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Evolving Protein Interaction Networks through Gene Duplication

Author

Listed:
  • Romualdo Pastor-Satorras
  • Eric Smith
  • Ricard V. Solé

Abstract

The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein-protein interactions is highly heterogeneous, with many proteins having few links while a few of them are heavily connected. This particular topology is shared by other cellular networks, such as metabolic pathways, and it has been suggested to be responsible for the high mutational homeostasis displayed by the genome of some organisms. In this paper we explore a recent model of proteome evolution that has been shown to reproduce many of the features displayed by its real counterparts. The model is based on gene duplication plus re-wiring of the newly created genes. The statistical features displayed by the proteome of well-known organisms are reproduced, suggesting that the overall topology of the protein maps naturally emerges from the two leading mechanisms considered by the model.

Suggested Citation

  • Romualdo Pastor-Satorras & Eric Smith & Ricard V. Solé, 2002. "Evolving Protein Interaction Networks through Gene Duplication," Working Papers 02-02-008, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:02-02-008
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    References listed on IDEAS

    as
    1. Richard J. Williams & Neo D. Martinez & Eric L. Berlow & Jennifer A. Dunne & Albert-Laszlo Barabasi, 2001. "Two Degrees of Separation in Complex Food Webs," Working Papers 01-07-036, Santa Fe Institute.
    2. Petra Ross-Macdonald & Paulo S. R. Coelho & Terry Roemer & Seema Agarwal & Anuj Kumar & Ronald Jansen & Kei-Hoi Cheung & Amy Sheehan & Dawn Symoniatis & Lara Umansky & Matthew Heidtman & F. Kenneth Ne, 1999. "Large-scale analysis of the yeast genome by transposon tagging and gene disruption," Nature, Nature, vol. 402(6760), pages 413-418, November.
    3. Ricard V. Solé & Romualdo Pastor-Satorras & Eric Smith & Thomas B. Kepler, 2002. "A Model Of Large-Scale Proteome Evolution," Advances in Complex Systems (ACS), World Scientific Publishing Co. Pte. Ltd., vol. 5(01), pages 43-54.
    4. Réka Albert & Hawoong Jeong & Albert-László Barabási, 2000. "Error and attack tolerance of complex networks," Nature, Nature, vol. 406(6794), pages 378-382, July.
    5. Leland H. Hartwell & John J. Hopfield & Stanislas Leibler & Andrew W. Murray, 1999. "From molecular to modular cell biology," Nature, Nature, vol. 402(6761), pages 47-52, December.
    6. Andreas Wagner, 2001. "Estimating Coarse Gene Network Structure from Large-Scale Gene Perturbation Data," Working Papers 01-09-051, Santa Fe Institute.
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