Optimized protein–protein interaction network usage with context filtering

Abstract

Protein–protein interaction networks (PPIs) collect information on physical—and in some cases–functional interactions between proteins. Most PPIs are annotated with confidence scores, which reflect the probability that a reported interaction is a true interaction. These scores, however, do not allow users to isolate interactions relevant in a particular biological context. Here, we describe solutions for performing context filtering on PPIs to allow biological data interpretation and functional inference in two publicly available PPIs resources (HIPPIE and STRING) and in the proprietary pathway analysis tool and knowledge base Ingenuity Pathway Analysis.