EnhancerDB

EnhancerDB catalogs enhancer-centered regulatory relationships to support analysis of transcriptional regulation, enhancer–gene and enhancer–miRNA interactions, transcription factor (TF) binding relationships, and enhancer-associated sequence variation.

Key Features:

• Comprehensive relationship counts: The repository contains 131,054,581 TF–enhancer relationships, 17,059 enhancer–miRNA associations, 318,993 enhancer–gene connections, 4,639,558 TF–miRNA links, and 1,059,695 TF–gene interactions.
• Enhancer variation annotation: The database includes 11,439,394 enhancer single-nucleotide polymorphisms (SNPs) and links to 23,334 genes associated with expression quantitative trait loci (eQTL) SNPs.
• Expression profiles: TF, gene, and miRNA expression profiles are provided across multiple human tissues and cell lines.
• Tissue-specific enhancer scoring: Tissue-specific enhancers can be defined by applying a threshold on a tissue-specificity score.

Scientific Applications:

• Regulatory network mapping: Reconstruction and analysis of enhancer-mediated regulatory networks involving TFs, genes, and miRNAs.
• Gene and miRNA regulation studies: Investigation of enhancer roles in regulating protein-coding genes and microRNAs.
• Variant impact analysis: Examination of enhancer-associated SNPs and eQTLs and assessment of potential impacts of mutations in TF binding sites on disease, including cancer.
• Tissue-specific regulatory analysis: Identification of tissue- or cell-line-specific enhancers using adjustable tissue-specificity thresholds.

Methodology:

Tissue-specific enhancers are defined by applying a threshold on a tissue-specificity score; TF, gene, and miRNA expression profiles across human tissues and cell lines are incorporated; regulatory relationships and enhancer-associated SNP and eQTL annotations are compiled into the repository.