the UCSC Genome Browser to identify statistically significant epigenomic feature enrichments across tissues, cell types, and cell lines in human and mouse genomes.

Key Features:

• Integration with public databases: Leverages annotations from Blueprint, RoadMap, GENCODE, and the UCSC Genome Browser.
• Database update automation: Annotations are regularly updated through custom scripts.
• Epigenomic coverage: Supports thousands of tracks spanning diverse tissues, cell types, and cell lines for human and mouse genomes.
• Region-based enrichment analysis: Compares selected genomic regions against background regions to detect enriched epigenomic features.
• High-throughput data handling: Designed to scale to large epigenomic datasets for high-throughput analyses.

Scientific Applications:

• Epigenetic modification analysis: Identify context-specific epigenomic modifications across tissues and cell types.
• Genomics: Interpret enrichment of epigenomic features in genomic studies.
• Transcriptomics and systems biology: Integrate epigenomic enrichment results with transcriptomic and systems-level analyses to reveal biological associations.

Methodology:

Users provide sets of selected regions and background regions; the software uses integrated annotations to compare the frequency of specific epigenomic features between selected and background regions and reports statistically significant enrichments, with annotations maintained via custom update scripts.