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This article is part of the supplement: Proceedings of the 23rd International Conference on Genome Informatics (GIW 2012)

Open Access Proceedings

Supervised maximum-likelihood weighting of composite protein networks for complex prediction

Chern Han Yong1*, Guimei Liu2, Hon Nian Chua3 and Limsoon Wong2

Author Affiliations

1 Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore

2 School of Computing, National University of Singapore, Singapore

3 Institute for Infocomm Research, Singapore

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BMC Systems Biology 2012, 6(Suppl 2):S13  doi:10.1186/1752-0509-6-S2-S13

Published: 12 December 2012

Abstract

Background

Protein complexes participate in many important cellular functions, so finding the set of existent complexes is essential for understanding the organization and regulation of processes in the cell. With the availability of large amounts of high-throughput protein-protein interaction (PPI) data, many algorithms have been proposed to discover protein complexes from PPI networks. However, such approaches are hindered by the high rate of noise in high-throughput PPI data, including spurious and missing interactions. Furthermore, many transient interactions are detected between proteins that are not from the same complex, while not all proteins from the same complex may actually interact. As a result, predicted complexes often do not match true complexes well, and many true complexes go undetected.

Results

We address these challenges by integrating PPI data with other heterogeneous data sources to construct a composite protein network, and using a supervised maximum-likelihood approach to weight each edge based on its posterior probability of belonging to a complex. We then use six different clustering algorithms, and an aggregative clustering strategy, to discover complexes in the weighted network. We test our method on Saccharomyces cerevisiae and Homo sapiens, and show that complex discovery is improved: compared to previously proposed supervised and unsupervised weighting approaches, our method recalls more known complexes, achieves higher precision at all recall levels, and generates novel complexes of greater functional similarity. Furthermore, our maximum-likelihood approach allows learned parameters to be used to visualize and evaluate the evidence of novel predictions, aiding human judgment of their credibility.

Conclusions

Our approach integrates multiple data sources with supervised learning to create a weighted composite protein network, and uses six clustering algorithms with an aggregative clustering strategy to discover novel complexes. We show improved performance over previous approaches in terms of precision, recall, and number and quality of novel predictions. We present and visualize two novel predicted complexes in yeast and human, and find external evidence supporting these predictions.