Methodology article

A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge

Young-Rae Cho¹ , Lei Shi¹ , Murali Ramanathan² and Aidong Zhang¹

¹  Department of Computer Science and Engineering, State University of New York, Buffalo, NY, USA

²  Department of Pharmaceutical Sciences, State University of New York, Buffalo, NY, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:382doi:10.1186/1471-2105-9-382

Published:	18 September 2008

Abstract

Background

The functional characterization of newly discovered proteins has been a challenge in the post-genomic era. Protein-protein interactions provide insights into the functional analysis because the function of unknown proteins can be postulated on the basis of their interaction evidence with known proteins. The protein-protein interaction data sets have been enriched by high-throughput experimental methods. However, the functional analysis using the interaction data has a limitation in accuracy because of the presence of the false positive data experimentally generated and the interactions that are a lack of functional linkage.

Results

Protein-protein interaction data can be integrated with the functional knowledge existing in the Gene Ontology (GO) database. We apply similarity measures to assess the functional similarity between interacting proteins. We present a probabilistic framework for predicting functions of unknown proteins based on the functional similarity. We use the leave-one-out cross validation to compare the performance. The experimental results demonstrate that our algorithm performs better than other competing methods in terms of prediction accuracy. In particular, it handles the high false positive rates of current interaction data well.

Conclusion

The experimentally determined protein-protein interactions are erroneous to uncover the functional associations among proteins. The performance of function prediction for uncharacterized proteins can be enhanced by the integration of multiple data sources available.