STRINGdb

STRINGdb provides, in version 9.1, a comprehensive, scored resource of known and predicted protein-protein interactions and functional associations across more than 1100 organisms to support analysis of cellular mechanisms.

Key Features:

• Integration of interaction data: Aggregates experimental data, computational predictions, and lower-quality datasets to produce a combined protein association network.
• Scoring system: Assigns confidence scores to each association based on evidence type and reliability.
• Automated text mining: Extracts interaction information from scientific literature, including full-text articles, using automated text-mining algorithms.
• Cross-species interaction transfer: Employs a re-designed algorithm to transfer interactions between model organisms for comparative analyses.
• Functional enrichment analysis: Provides statistical enrichment calculations for biological processes and pathways within protein networks.
• Organismal coverage: Contains interaction and association data spanning more than 1100 organisms.

Scientific Applications:

• Functional genomics: Elucidates gene and protein functions by analyzing interaction partners and network context.
• Pathway analysis: Maps proteins onto biological pathways by integrating interaction data with pathway databases.
• Comparative biology: Enables cross-species network comparisons and inference of conserved mechanisms via transferred interactions.

Methodology:

Computational methods include integration and scoring of diverse interaction data sources, automated text mining of scientific literature including full-text articles, and a re-designed algorithm for transferring interactions between model organisms.