Journal of Biomedicine and Biotechnology
Volume 2008 (2008), Article ID 860270, 10 pages
doi:10.1155/2008/860270
Research Article

An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

Guangyu Cui,1 Yu Chen,1 De-Shuang Huang,2 and Kyungsook Han1

1School of Computer Science and Engineering, Inha University, Incheon 402-751, South Korea
2Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, China

Received 1 September 2007; Revised 12 November 2007; Accepted 24 December 2007

Academic Editor: Daniel Howard

Copyright © 2008 Guangyu Cui 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.

Linked References

  1. D. Bu, Y. Zhao, L. Cai, et al., “Topological structure analysis of the protein-protein interaction network in budding yeast,” Nucleic Acids Research, vol. 31, no. 9, pp. 2443–2450, 2003. View at Publisher · View at Google Scholar
  2. R. Battiti and M. Protasi, “Reactive local search for the maximum clique problem,” Algorithmica, vol. 29, no. 4, pp. 610–637, 2001.
  3. K. Katayama, A. Hamamoto, and H. Narihisa, “An effective local search for the maximum clique problem,” Information Processing Letters, vol. 95, no. 5, pp. 503–511, 2005. View at Publisher · View at Google Scholar · View at MathSciNet
  4. B. Adamcsek, G. Palla, I. Farkas, I. Derényi, and T. Vicsek, “CFinder: locating cliques and overlapping modules in biological networks,” Bioinformatics, vol. 22, no. 8, pp. 1021–1023, 2006. View at Publisher · View at Google Scholar · View at PubMed
  5. G. Palla, I. Derényi, I. Farkas, and T. Vicsek, “Uncovering the overlapping community structure of complex networks in nature and society,” Nature, vol. 435, no. 7043, pp. 814–818, 2005. View at Publisher · View at Google Scholar · View at PubMed
  6. B.-H. Ju and K. Han, “Complexity management in visualizing protein interaction networks,” Bioinformatics, vol. 19, pp. i177–i179, 2003. View at Publisher · View at Google Scholar
  7. F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, and D. Paris, “Defining and identifying communities in networks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 9, pp. 2658–2663, 2004. View at Publisher · View at Google Scholar · View at PubMed
  8. V. Spirin and L. A. Mirny, “Protein complexes and functional modules in molecular networks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 21, pp. 12123–12126, 2003. View at Publisher · View at Google Scholar · View at PubMed
  9. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki, “A comprehensive two-hybrid analysis to explore the yeast protein interactome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 8, pp. 4569–4574, 2001. View at Publisher · View at Google Scholar · View at PubMed
  10. P. Uetz, L. Giot, G. Cagney, et al., “A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae,” Nature, vol. 403, no. 6770, pp. 623–627, 2000. View at Publisher · View at Google Scholar · View at PubMed
  11. A. Ruepp, A. Zollner, D. Maier, et al., “The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes,” Nucleic Acids Research, vol. 32, no. 18, pp. 5539–5545, 2004. View at Publisher · View at Google Scholar · View at PubMed