STRING

STRING integrates known and predicted protein-protein interactions (Search Tool for the Retrieval of Interacting Genes/Proteins) to characterize direct physical associations and indirect functional connections for analysis of cellular processes in molecular systems biology.

Key Features:

• Integrated interaction data: Combines known and predicted protein-protein interactions encompassing direct physical associations and indirect functional connections.
• Organism coverage: Includes interaction data across more than 2000 organisms and supports transfer of interaction information between species.
• Cross-species transfer algorithms: Implements novel, scalable algorithms to transfer interaction information between species.
• Orthology annotations: Uses hierarchical and self-consistent orthology annotations to organize interacting proteins into families at varying levels of phylogenetic resolution.
• Prediction pipeline (version 10.0): Features a redesigned prediction pipeline that infers protein-protein associations from co-expression data.
• Programmatic access: Provides an API for the R computing environment.
• Statistical analysis: Offers improved statistical analysis tools for enrichment tests within user-defined networks.

Scientific Applications:

• Protein interaction mapping: Characterizing networks of protein-protein interactions including physical and functional links.
• Molecular systems biology: Analyzing cellular processes and systems-level relationships among proteins.
• Comparative interactomics: Transferring and comparing interaction information across species using orthology-based methods.
• Network enrichment analysis: Performing enrichment tests and statistical evaluation on user-defined protein interaction networks.

Methodology:

Integration of known and predicted interactions; novel, scalable algorithms for cross-species transfer; hierarchical, self-consistent orthology annotations organizing proteins into families; a prediction pipeline that infers associations from co-expression data; statistical enrichment tests for user-defined networks.