Volume 7 Number 7 (Jul. 2012)
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JCP 2012 Vol.7(7): 1761-1768 ISSN: 1796-203X
doi: 10.4304/jcp.7.7.1761-1768

Detecting Protein Complexes by an Improved Affinity Propagation Algorithm in Protein-Protein Interaction Networks

Yu Wang, Lin Gao
School of Computer Science and Technology, Xidian University, Xi’an, China
Abstract—Identification of protein complexes in protein-protein interaction (PPI) networks is important in understanding cellular processes. In this paper, we propose a computationally efficient algorithm, named by Overlapped Affinity Propagation (OAP), which is based on Affinity Propagation algorithm (AP) to detect protein complexes. First, AP algorithm is adopted to obtain a hard partition of the network. Then the candidate overlapping proteins for each community are identified. Finally, a strategy is constructed with an immediate purpose to filter noise in these detected protein complexes. We apply the OAP to the Saccharomyces cerevisiae PPI network, and the experimental results demonstrate that our algorithm can discover protein complexes with high precision by compared with the AP, MCL, CoAch and CPM algorithms. Our proposed method is validated as an effective algorithm in identifying protein complexes and can provide more insights for future biological study.

Index Terms—Protein-protein interaction networks, graph clustering, protein complexes, affinity propagation.

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Cite: Yu Wang, Lin Gao, "Detecting Protein Complexes by an Improved Affinity Propagation Algorithm in Protein-Protein Interaction Networks," Journal of Computers vol. 7, no. 7, pp. 1761-1768, 2012.

General Information

ISSN: 1796-203X
Abbreviated Title: J.Comput.
Frequency: Bimonthly
Editor-in-Chief: Prof. Liansheng Tan
Executive Editor: Ms. Nina Lee
Abstracting/ Indexing: DBLP, EBSCO,  ProQuest, INSPEC, ULRICH's Periodicals Directory, WorldCat,etc
E-mail: jcp@iap.org
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