Chaotic gene regulatory networks can be robust against mutations and noise

Journal of Theoretical Biology

Volumn 253, Issue 2, 2008, Pages 323-332

  Sevim, Volkan ^a,b   Rikvold, Per Arne ^a,b,c  

^a FLORIDA STATE UNIVERSITY   (United States)

^b Florida State University   (United States)

^c FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Gene regulatory network; Random threshold network; Robustness; State space structure

Indexed keywords

DAMAGE; GENE EXPRESSION; MUTATION; NOISE; PHENOTYPE;

ARTICLE; GENE EXPRESSION; GENE MUTATION; GENE REGULATORY NETWORK; NOISE; PHENOTYPE; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

ANIMALS; EVOLUTION; GENE REGULATORY NETWORKS; MODELS, GENETIC; MUTATION; SELECTION (GENETICS);

EID: 45649084243     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.03.003     Document Type: Article

References (45)

1. Albert R., and Othmer H.G. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol. 223 1 (2003) 1-18
2. Aldana M. Boolean dynamics of networks with scale-free topology. Physica D 185 1 (2003) 45-66
3. Aldana M., Coppersmith S., and Kadanoff L.P. Boolean dynamics with random couplings. In: Kaplan E., Marsden J.E., and Sreenivasan K.R. (Eds). Perspectives and Problems in Nonlinear Science. A Celebratory Volume in Honor of Lawrence Sirovich (2003), Springer, Berlin, Heidelberg, New York 23-89
4. Alon U., Surette M.G., Barkai N., and Leibler S. Robustness in bacterial chemotaxis. Nature (London) 397 6715 (1999) 168-171
5. Azevedo R.B.R., Lohaus R., Srinivasan S., Dang K.K., and Burch C.L. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature (London) 440 7080 (2006) 87-90
6. Balcan D., Kabakçi{dotless}oǧlu A., Mungan M., and Erzan A. The information coded in the yeast response elements accounts for most of the topological properties of its transcriptional regulation network. PLoS ONE 2 6 (2007) e501
7. Barkai N., and Leibler S. Robustness in simple biochemical networks. Nature (London) 387 6636 (1997) 913-917
8. Bergman A., and Siegal M.L. Evolutionary capacitance as a general feature of complex gene networks. Nature (London) 424 6948 (2003) 549-552
9. Chaves M., Albert R., and Sontag E.D. Robustness and fragility of Boolean models for genetic regulatory networks. J. Theor. Biol. 235 3 (2005) 431-449
10. Ciliberti S., Martin O.C., and Wagner A. Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput. Biol. 3 2 (2007) 164-173
11. de Visser J.A.G.M., Hermisson J., Wagner G.P., Meyers L.A., Bagheri-Chaichian H., Blanchard J.L., Chao L., Cheverud J.M., Elena S.F., Fontana W., Gibson G., Hansen T.F., Krakauer D., Lewontin R.C., Ofria C., Rice S.H., von Dassow G., Wagner A., and Whitlock M.C. Perspective: evolution and detection of genetic robustness. Evolution 57 9 (2003) 1959-1972
12. Derrida B., and Pomeau Y. Random networks of automata-a simple annealed approximation. Europhys. Lett. 1 2 (1986) 45-49
13. Drossel B. Random Boolean networks. In: Schuster H.G. (Ed). Annual Review of Nonlinear Dynamics and Complexity vol. 1 (2007), Wiley-VCH, Weinheim preprint: arXiv:0706.3351
14. Ellson J., Gansner E.R., Koutsofios E., North S.C., and Woodhull G. Graphviz and dynagraph-static and dynamic graph drawing tools. In: Junger M., and Mutzel P. (Eds). Graph Drawing Software (2003), Springer-Verlag, Berlin, Heidelberg, New York 127-148
15. Foster D.V., Kauffman S.A., and Socolar J.E.S. Network growth models and genetic regulatory networks. Phys. Rev. E 73 3 (2006) 031912
