GWASdb

GWASdb provides a comprehensive catalog of human genetic variants (GVs) identified by genome-wide association studies (GWAS), including variants with moderate statistical significance (P < 1.0 × 10^(-3)), and annotates their genomic, regulatory, evolutionary, expression, and disease contexts to support pathway and protein–protein interaction analyses.

Key Features:

• Database expansion: A twenty-fold expansion relative to the NHGRI GWAS Catalog, incorporating GVs with P < 1.0 × 10^(-3).
• Literature curation: Variant records are curated from the scientific literature to assemble GWAS-identified GVs.
• Genomic mapping: Provides genomic mapping details for each variant.
• Regulatory annotations: Annotates regulatory effects including transcription factor binding sites, microRNA target sites, and splicing sites.
• Amino acid substitutions: Reports coding changes and amino acid substitutions associated with variants.
• Evolutionary data: Includes evolutionary context information for variants.
• Gene expression profiles: Links variants to gene expression data where available.
• Disease classification: Classifies variant–disease associations using Disease-Ontology Lite and Human Phenotype Ontology.
• Pathway and network analysis: Supports pathway enrichment analysis and protein–protein interaction (PPI) network association studies related to diseases.

Scientific Applications:

• Variant annotation and interpretation: Interprets functional consequences of GWAS-identified variants using genomic, regulatory, coding, evolutionary, and expression annotations.
• Disease–variant association analysis: Enables classification and exploration of variant associations with diseases using Disease-Ontology Lite and Human Phenotype Ontology.
• Pathway enrichment: Facilitates identification of enriched biological pathways linked to disease-associated variants.
• Network-based investigation: Supports PPI network association studies to investigate network-level relationships of disease-associated variants.

Methodology:

Curated GWAS variants from the scientific literature and annotated them for genomic mapping, regulatory effects (transcription factor binding sites, microRNA target sites, splicing sites), amino acid substitutions, evolutionary data, and gene expression; classified disease associations using Disease-Ontology Lite and Human Phenotype Ontology; and provided pathway enrichment and PPI network association analyses.