EnhancerAtlas

EnhancerAtlas annotates and catalogs enhancers across nine species, including human, mouse, and Drosophila, to identify distal cis-regulatory elements and support study of their roles in activating gene transcription.

Key Features:

• Species coverage: Covers nine species, explicitly including human, mouse, and Drosophila.
• Dataset scale: Integrates 16,055 genome-wide profiling datasets.
• Experimental methods: Incorporates data from twelve high-throughput methods, including H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq, and MPRA.
• Enhancer catalog: Identifies 13,494,603 enhancers.
• Tissue and cell-type diversity: Profiles enhancers across 586 tissue/cell types, including normal tissues, cancer cell lines, and cells at various developmental stages.
• Enhancer–target prediction: Predicts enhancer–target gene relationships in human, mouse, and Drosophila.

Scientific Applications:

• Functional genomics: Enables analysis of enhancer activity and its impact on gene transcription.
• Comparative genomics: Supports cross-species comparisons of enhancer repertoires.
• Evolutionary biology: Facilitates studies of enhancer evolution and conservation across species.
• Development and disease research: Supports investigation of enhancers in embryogenesis, development, homeostasis, and cancer cell lines.

Methodology:

Integrates 16,055 genome-wide profiling datasets from twelve high-throughput experimental methods (H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq, MPRA, etc.) to identify enhancers and predict enhancer–target gene relationships for human, mouse, and Drosophila.