Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Research article

Mining protein networks for synthetic genetic interactions

Sri R Paladugu13, Shan Zhao2, Animesh Ray1 and Alpan Raval13*

Author Affiliations

1 Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA

2 Virtual Endoscopy and Computer-Aided Diagnosis Laboratory, Department of Radiology, National Institutes of Health Clinical Center, Bethesda, MD 20892-1182, USA

3 School of Mathematical Sciences, Claremont Graduate University, 710 N. College Avenue, Claremont, CA 91711, USA

For all author emails, please log on.

BMC Bioinformatics 2008, 9:426  doi:10.1186/1471-2105-9-426

Published: 9 October 2008

Abstract

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-interacting gene pairs culled from large scale genetic screens as well as literature-curated data. We find that the method is capable of predicting synthetic genetic interactions with sensitivity and specificity both exceeding 85%. We further find that the prediction performance is reasonably robust with respect to errors in the protein interaction network and with respect to changes in the features of test datasets. Using the prediction system, we carried out novel predictions of synthetic sick/lethal gene pairs at a genome-wide scale. These pairs appear to have functional properties that are similar to those that characterize the known synthetic lethal gene pairs.

Conclusion

Our analysis shows that protein interaction networks can be used to predict synthetic lethal interactions with accuracies on par with or exceeding that of other computational methods that use a variety of input features, including functional annotations. This indicates that protein interaction networks could plausibly be rich sources of information about epistatic effects among genes.