Detecting protein complexes by an improved Affinity Propagation algorithm in protein-protein interaction networks

作者：Wang Yu^*; Gao Lin

来源：Journal of Computers, 2012, 7(7): 1761-1768.

DOI：10.4304/jcp.7.7.1761-1768

• Affinity propagation
• AP algorithm
• Biological studies
• Cellular process
• Computationally efficient
• CPM algorithms
• Effective algorithms
• Filter noise
• Graph clustering
• High precision
• Identification of proteins
• Protein complexes
• Protein-protein interaction networks

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.

• 出版日期2012
• 单位西安电子科技大学