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EURASIP Journal on Bioinformatics and Systems Biology
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Comparison of Gene Regulatory Networks via Steady-State Trajectories

EURASIP Journal on Bioinformatics and Systems Biology volume 2007, Article number: 82702 (2007) Cite this article

Abstract

The modeling of genetic regulatory networks is becoming increasingly widespread in the study of biological systems. In the abstract, one would prefer quantitatively comprehensive models, such as a differential-equation model, to coarse models; however, in practice, detailed models require more accurate measurements for inference and more computational power to analyze than coarse-scale models. It is crucial to address the issue of model complexity in the framework of a basic scientific paradigm: the model should be of minimal complexity to provide the necessary predictive power. Addressing this issue requires a metric by which to compare networks. This paper proposes the use of a classical measure of difference between amplitude distributions for periodic signals to compare two networks according to the differences of their trajectories in the steady state. The metric is applicable to networks with both continuous and discrete values for both time and state, and it possesses the critical property that it allows the comparison of networks of different natures. We demonstrate application of the metric by comparing a continuous-valued reference network against simplified versions obtained via quantization.

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Authors and Affiliations

  1. Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA

    Marcel Brun, Seungchan Kim & Edward R Dougherty

  2. School of Computing and Informatics, Ira A. Fulton School of Engineering, Arizona State University, Tempe, AZ, 85287, USA

    Seungchan Kim

  3. Department of Mathematics and Statistics, College of Liberal Arts and Sciences, Arizona State University, Tempe, AZ, 85287, USA

    Woonjung Choi

  4. Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA

    Edward R Dougherty

  5. Cancer Genomics Laboratory, Department of Pathology, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA

    Edward R Dougherty

Authors
  1. Marcel Brun
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  2. Seungchan Kim
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  3. Woonjung Choi
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  4. Edward R Dougherty
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Correspondence to Marcel Brun.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Brun, M., Kim, S., Choi, W. et al. Comparison of Gene Regulatory Networks via Steady-State Trajectories. J Bioinform Sys Biology 2007, 82702 (2007). https://doi.org/10.1155/2007/82702

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  • DOI: https://doi.org/10.1155/2007/82702

Keywords

  • Predictive Power
  • Regulatory Network
  • Model Complexity
  • System Biology
  • Computational Power