GREAP: a comprehensive enrichment analysis software for human genomic regions.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-throughput sequencing has generated vast amounts of functional genomic region data.
• Existing analysis tools lack comprehensive annotation and enrichment capabilities for these regions.
• Understanding human functional genomic regions is crucial but challenging.

Purpose of the Study:

• To develop a novel software platform, GREAP, for comprehensive genomic region analysis.
• To provide extensive annotation and enrichment analysis functionalities for functional genomic regions.
• To facilitate the understanding and research of human functional genomic data.

Main Methods:

• Designed and implemented the Genomic Region sets Enrichment Analysis Platform (GREAP).
• Integrated 85,370 genomic region reference sets covering over 634 million regions across 11 data types.
• Utilized hypergeometric test and Locus Overlap Analysis for enrichment significance.
• Developed a customizable genome browser with over 400 million customizable tracks.

Main Results:

• GREAP supports extensive annotation and enrichment analysis of genomic regions.
• The platform includes a large collection of diverse genomic region sets (e.g., super enhancers, transcription factors, accessible chromatins).
• A user-friendly, customizable genome browser is integrated for data visualization.

Conclusions:

• GREAP is a powerful, freely available platform for genomic region annotation and enrichment analysis.
• It addresses the limitations of existing tools by offering comprehensive capabilities.
• The platform aids researchers in exploring and interpreting large-scale functional genomic data.