Mining protein networks for synthetic genetic interactions

Background: The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its essentiality or dispensability. It is therefore of interest to extend this observation and examine whether network properties of two proteins considered simultaneously can determine their joint dispensability, i.e., their propensity for synthetic sick/lethal interaction. Accordingly, we examine the predictive power of protein interaction networks for synthetic genetic interaction in Saccharomyces cerevisiae, an organism in which high confidence protein interaction networks are available and synthetic sick/ lethal gene pairs have been extensively identified. Results: We design a support vector machine system that uses graph-theoretic properties of two proteins in a protein interaction network as input features for prediction of synthetic sick/lethal interactions. The system is trained on interacting and non-int...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Sri R. Paladugu, Shan Zhao, Animesh Ray, Alpan Raval
• Keywords: BMCBI 2008, Gene Pairs, Protein Interaction Networks, Synthetic Genetic Interactions