wppi

wppi weights protein-protein interactions by predicting functional relevance based on functional annotations and prioritizes genes using network topology, functional scores, and a path search algorithm.

Key Features:

• Functional relevance prediction: Predicts functional relevance of protein-protein interactions using functional annotations such as Human Phenotype Ontology and Gene Ontology.
• Gene prioritization: Prioritizes genes based on network topology, functional scores, and a path search algorithm.
• Context-aware weighting: Addresses the limitation that database knowledge is general and not specific for cell type, physiological condition, or other contexts determining functional connections.

Scientific Applications:

• Omics data analysis: Supports omics data analysis and modeling by providing weighted protein-protein interaction data.
• Signaling network modeling: Helps identify functional connections that contribute to signaling in specific biological contexts.

Methodology:

The package uses functional annotations including Human Phenotype Ontology and Gene Ontology to evaluate interaction relevance, and applies network topology, functional scores, and a path search algorithm for gene prioritization.