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Fault tolerance of information processing in gene networks

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  • Emmert-Streib, Frank
  • Dehmer, Matthias

Abstract

The major objective of this paper is to study the fault tolerance of gene networks. For single gene knockouts we investigate the disturbance of the communication abilities of gene networks globally. For our study we use directed scale-free networks resembling important properties of gene networks, e.g., signaling, or transcriptional regulatory networks, as well as metabolic networks and define a Markov chain on the network to model the communication dynamics. This allows us to evaluate the spread of information in the network and, hence, detect differences due to single gene knockouts in the gene-to-gene communication asymptotically regarding the limiting stationary distributions governed by the Markov chain. Further, we study the connection of the global effect of the perturbations with local properties of the network topology by means of statistical hypothesis tests.

Suggested Citation

  • Emmert-Streib, Frank & Dehmer, Matthias, 2009. "Fault tolerance of information processing in gene networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(4), pages 541-548.
    • Handle: RePEc:eee:phsmap:v:388:y:2009:i:4:p:541-548
    DOI: 10.1016/j.physa.2008.10.032
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    1. Réka Albert & Hawoong Jeong & Albert-László Barabási, 1999. "Diameter of the World-Wide Web," Nature, Nature, vol. 401(6749), pages 130-131, September.
    2. Réka Albert & Hawoong Jeong & Albert-László Barabási, 2000. "Error and attack tolerance of complex networks," Nature, Nature, vol. 406(6794), pages 378-382, July.
    3. H. Jeong & B. Tombor & R. Albert & Z. N. Oltvai & A.-L. Barabási, 2000. "The large-scale organization of metabolic networks," Nature, Nature, vol. 407(6804), pages 651-654, October.
    4. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
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