I2D

I2D integrates known, experimental, and predicted protein-protein interactions (PPIs) for Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, and humans to enable comparative interactome analysis and interolog-based inference of human interactions.

Key Features:

• Multi-species PPI integration: Combines known, experimental, and predicted PPIs across five model organisms and humans.
• Interolog transfer: Uses interologs to transfer conserved interactions between species to supplement interactomes.
• Evolutionary conservation analysis: Reports that protein complexes are preferentially conserved across species and shows a positive correlation between number of interacting proteins and evolutionary conservation when mapping human proteins onto yeast.
• Literature-derived data sources: Incorporates interactions from databases including BIND, HPRD, and MINT.
• Domain-based evaluation: Evaluates predicted interactions using protein domain information.
• Co-expression evaluation: Evaluates predicted interactions using gene co-expression patterns.
• GO-term evaluation: Evaluates predicted interactions using Gene Ontology (GO) terms.
• Predicted human interactions: Contains a set of 23,889 predicted human interactions.
• Querying: Supports queries using single or multiple identifiers.
• Network visualization and export: Provides custom graph visualization of query results and supports export in tab-delimited and PSI-MI formats.

Scientific Applications:

• Comparative interactomics: Comparative analysis of interactomes across Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, and humans.
• Interolog-based interactome expansion: Expansion of the human interactome through conserved interactions inferred from model organisms.
• Conservation studies: Investigation of conservation patterns distinguishing protein complexes from transient interactions.
• Systems biology analyses: Network-level studies of PPI organization and evolution.
• Experimental planning and validation: Prioritization and selection of predicted PPIs for experimental follow-up using domain, co-expression, and GO evidence.

Methodology:

Integrates known, experimental, and predicted PPIs; transfers interactions across species via interologs; incorporates literature-derived interactions from BIND, HPRD, and MINT; and evaluates predicted interactions using protein domains, gene co-expression patterns, and Gene Ontology (GO) terms.