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Spectral analysis of protein-protein interactions in Drosophila melanogaster

Christel Kamp*

Kim Christensen†

  • Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2AZ, United Kingdom

  • Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2AZ, United Kingdom
  • and Physics of Geological Processes, University of Oslo, P. O. Box 1048, Blindern, N-0316 Oslo, Norway

  • *Electronic address: mail@christelkamp.de; c.kamp@imperial.ac.uk
  • †Electronic address: k.christensen@imperial.ac.uk
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Phys. Rev. E 71, 041911 – Published 21 April, 2005

DOI: https://doi.org/10.1103/PhysRevE.71.041911

Abstract

Within a case study on the protein-protein interaction network (PIN) of Drosophila melanogaster we investigate the relation between the network’s spectral properties and its structural features. The frequencies of loops of any size within the network can be derived from the spectrum; also the prevalence of specific subgraphs as a result of the network’s evolutionary history affects its spectrum. The discrete part of the spectral density shows fingerprints of the PIN’s topological features including a preference for loop structures. Duplicate nodes are also characteristic for PINs and we discuss their representation in the PIN’s spectrum as well as their biological implications.

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References (34)

  1. S. H. Strogatz, Nature (London) 410, 268 (2001).
  2. B. Bollobás, Modern Graph Theory (Springer, New York, 1998).
  3. B. Bollobás, Random Graphs (Cambridge University Press, Cambridge, U.K., 2001).
  4. R. Albert and A.-L. Barabási, Rev. Mod. Phys. 74, 47 (2002).
  5. F. Chung, Spectral Graph Theory, Regional Conference Series in Mathematics Vol. 92 (American Mathematical Society, Providence, RI, 1994).
  6. D. Cvetković, M. Doob, and H. Sachs, Spectra of Graphs, Pure and Applied Mathematics, Vol. 87 (Academic Press, New York, 1980).
  7. D. Cvetković, M. Doob, I. Gutman, and A. Torgašev, Recent Results in the Theory of Graph Spectra, Annals of Discrete Mathematics Vol. 36 (North-Holland, Amsterdam, 1988).
  8. N. Biggs, Algebraic Graph Theory (Cambridge University Press, Cambridge, U.K., 1996).
  9. Introductions to spectral analysis and spectral graph theory of varying levels can be found at http://www.sosmath.com/matrix/eigen0/eigen0.html, http://en.wikipedia.org/wiki/Eigenvalue, http://en.wikipedia.org/wiki/Adjacency_matrix, and http://www.win.tue.nl/~aeb/srgbk/node5.html
  10. M. Bauer and O. Golinelli, J. Stat. Phys. 103, 301 (2001).
  11. I. Farkas, I. Derényi, A.-L. Barabási, and T. Vicsek, Phys. Rev. E 64, 026704 (2001).
  12. S. Dorogovtsev, A. Goltsev, J. Mendes, and A. Samukhin, Phys. Rev. E 68, 046109 (2003).
  13. F. Chung, L. Lu, and V. Vu, Ann. Comb. 7, 21 (2003).
  14. F. Chung, L. Lu, and V. Vu, Proc. Natl. Acad. Sci. U.S.A. 100, 6313 (2003).
  15. M. Mihail and C. Papadimitriou, in Proceedings of the 6th International Workshop on Randomization and Approximation Techniques, 2002 Lecture Notes in Comp. Sci., Vol. 2483 (Springer, New York) pp. 254–262.
  16. K.-I. Goh, B. Kahng, and D. Kim, Phys. Rev. E 64, 051903 (2001).
  17. O. Golinelli, e-print cond-mat/0301437.
  18. S. Kirkpatrick and T. Eggarter, Phys. Rev. B 6, 3598 (1972).
  19. S. Evangelou, Phys. Rev. B 27, 1397 (1983).
  20. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, Science 298, 824 (2002).
  21. S. Milo, R. Itzkovitz, N. Kashtan, R. Levitt, S. Shen-Orr, I. Ayzenshtat, M. Sheffer, and U. Alon, Science 303, 1538 (2004).
  22. L. Giot et al., Science 302, 1727 (2003).
  23. Database of Interacting Proteins (DIP), available at http://dip.doe-mbi.ucla.edu/
  24. S. Maslov and K. Sneppen, Science 296, 910 (2002).
  25. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, Computer code MFINDER, available at http://www.weizmann.ac.il/mcb/UriAlon/groupDownloadableData.html
  26. S. Ohno, Evolution by Gene Duplication (Springer, Berlin, 1970).
  27. S. Teichmann and M. Babu, Nat. Genet. 36, 492 (2004).
  28. G. Amoutzias, D. Robertson, S. Oliver, and E. Bornberg-Bauer, EMBO Rep. 5, 1 (2004).
  29. G. Amoutzias, D. Robertson, and E. Bornberg-Bauer, Comput. and Funct. Genomics 5, 79 (2004).
  30. N. Kashtan, S. Itzkovitz, R. Milo, and U. Alon, Bioinformatics 20, 1746 (2004).
  31. FlyBase, A Database of the Drosophila Genome, available at http://flybase.bio.indiana.edu/
  32. http://www.cmth.ph.ic.ac.uk/people/k.christensen/PRE/supp.html
  33. M. Samanta and S. Liang, Proc. Natl. Acad. Sci. U.S.A. 100, 12579 (2003).
  34. S. Itzkovitz, R. Milo, N. Kashtan, G. Ziv, and U. Alon, Phys. Rev. E 68, 026127 (2003).

Outline

Information

Phys. Rev. E 71, 041911– Published 21 April, 2005
  • Received 26 May 2004

© 2005 American Physical Society

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