ENdb

ENdb curates experimentally validated enhancers in human and mouse genomes, providing detailed annotations that link enhancers to target genes, transcription factors, biological functions, and disease associations.

Key Features:

• Species coverage: Contains enhancer entries from human and mouse genomes.
• Experimental validation focus: Emphasizes low-throughput experimental evidence to support enhancer annotations.
• Documented enhancers: Records 737 experimentally validated enhancers.
• Target gene annotations: Associates 384 target genes with curated enhancers.
• Transcription factor bindings: Includes information on 263 transcription factors that bind to these enhancers.
• Disease associations: Links enhancers to 110 diseases documented in the curated dataset.
• Functional annotations: Describes 153 biological functions influenced by the curated enhancers.
• Enhancer locations and mechanism: Annotates enhancers located in intergenic regions, introns, and exons and notes their role as cis-regulatory elements that modulate transcription via physical looping.
• Experimental methods recorded: Captures validation techniques including RNA interference (RNAi), in vitro knockdown assays, western blot, quantitative RT-PCR (qRT-PCR), luciferase reporter assays, chromatin conformation capture (3C), and 4C assays.

Scientific Applications:

• Gene regulation studies: Supports analysis of enhancer-mediated regulation and enhancer–target gene relationships in human and mouse.
• Disease mechanism research: Enables investigation of regulatory contributions of enhancers to 110 documented diseases.
• Transcription factor research: Facilitates study of TF–enhancer interactions for 263 transcription factors.
• Functional genomics: Assists characterization of enhancer roles across 153 annotated biological functions.
• Enhancer location studies: Supports examination of enhancer presence in intergenic regions, introns, and exons and their looping interactions with targets.

Methodology:

Manual literature curation of experimentally validated enhancers based on low-throughput evidence, including RNAi, in vitro knockdown, western blot, qRT-PCR, luciferase reporter assays, 3C, and 4C.