SEA

SEA catalogs and annotates super-enhancers across multiple species to support analysis of their roles in regulating gene expression and maintaining cell identity.

Key Features:

• Extensive database: Contains 83,996 super-enhancers identified across 134 cell types, tissues, and diseases including Human: 75,439 (three experimentally validated), Mouse: 5,879 (five experimentally validated), Drosophila melanogaster: 1,774, and Caenorhabditis elegans: 904.
• Comprehensive annotations: Records cell type specificity, nearby genes, transcription factor binding sites, CRISPR/Cas9 target sites, evolutionary conservation data, single nucleotide polymorphisms (SNPs), histone modification markers such as H3K27ac, and DNA methylation patterns.
• Gene expression and ChIP-seq integration: Integrates gene expression profiles and transcription factor ChIP-seq data to contextualize super-enhancer activity.
• Analytical tools: Provides analytical capabilities for investigating functional roles of super-enhancers and their contributions to cell identity and disease.

Scientific Applications:

• Developmental gene regulation: Investigating super-enhancer–mediated regulation of gene expression during development and establishment of cell identity.
• Disease and tumorigenesis studies: Examining how super-enhancers and annotated variants contribute to tumorigenesis and other disease processes.
• Comparative and evolutionary analyses: Performing cross-species comparisons to assess evolutionary conservation and divergence of super-enhancer elements.

Methodology:

Identification and integration of super-enhancers across species with annotation of cell type specificity, nearby genes, transcription factor binding sites, CRISPR/Cas9 target sites, evolutionary conservation, SNPs, H3K27ac and DNA methylation data, and incorporation of gene expression profiles and transcription factor ChIP-seq data.