APID Interactomes

APID Interactomes provides integrated, experimentally validated protein-protein interaction (PPI) networks across more than 1,100 species (including over 30 species with >500 interactions each) to support analysis of molecular interaction networks and proteome coverage.

Key Features:

• Integration of Diverse Data Sources: Aggregates PPIs from primary databases BIND, BioGRID, DIP, HPRD, IntAct, MINT and includes experimentally resolved 3D structures from the Protein Data Bank (PDB), including interactions identified in complexes with more than two distinct proteins.
• Quality and Coverage: Reports quality levels and proteome coverage for each organism and enables filtering of PPIs based on the reliability of experimental validation.
• Graph-based Network Visualization: Provides a graph tool based on Cytoscape.js for visualization, analysis, and construction of sub-interactomes from query protein lists.
• Experimental Evidence Classification: Categorizes interactions into 'binary' direct detection methods and 'indirect' methods and records detailed experimental evidence for each PPI.
• Comprehensive Data Repository: Maintains a global compendium of 90,379 distinct proteins and 678,441 singular interactions with procedures to eliminate false duplicates and incorporate new data sources.

Scientific Applications:

• Systems Biology: Mapping and analysis of interaction networks to investigate the architecture of cellular processes.
• Drug Discovery and Development: Identification and characterization of candidate drug targets and interaction partners within disease-related pathways.
• Functional Genomics: Inferring gene function and regulatory relationships through protein interaction context.
• Comparative Proteomics: Comparative analysis of interactomes to study evolutionary conservation and functional divergence across species.

Methodology:

APID integrates PPI data from multiple primary databases and PDB structures, applies data mining and integration procedures, evaluates experimental validation to assign quality levels and proteome coverage, and standardizes data representation using HUPO PSI-MI controlled vocabularies and ontologies; network visualization is provided via Cytoscape.js.