Modeling pathways of differentiation in genetic regulatory networks with Boolean networks

We have carried out the first examination of pathways of cell differentiation in model genetic networks in which cell types are assumed to be attractors of the nonlinear dynamics, and differentiation corresponds to a transition of the cell to a new basin of attraction, which may be induced by a signal or noise perturbation. The associated flow along a transient to a new attractor corresponds to a pathway of differentiation. We have measured a variety of features of such model pathways of differentiation, most of which should be observable using gene array techniques. © 2005 Wiley Periodicals, Inc. Complexity 11: 52–60, 2005

[1]  C. Espinosa-Soto,et al.  A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profilesw⃞ , 2004, The Plant Cell Online.

[2]  S. Kauffman.  Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[3]  S. Kauffman.  Gene regulation networks: a theory for their global structure and behaviors. , 1971, Current topics in developmental biology.

[4]  Jacques Monod,et al.  On the Regulation of Gene Activity , 1961 .

[5]  Bernard Derrida,et al.  Distribution of local magnetisations in random networks of automata , 1987 .

[6]  S. Kauffman.  The large scale structure and dynamics of gene control circuits: an ensemble approach. , 1974, Journal of theoretical biology.

[7]  P. Andrews,et al.  From teratocarcinomas to embryonic stem cells. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[8]  B. Derrida,et al.  Random networks of automata: a simple annealed approximation , 1986 .

[9]  S A Kauffman,et al.  Developmental logic and its evolution. , 1987, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  Jacques Monod,et al.  Genetic Repression, Allosteric Inhibition, and Cellular Differentiation , 1963 .

[11]  Q. Ouyang,et al.  The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[13]  H. Othmer,et al.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.