Literature DB >> 15572453

Genetic networks with canalyzing Boolean rules are always stable.

Stuart Kauffman1, Carsten Peterson, Björn Samuelsson, Carl Troein.   

Abstract

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are dynamically stable. Furthermore, for architectures with few inputs per node, the dynamics of the networks is close to critical. In addition, the fraction of genes that are active decreases with the number of inputs per node. These results are based upon investigating ensembles of networks using analytical methods. Also, for different in-degree distributions, the numbers of fixed points and cycles are calculated, with results intuitively consistent with stability analysis; fewer inputs per node implies more cycles, and vice versa. There are hints that genetic networks acquire broader degree distributions with evolution, and hence our results indicate that for single cells, the dynamics should become more stable with evolution. However, such an effect is very likely compensated for by multicellular dynamics, because one expects less stability when interactions among cells are included. We verify this by simulations of a simple model for interactions among cells.

Mesh:

Year:  2004        PMID: 15572453      PMCID: PMC534611          DOI: 10.1073/pnas.0407783101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  7 in total

1.  Superpolynomial growth in the number of attractors in Kauffman networks.

Authors:  Björn Samuelsson; Carl Troein
Journal:  Phys Rev Lett       Date:  2003-03-04       Impact factor: 9.161

2.  Random Boolean network models and the yeast transcriptional network.

Authors:  Stuart Kauffman; Carsten Peterson; Björn Samuelsson; Carl Troein
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-01       Impact factor: 11.205

3.  From topology to dynamics in biochemical networks.

Authors:  Jeffrey J. Fox; Colin C. Hill
Journal:  Chaos       Date:  2001-12       Impact factor: 3.642

4.  A natural class of robust networks.

Authors:  Maximino Aldana; Philippe Cluzel
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-09       Impact factor: 11.205

5.  RegulonDB: a database on transcriptional regulation in Escherichia coli.

Authors:  A M Huerta; H Salgado; D Thieffry; J Collado-Vides
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

6.  A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

Authors:  P Uetz; L Giot; G Cagney; T A Mansfield; R S Judson; J R Knight; D Lockshon; V Narayan; M Srinivasan; P Pochart; A Qureshi-Emili; Y Li; B Godwin; D Conover; T Kalbfleisch; G Vijayadamodar; M Yang; M Johnston; S Fields; J M Rothberg
Journal:  Nature       Date:  2000-02-10       Impact factor: 49.962

7.  Transcriptional regulatory networks in Saccharomyces cerevisiae.

Authors:  Tong Ihn Lee; Nicola J Rinaldi; François Robert; Duncan T Odom; Ziv Bar-Joseph; Georg K Gerber; Nancy M Hannett; Christopher T Harbison; Craig M Thompson; Itamar Simon; Julia Zeitlinger; Ezra G Jennings; Heather L Murray; D Benjamin Gordon; Bing Ren; John J Wyrick; Jean-Bosco Tagne; Thomas L Volkert; Ernest Fraenkel; David K Gifford; Richard A Young
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

  7 in total
  63 in total

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Journal:  Microbiol Mol Biol Rev       Date:  2015-11-25       Impact factor: 11.056

2.  Topology of biological networks and reliability of information processing.

Authors:  Konstantin Klemm; Stefan Bornholdt
Journal:  Proc Natl Acad Sci U S A       Date:  2005-12-08       Impact factor: 11.205

3.  Boolean dynamics of biological networks with multiple coupled feedback loops.

Authors:  Yung-Keun Kwon; Kwang-Hyun Cho
Journal:  Biophys J       Date:  2007-01-26       Impact factor: 4.033

Review 4.  A boolean network modelling of receptor mosaics relevance of topology and cooperativity.

Authors:  L F Agnati; D Guidolin; G Leo; K Fuxe
Journal:  J Neural Transm (Vienna)       Date:  2006-09-12       Impact factor: 3.575

5.  Robustness, canalyzing functions and systems design.

Authors:  Johannes Rauh; Nihat Ay
Journal:  Theory Biosci       Date:  2013-09-18       Impact factor: 1.919

Review 6.  Boolean network models of cellular regulation: prospects and limitations.

Authors:  Stefan Bornholdt
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

7.  Nested Canalyzing, Unate Cascade, and Polynomial Functions.

Authors:  Abdul Salam Jarrah; Blessilda Raposa; Reinhard Laubenbacher
Journal:  Physica D       Date:  2007-09-15       Impact factor: 2.300

8.  Canalization and control in automata networks: body segmentation in Drosophila melanogaster.

Authors:  Manuel Marques-Pita; Luis M Rocha
Journal:  PLoS One       Date:  2013-03-08       Impact factor: 3.240

9.  A tutorial on analysis and simulation of boolean gene regulatory network models.

Authors:  Yufei Xiao
Journal:  Curr Genomics       Date:  2009-11       Impact factor: 2.236

10.  Robustness in regulatory interaction networks. A generic approach with applications at different levels: physiologic, metabolic and genetic.

Authors:  Jacques Demongeot; Hedi Ben Amor; Adrien Elena; Pierre Gillois; Mathilde Noual; Sylvain Sené
Journal:  Int J Mol Sci       Date:  2009-11-20       Impact factor: 6.208

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