SEdb 2.0

SEdb 2.0 catalogs super-enhancers in human and mouse genomes and provides annotated datasets to support analysis of their roles in gene transcription regulation.

Key Features:

• Expanded Dataset: Contains 1,167,518 super-enhancers from 1,739 human H3K27ac ChIP-seq samples and 550,226 super-enhancers from 931 mouse H3K27ac ChIP-seq samples.
• Transcription Factor Binding Sites (TFBSs): Incorporates TFBS annotations identified through TF motifs and TF ChIP-seq data to link transcription factors to super-enhancer regions.
• Comprehensive (epi)genetic Annotations: Integrates chromatin accessibility regions, DNA methylation sites, chromatin interaction regions, and topologically associating domains (TADs) for each super-enhancer.
• Search and Analysis Tools: Provides analytical functions including 'Search SE by TF-based', 'Differential-Overlapping-SE analysis', and 'SE-based TF-Gene analysis' for TF–SE associations, comparative SE studies, and linking SEs to target genes.
• Quality Control Metrics: Includes quality control metrics for ChIP-seq data processing.

Scientific Applications:

• Transcriptional regulation studies: Support investigation of super-enhancer roles in regulating gene transcription across conditions and cell types.
• Comparative genomics: Enable comparison of super-enhancer landscapes between human and mouse genomes.
• Epigenetic research: Facilitate study of chromatin accessibility, DNA methylation, chromatin interactions, and TAD context around super-enhancers.
• Cell-type-specific expression analysis: Aid analysis of cell-specific super-enhancers, their associated transcription factors, and putative target genes.

Methodology:

Super-enhancers were identified from H3K27ac ChIP-seq samples; TFBSs were identified using TF motifs and TF ChIP-seq data; annotations integrated chromatin accessibility, DNA methylation sites, chromatin interaction regions, and topologically associating domains (TADs); ChIP-seq processing included quality control metrics.