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Estimating Coarse Gene Network Structure from Large-Scale Gene Perturbation Data

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  • Andreas Wagner

Abstract

Large scale gene perturbation experiments generate information about the number of genes whose activity is directly or indirectly affected by a gene perturbation. From this information, one can numerically estimate coarse structural network features such as the total number of direct regulatory interactions and the number of isolated subnetworks in a transcriptional regulation network. Applied to the results of a large-scale gene knockout experiment in the yeast Saccharomyces cerevisiae, the results suggests that the yeast transcriptional regulatory network is very sparse, containing no more direct regulatory interactions than genes. The network comprises more than one hundred independent sub-networks.

Suggested Citation

  • Andreas Wagner, 2001. "Estimating Coarse Gene Network Structure from Large-Scale Gene Perturbation Data," Working Papers 01-09-051, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:01-09-051
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    References listed on IDEAS

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    1. David J. Lockhart & Elizabeth A. Winzeler, 2000. "Genomics, gene expression and DNA arrays," Nature, Nature, vol. 405(6788), pages 827-836, June.
    2. Gernot Grabher & Walter W. Powell (ed.), 2004. "Networks," Books, Edward Elgar Publishing, volume 0, number 2771.
    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. Santiago F. Elena & Richard E. Lenski, 1997. "Test of synergistic interactions among deleterious mutations in bacteria," Nature, Nature, vol. 390(6658), pages 395-398, November.
    5. Andreas Wagner & David Fell, 2000. "The Small World Inside Large Metabolic Networks," Working Papers 00-07-041, Santa Fe Institute.
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    Cited by:

    1. Romualdo Pastor-Satorras & Eric Smith & Ricard V. Solé, 2002. "Evolving Protein Interaction Networks through Gene Duplication," Working Papers 02-02-008, Santa Fe Institute.

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