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Large-scale inference and graph-theoretical analysis of gene-regulatory networks in B. Subtilis

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  • Christensen, Claire
  • Gupta, Anshuman
  • Maranas, Costas D.
  • Albert, Réka

Abstract

We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B.subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. By employing a computational, linear correlative procedure to generate these networks, and by analyzing the networks from a graph theoretical perspective, we are able to verify the biological viability of our inferred networks, and we demonstrate that our networks’ graph-theoretical properties are remarkably similar to those of other biological systems. In addition, by comparing our inferred networks to those of a previous, noisier implementation of the linear inference process [A. Gupta, J.D. Varner, C.D. Maranas, Comput. Chem. Eng. 29 (2005) 565], we are able to identify trends in graph-theoretical behavior that occur both in our networks as well as in their perturbed counterparts. These commonalities in behavior at multiple levels of complexity allow us to ascertain the level of complexity to which our process is robust to noise.

Suggested Citation

  • Christensen, Claire & Gupta, Anshuman & Maranas, Costas D. & Albert, Réka, 2007. "Large-scale inference and graph-theoretical analysis of gene-regulatory networks in B. Subtilis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 373(C), pages 796-810.
    • Handle: RePEc:eee:phsmap:v:373:y:2007:i:c:p:796-810
    DOI: 10.1016/j.physa.2006.04.118
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    Cited by:

    1. Salcedo-Sanz, S. & Cuadra, L., 2019. "Quasi scale-free geographically embedded networks over DLA-generated aggregates," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 523(C), pages 1286-1305.
    2. Radillo-Ochoa, Diego & Rodríguez-Hernández, Andrea & Terrero-Escalante, César A., 2023. "Bifurcation in cellular evolution," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 615(C).

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