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Networks and Heterogeneous Media

2008, Volume 3, Issue 2: 333-343. doi: 10.3934/nhm.2008.3.333
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The simulation of gene knock-out in scale-free random Boolean models of genetic networks

  • 1.
    Dipartimento di scienze sociali, cognitive e quantitative, Università di Modena e Reggio Emilia, Via Allegri 9, 42100 Reggio Emilia
  • 2.
    Excellence Environmental Carcinogenesis, Environmental Protection and Health Prevention Agency, Emilia-Romagna, viale Filopanti 22, Bologna
  • 3.
    Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4
  • Received: 01 August 2007 Revised: 01 February 2008

  • Primary: 92D10, 37B99; Secondary: 92C40, 94C15.

  • This paper describes the effects of perturbations, which simulate the knock-out of single genes, one at a time, in random Boolean models of genetic networks (RBN). The analysis concentrates on the probability distribution of so-called avalanches (defined in the text) in gene expression. The topology of the random Boolean networks considered here is of the scale-free type, with a power-law distribution of outgoing connectivities. The results for these scale-free random Boolean networks (SFRBN) are compared with those of classical RBNs, which had been previously analyzed, and with experimental data on S. cerevisiae. It is shown that, while both models approximate the main features of the distribution of experimental data, SFRBNs tend to overestimate the number of large avalanches.

    Citation: Roberto Serra, Marco Villani, Alex Graudenzi, Annamaria Colacci, Stuart A. Kauffman. The simulation of gene knock-out in scale-free random Boolean models of genetic networks[J]. Networks and Heterogeneous Media, 2008, 3(2): 333-343. doi: 10.3934/nhm.2008.3.333

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  • This paper describes the effects of perturbations, which simulate the knock-out of single genes, one at a time, in random Boolean models of genetic networks (RBN). The analysis concentrates on the probability distribution of so-called avalanches (defined in the text) in gene expression. The topology of the random Boolean networks considered here is of the scale-free type, with a power-law distribution of outgoing connectivities. The results for these scale-free random Boolean networks (SFRBN) are compared with those of classical RBNs, which had been previously analyzed, and with experimental data on S. cerevisiae. It is shown that, while both models approximate the main features of the distribution of experimental data, SFRBNs tend to overestimate the number of large avalanches.


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    1. Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis, Marco Antoniotti, CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer, 2015, 14s4, 1176-9351, CIN.S19965, 10.4137/CIN.S19965
    2. Marco Villani, Luca La Rocca, Stuart Alan Kauffman, Roberto Serra, Dynamical Criticality in Gene Regulatory Networks, 2018, 2018, 1076-2787, 1, 10.1155/2018/5980636
    3. Marco Villani, Salvatore Magrì, Andrea Roli, Roberto Serra, 2020, Chapter 2, 978-3-030-45015-1, 7, 10.1007/978-3-030-45016-8_2
    4. A. Graudenzi, R. Serra, M. Villani, A. Colacci, S.A. Kauffman, Robustness Analysis of a Boolean Model of Gene Regulatory Network with Memory, 2011, 18, 1066-5277, 559, 10.1089/cmb.2010.0224
    5. Junxiu Liu, Jufang Dai, Min Su, Shunsheng Zhang, Yifan Hua, Yanhu Wang, Haiping Shu, 2022, De-redundancy in a random boolean network using knockout, 9781450392686, 132, 10.1145/3520304.3528997
    6. Marco Villani, Davide Campioli, Chiara Damiani, Andrea Roli, Alessandro Filisetti, Roberto Serra, Dynamical regimes in non-ergodic random Boolean networks, 2017, 16, 1567-7818, 353, 10.1007/s11047-016-9552-7
    7. Marco Villani, Roberto Serra, On the dynamical properties of a model of cell differentiation, 2013, 2013, 1687-4153, 10.1186/1687-4153-2013-4
    8. Salvatore Magrì, Marco Villani, Andrea Roli, Roberto Serra, 2019, Chapter 2, 978-3-030-21732-7, 17, 10.1007/978-3-030-21733-4_2
    9. Alberto Vezzani, Marco Villani, Roberto Serra, 2020, Chapter 3, 978-3-030-45015-1, 17, 10.1007/978-3-030-45016-8_3
    10. Alex Graudenzi, Roberto Serra, Marco Villani, Chiara Damiani, Annamaria Colacci, Stuart A. Kauffman, Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory, 2011, 18, 1066-5277, 1291, 10.1089/cmb.2010.0069
    11. Sara Montagna, Michele Braccini, Andrea Roli, 2018, Chapter 8, 978-3-319-78657-5, 104, 10.1007/978-3-319-78658-2_8
    12. Roberto Serra, 2014, Chapter 16, 978-3-319-12744-6, 201, 10.1007/978-3-319-12745-3_16
    13. Marco Antonio Leonel Caetano, Takashi Yoneyama, The effects of node exclusion on the centrality measures in graph models of interacting economic agents, 2015, 430, 03784371, 216, 10.1016/j.physa.2015.02.093
    14. Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti, 2014, Chapter 13, 978-3-319-12744-6, 151, 10.1007/978-3-319-12745-3_13
    15. Roberto Serra, Marco Villani, 2013, Chapter 3, 978-94-007-6802-4, 65, 10.1007/978-94-007-6803-1_3
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  • © 2008 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
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