Density based merging search of functional modules in protein-protein interaction (PPI) networks

  • Authors:

  • Wei Wang;Jinwen Ma

  • Affiliations:

  • Department of Information Science, School of Mathematical Sciences and LMAM, Peking University, Beijing, China;Department of Information Science, School of Mathematical Sciences and LMAM, Peking University, Beijing, China

  • Venue:
  • ICIC'10 Proceedings of the 6th international conference on Advanced intelligent computing theories and applications: intelligent computing
  • Year:
  • 2010

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Abstract

Discovering functional modules in a protein-protein interaction (PPI) network is very important for understanding the organization and function of the related biological system. The main strategy for this discovery is to translate the PPI network into a mathematical graph which can be analyzed with graph theory. In this paper, we propose a Density Based Merging Search (DBMS) algorithm to discover the complexes of a PPI graph corresponding to the functional modules in the PPI network. The DBMS algorithm starts from a single vertex with the highest density of connecting, then adds it's neighbor vertexes with the sufficiently high density of connecting one by one, and finally obtain one complex when there is no vertex to be added. The same DBMS procedure can be conducted on the rest of the vertexes in the PPI graph till all the complexes are found out. It is demonstrated by the experiments on six PPI datasets that the DBMS algorithm is efficient for discovering the complexes of a PPI network.