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The Scientific World Journal
Volume 2012 (2012), Article ID 523706, 8 pages
http://dx.doi.org/10.1100/2012/523706
Research Article

Hierarchical Modular Structure Identification with Its Applications in Gene Coexpression Networks

Center for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai 200433, China

Received 2 November 2012; Accepted 25 November 2012

Academic Editors: R. Jiang, W. Tian, J. Wan, and X. Zhao

Copyright © 2012 Shuqin Zhang. 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. R. Guimerà and L. A. N. Amaral, “Functional cartography of complex metabolic networks,” Nature, vol. 433, no. 7028, pp. 895–900, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. M. Girvan and M. E. J. Newman, “Community structure in social and biological networks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 12, pp. 7821–7826, 2002. View at Publisher · View at Google Scholar
  3. A. Arenas, J. Borge-Holthoefer, S. Gómez, and G. Zamora-López, “Optimal map of the modular structure of complex networks,” New Journal of Physics, vol. 12, Article ID 053009, 2010. View at Publisher · View at Google Scholar
  4. J. Dong and S. Horvath, “Understanding network concepts in modules,” BMC Systems Biology, vol. 1, article 24, 2007. View at Publisher · View at Google Scholar
  5. E. Estrada and N. Hatano, “Communicability in complex networks,” Physical Review E, vol. 77, no. 3, Article ID 036111, 2008. View at Publisher · View at Google Scholar
  6. S. Fortunato, “Community detection in graphs,” Physics Reports, vol. 486, no. 3–5, pp. 75–174, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. M. E. J. Newman, “Finding community structure in networks using the eigenvectors of matrices,” Physical Review E, vol. 74, no. 3, Article ID 036104, 2006. View at Publisher · View at Google Scholar
  8. M. E. J. Newman, “Modularity and community structure in networks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 23, pp. 8577–8582, 2006. View at Publisher · View at Google Scholar
  9. M. A. Porter, J. P. Onnela, and P. J. Mucha., “Communities in networks,” Notices of the American Mathematical Society, vol. 56, no. 9, pp. 1082–1102, 2010. View at Google Scholar
  10. 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
  11. Z. Li, S. Zhang, R.-S. Wang, X.-S. Zhang, and L. Chen, “Quantitative function for community detection,” Physical Review E, vol. 77, no. 3, Article ID 036109, 2008. View at Publisher · View at Google Scholar
  12. M. Rosvall and C. T. Bergstrom, “An information-theoretic framework for resolving community structure in complex networks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 18, pp. 7327–7331, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. L. Danon, A. Díaz-Guilera, J. Duch, and A. Arenas, “Comparing community structure identification,” Journal of Statistical Mechanics, no. 9, Article ID 09008, pp. 219–228, 2005. View at Publisher · View at Google Scholar
  14. S. Zhang and H. Zhao, “Community identification in networks with unbalanced structure,” Physical Review E, vol. 85, no. 6, Article ID 066114, 2012. View at Publisher · View at Google Scholar
  15. P. J. Bickel and A. Chen, “A nonparametric view of network models and Newman-Girvan and other modularities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 50, pp. 21068–21073, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. A. Arenas, A. Díaz-Guilera, and C. J. Pérez-Vicente, “Synchronization reveals topological scales in complex networks,” Physical Review Letters, vol. 96, no. 11, Article ID 114102, 2006. View at Publisher · View at Google Scholar
  17. D. Meunier, R. Lambiotte, and E. T. Bullmore, “Modular and hierarchically modular organization of brain networks,” Frontiers Neuroscience, vol. 4, no. 200, 2010. View at Google Scholar
  18. H. Shen, X. Cheng, K. Cai, and M.-B. Hu, “Detect overlapping and hierarchical community structure in networks,” Physica A, vol. 388, no. 8, pp. 1706–1712, 2009. View at Publisher · View at Google Scholar
  19. A. Lancichinetti, S. Fortunato, and J. Kertész, “Detecting the overlapping and hierarchical community structure in complex networks,” New Journal of Physics, vol. 11, Article ID 033015, 2009. View at Publisher · View at Google Scholar
  20. E. Ravasz, “Detecting hierarchical modularity in biological networks,” Computational Systems Biology, vol. 54, pp. 145–160, 2009. View at Google Scholar
  21. P. Erdős and A. R. Rényi, “On random graphs. I,” Publicationes Mathematicae, vol. 6, pp. 290–297, 1959. View at Google Scholar
  22. W. W. Zachary, “An information flow model for conflict and fission in small groups,” Journal of Anthropological Research, vol. 33, pp. 452–473, 1977. View at Google Scholar
  23. R. B. Brem and L. Kruglyak, “The landscape of genetic complexity across 5,700 gene expression traits in yeast,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 5, pp. 1572–1577, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. B. Zhang and S. Horvath, “A general framework for weighted gene co-expression network analysis,” Statistical Applications in Genetics and Molecular Biology, vol. 4, no. 1, article 17, 2005. View at Google Scholar
  25. M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: tool for the unification of biology, the gene ontology consortium,” Nature Genetics, vol. 25, no. 1, pp. 25–29, 2000. View at Publisher · View at Google Scholar
  26. F. Supek, M. Bošnjak, N. Škunca, and T. Šmuc, “REVIGO summarizes and visualizes long lists of gene ontology terms,” PLoS ONE, vol. 6, no. 7, Article ID 21800, 2011. View at Publisher · View at Google Scholar