dbSUPER

dbSUPER provides an integrated database of super-enhancers in human and mouse genomes to support analysis of cell-type-specific gene regulation and mapping of disease-associated regulatory variation.

Key Features:

• Comprehensive Data Integration: Consolidates super-enhancer annotations from multiple published studies across over 100 human and mouse cell types.
• Data export and interoperability: Exports super-enhancer regions in various formats and enables direct submission to Galaxy, GREAT, and Cistrome for downstream analysis.
• UCSC Genome Browser visualization: Supports automatic creation of custom tracks for visualization of super-enhancer regions in the UCSC Genome Browser.
• Gene association and external links: Lists genes associated with super-enhancers and provides cross-references to GeneCards, UniProt, and Entrez.
• Overlap analysis: Includes an overlap-analysis tool to annotate user-defined genomic regions against the super-enhancer dataset.

Scientific Applications:

• Transcriptional control studies: Enables investigation of super-enhancer clusters in regulating cell identity and transcriptional programs.
• Disease research: Facilitates linking disease-associated sequence variations to super-enhancers to prioritize candidate biomarkers and therapeutic targets in relevant cell types.

Methodology:

Integration of super-enhancer data from numerous published studies into a unified database, provision of an overlap-analysis annotation tool, and support for exporting regions to Galaxy/GREAT/Cistrome and for automatic UCSC Genome Browser custom-track creation.