Inferring edge function in protein-protein interaction networks

Motivation: Post-translational modifications (PTMs) regulate many key cellular processes. Numerous studies have linked the topology of protein-protein interaction (PPI) networks to many biological phenomena such as key regulatory processes and disease. However, these methods fail to give insight in the functional nature of these interactions. On the other hand, pathways are commonly used to gain biological insight into the function of PPIs in the context of cascading interactions, sacrificing the coverage of networks for rich functional annotations on each PPI. We present a machine learning approach that uses Gene Ontology, InterPro and Pfam annotations to infer the edge functions in PPI networks, allowing us to combine the high coverage of networks with the information richness of pathways.\n\nResults: An ensemble method with a combination Logistic Regression and Random Forest classifiers trained on a high-quality set of annotated interactions, with a total of 18 unique labels, achieves high a average F1 score 0.88 despite not taking advantage of multi-label dependencies. When applied to the human interactome, our method confidently classifies 62% of interactions at a probability of 0.7 or higher.\n\nAvailability: Software and data are available at https://github.com/DavisLaboratory/pyPPI\n\nContact: davis.m@wehi.edu.au\n\nSupplementary information: Supplementary data are available at Bioinformatics online.