A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks

  • Min Li
  • Jianxin Wang
  • Jianer Chen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)


Identification of functional modules in large protein interaction networks is crucial to understand principles of cellular organization, processes and functions. As a protein can perform different functions, functional modules overlap with each other. In this paper, we presented a new algorithm OMFinder for mining overlapping functional modules in protein interaction networks by using graph split and reduction. We applied algorithm OMFinder to the core protein interaction network of budding yeast collected from DIP database. The experimental results showed that algorithm OMFinder detected many significant overlapping functional modules with various topologies. The significances of identified modules were evaluated by using functional categories from MIPS database. Most importantly, our algorithm had very low discard rate compared to other approaches of detecting overlapping modules.


protein interaction network functional module graph 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Min Li
    • 1
  • Jianxin Wang
    • 1
  • Jianer Chen
    • 1
    • 2
  1. 1.School of Information Science and EngineeringCentral South UniversityChangshaP.R. China
  2. 2.Department of Computer ScienceTexas A&M UniversityCollege StationUSA

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