Animal-eRNAdb

Animal-eRNAdb catalogs enhancer RNAs (eRNAs) across multiple animal species to provide expression profiles and comparative analyses for studies of gene regulation and complex traits.

Key Features:

• Comprehensive Data Repository: Contains 185,177 eRNAs identified from 5,085 RNA-seq samples across ten animal species.
• eRNA Identification by RNA-seq Mapping: eRNAs were identified by mapping RNA sequencing data to known enhancer regions.
• Tissue-specific Expression Landscape: Provides expansive expression profiles of eRNAs across various tissues.
• Evolutionary Conservation Analysis: Includes sequence similarity analyses among multiple species to assess evolutionary conservation of eRNAs.
• Associations with Transcription Factors and Nearby Genes: Reports associations between eRNAs and transcription factors (TFs) or nearby genes to infer regulatory interactions.
• Trait-Related eRNA Characterization: Characterizes trait-related eRNAs to link eRNA presence or expression with biological traits.

Scientific Applications:

• Non-coding RNA and Gene Regulation Studies: Enables analysis of enhancer RNA roles in gene regulation and regulatory network inference.
• Evolutionary and Comparative Genomics: Supports investigation of evolutionary conservation and cross-species comparisons of eRNAs using sequence similarity analyses.
• Complex Trait Genetics: Facilitates linking eRNAs to phenotypic traits and trait-related regulatory mechanisms.
• Tissue-specific Expression and Functional Prediction: Allows exploration of tissue-specific eRNA expression profiles to infer functional contexts.
• TF–eRNA–Target Interaction Analysis: Permits analysis of associations between eRNAs, transcription factors, and nearby genes to identify candidate regulatory interactions.

Methodology:

Mapping of RNA-seq data to known enhancer regions to identify 185,177 eRNAs from 5,085 samples across ten species; sequence similarity analyses for evolutionary conservation; association analyses between eRNAs and transcription factors (TFs) or nearby genes; and characterization of trait-related and tissue-specific eRNA expression.