GREAP

GREAP performs comprehensive annotation and enrichment analysis of human genomic regions to identify regulatory elements and quantify their statistical enrichment.

Key Features:

• Extensive Reference Sets: Supports 85,370 genomic region reference sets comprising 634,681,107 regions across 11 data types, including super enhancers, transcription factors, and accessible chromatin.
• Annotation and Enrichment Analysis: Provides annotation of genomic regions and enrichment testing using the hypergeometric test to assess significance.
• Locus Overlap Analysis: Performs locus overlap analysis to evaluate overlaps between different genomic loci.
• Genome Track Integration: Supports integration of over 400 million genome tracks for association with annotated region sets.

Scientific Applications:

• Regulatory Element Identification: Identify regulatory elements associated with specific genomic functions through annotation and enrichment of region sets.
• Interaction and Overlap Analysis: Analyze overlaps and interactions among diverse genomic region types using locus overlap analysis.
• Super-enhancer and Transcription Factor Studies: Investigate the roles of super enhancers and transcription factors in gene regulation via annotation and enrichment analysis.

Methodology:

Enrichment significance is evaluated with the hypergeometric test; overlaps are assessed via locus overlap analysis; the system integrates 85,370 reference region sets (634,681,107 regions) across 11 data types and supports over 400 million genome tracks.