eRNAbase

eRNAbase catalogs enhancer RNAs (eRNAs) and integrates their annotations and analyses to support study of gene regulatory mechanisms in human and mouse genomes.

Key Features:

• Extensive Data Repository: The database contains 10,399,928 eRNAs derived from 1,012 samples (858 human and 154 mouse) collected from 14 eRNA-related experiment types and sourced from GEO/SRA and ENCODE.
• Comprehensive Annotation: eRNAs are annotated with (epi)genetic features including super enhancers, common single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, CRISPR/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, methylation sites, chromatin interactions regions, topologically associating domains, and RNA spatial interactions.
• Innovative Analytical Tools: The platform implements three analyses—eRNA-mediated Pathway Regulatory Analysis, eRNA-based Variation Interpretation Analysis, and eRNA-mediated TF-Target Gene Analysis—to investigate pathway regulation, variation interpretation, and transcription factor–target relationships mediated by eRNAs.

Scientific Applications:

• Gene Regulation Studies: Investigation of how eRNAs contribute to transcriptional regulation in human and mouse genomes.
• Genetic Variation Analysis: Interpretation of genetic variations located within eRNA regions and their potential regulatory consequences.
• Transcription Factor Interactions: Elucidation of interactions between transcription factors and target genes mediated by eRNAs.
• Pathway Analysis: Analysis of eRNA-mediated regulation of biological pathways to understand cellular processes.

Methodology:

eRNAs were identified and uniformly processed from diverse experimental types collected from GEO/SRA and ENCODE, and extensive (epi)genetic annotations were integrated for each eRNA.