ATACdb

ATACdb catalogs human chromatin accessibility regions from ATAC-seq datasets and annotates them with enhancers, transcription factors and TF footprints, SNPs (including risk-associated SNPs and eQTLs), linkage disequilibrium SNPs, DNA methylation, chromatin interactions, and topologically associating domains to support study of gene regulatory mechanisms.

Key Features:

• Extensive Data Collection: Documents 52,078,883 chromatin accessibility regions derived from over 1,400 ATAC-seq samples curated from more than 2,200 datasets in NCBI GEO and SRA.
• Quality Assurance and Control: Implements a rigorous quality assurance process comprising four distinct quality control (QC) metrics to validate dataset reliability.
• Comprehensive Annotations: Annotates accessibility regions with super-enhancers and typical enhancers, transcription factors and inferred TF footprints, SNPs (common, risk-associated, and eQTLs), linkage disequilibrium SNPs, DNA methylation, chromatin interactions, and TADs.
• Tissue/Cell Type-Specific Insights: Provides tissue- and cell type-specific annotation and illustration of potential regulatory roles of chromatin accessibility regions.

Scientific Applications:

• Gene regulation and epigenetics: Enables analysis of transcriptional regulation and epigenetic states through chromatin accessibility profiles.
• Identification of regulatory elements: Supports identification and characterization of super-enhancers, typical enhancers, and other regulatory elements.
• Transcription factor analysis: Facilitates inference of transcription factor binding and TF footprinting from ATAC-seq-derived accessibility regions.
• Genetic variant interpretation: Supports investigation of SNPs (common, risk-associated, eQTLs) and LD SNPs to link genetic variation with regulatory function and disease association.
• Chromatin architecture studies: Provides annotations of chromatin interactions and TADs to study 3D genome organization in regulatory contexts.

Methodology:

Curation of ATAC-seq datasets from NCBI GEO/SRA; processing of those datasets to identify 52,078,883 chromatin accessibility regions across >1,400 samples from >2,200 datasets; application of four distinct QC metrics; inference of TF footprints; and annotation of regions with super-enhancers, typical enhancers, TFs, SNPs (common, risk-associated, eQTLs), LD SNPs, DNA methylation, chromatin interactions, and TADs.