CSEA-DB

CSEA-DB maps cell type–specific associations between GWAS-derived genetic variants and single-cell transcriptomic profiles to enable interpretation of disease- and trait-associated genetic susceptibility at the cellular level.

Key Features:

• GWAS integration: Integrates 5,120 GWAS summary statistics datasets that were manually curated and subjected to rigorous quality control.
• Single-cell compendium: Incorporates over 900,000 single-cell transcriptomes from the Human Cell Landscape and the Human Cell Atlas covering 752 tissue cell types from 71 adult and fetal tissues across 11 human organ systems.
• Ontology-based annotation: Annotates tissues and cell types using Uberon for anatomical structures and Cell Ontology for cellular entities.
• Association analysis (deTS): Applies the deTS algorithm to perform trait–cell type association analyses and executed 10,250,480 association tests.
• Significant trait associations: Identified 598 (11.68%) GWAS traits that are significantly associated with at least one cell type.
• Integrated data types: Combines manually curated GWAS summary statistics with single-cell transcriptome resources for cross-reference analyses.

Scientific Applications:

• Cell type–specific interpretation: Map GWAS signals to specific cell types to interpret how genetic susceptibility manifests at the cellular level.
• Prioritization for functional follow-up: Prioritize candidate cell types for experimental validation of disease-associated loci.
• Investigation of cellular mechanisms: Elucidate cellular contexts of gene expression regulation underlying phenotypic diversity and disease susceptibility.
• Cross-tissue comparative analysis: Compare trait–cell type associations across 71 adult and fetal tissues and 11 human organ systems.

Methodology:

Manually curate and quality-control GWAS summary statistics; integrate single-cell transcriptomes from the Human Cell Landscape and the Human Cell Atlas; annotate entities with Uberon and Cell Ontology; apply the deTS algorithm to perform 10,250,480 trait–cell type association analyses, yielding 598 significant GWAS trait–cell type associations.