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BioMed Research International
Volume 2015, Article ID 259157, 9 pages
http://dx.doi.org/10.1155/2015/259157
Research Article

Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

1School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
2Information and Network Administration Center, Heilongjiang University, Harbin 150080, China

Received 29 September 2014; Revised 16 January 2015; Accepted 17 January 2015

Academic Editor: Tatsuya Akutsu

Copyright © 2015 Peng Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.