RAEdb

RAEdb aggregates and organizes enhancers identified by high-throughput reporter assays to provide a centralized resource of quantitative enhancer activity data.

Key Features:

• Comprehensive Data Collection: Aggregates enhancers from eight distinct studies, predominantly derived from six human cell lines, totaling 538,320 enhancers.
• Activity Scoring System: Assigns an activity score to each enhancer based on quantitative reporter assay measurements, reflecting relative regulatory strength.
• Epromoter Identification: Identifies and stores 7,658 epromoters, defined as promoters that exhibit enhancer activity.
• Search Capabilities: Supports study-based filtering by species and cell line and enhancer/epromoter queries by genomic position, activity score, sequence characteristics, and associated genes.
• Genome Browser Integration: Includes a genome browser for visualization and comparison of enhancers in genomic context, enabling spatial analysis relative to other genetic elements.

Scientific Applications:

• Gene Regulation Studies: Enables investigation of regulatory networks using enhancer activity scores and epromoter data.
• Comparative Genomics: Facilitates comparisons across species and cell lines to identify conserved regulatory elements and evolutionary patterns.
• Functional Genomics: Supports design and interpretation of functional experiments by providing enhancer genomic positions and quantitative activity scores.

Methodology:

Data derive from high-throughput reporter assays that quantitatively measure enhancer activity across thousands of regulatory elements, and activity scores are calculated from those quantitative assessments.