16. Hahn M.W., Conant G.C., and Wagner A. Molecular evolution in large genetic networks: does connectivity equal constraint?. J. Mol. Evol. 58 2 (2004) 203-211
17. Hansen T.F. The evolution of genetic architecture. Annu. Rev. Ecol. Evol. Systematics 37 (2006) 123-157
18. Huerta-Sanchez E., and Durrett R. Wagner's canalization model. Theor. Popul. Biol. 71 2 (2007) 121-130
19. Jeong H., Tombor B., Albert R., Oltvai Z.N., and Barabasi A.L. The large-scale organization of metabolic networks. Nature (London) 407 6804 (2000) 651-654
20. Jeong H., Mason S.P., Barabasi A.L., and Oltvai Z.N. Lethality and centrality in protein networks. Nature (London) 411 6833 (2001) 41-42
21. Kaneko K. Evolution of robustness to noise and mutation in gene expression dynamics. PLoS ONE 2 5 (2007) e434
22. Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22 3 (1969) 437-467
23. Kauffman S.A. The Origins of Order. Self-organization and Selection in Evolution (1993), Oxford University Press, Oxford
24. Krawitz P., and Shmulevich I. Basin entropy in Boolean network ensembles. Phys. Rev. Lett. 98 (2007) 158701
25. Kürten K.E. Correspondence between neural threshold networks and Kauffman Boolean cellular automata. J. Phys. A 21 11 (1988) L615-L619
26. Kürten K.E. Critical phenomena in model neural networks. Phys. Lett. A 129 3 (1988) 157-160
27. Langton C.G. Computation at the edge of chaos-phase-transitions and emergent computation. Physica D 42 1-3 (1990) 12-37
28. Lau K.-Y., Ganguli S., and Tang C. Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network. Phys. Rev. E 75 (2007) 051907
29. Li F., Long T., Lu Y., Qi O., and Tang C. The yeast cell-cycle network is robustly designed. Proc. Natl. Acad. Sci. USA 101 (2004) 4781-4786
30. Luque B., and Solé R.V. Phase transitions in random networks: simple analytical determination of critical points. Phys. Rev. E 55 1 (1997) 257-260
31. Luque B., and Solé R.V. Lyapunov exponents in random Boolean networks. Physica A 284 1-4 (2000) 33-45
32. Mitchell M., Hraber P.T., and Crutchfield J.P. Revisiting the edge of chaos: evolving cellular automata to perform computations. Complex Systems 7 2 (1993) 89-133
33. Oikonomou P., and Cluzel P. Effects of topology on network evolution. Nature Phys. 2 8 (2006) 532-536
34. Rohlf T., and Bornholdt S. Criticality in random threshold networks: annealed approximation and beyond. Physica A 310 1-2 (2002) 245-259
35. Shreim A., Grassberger P., Nadler W., Samuelsson B., Socolar J.E.S., and Paczuski M. Network analysis of the state space of discrete dynamical systems. Phys. Rev. Lett. 98 (2007) 198701
36. Siegal M.L., and Bergman A. Waddington's canalization revisited: developmental stability and evolution. Proc. Natl. Acad. Sci. USA 99 16 (2002) 10528-10532
37. Siegal M.L., Promislow D.E.L., and Bergman A. Functional and evolutionary inference in gene networks: does topology matter?. Genetica 129 1 (2007) 83-103
38. Smith V., Chou K.N., Lashkari D., Botstein D., and Brown P.O. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 274 5295 (1996) 2069-2074
39. Stearns S.C., Kaiser M., and Kawecki T.J. The differential genetic and environmental canalization of fitness components in Drosophila melanogaster. J. Evol. Biol. 8 5 (1995) 539-557
40. Szejka A., and Drossel B. Evolution of canalizing Boolean networks. Eur. Phys. J. B 56 (2007) 373-380
41. von Dassow G., and Odell G.M. Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches. J. Exp. Zool. 294 3 (2002) 179-215
42. von Dassow G., Meir E., Munro E.M., and Odell G.M. The segment polarity network is a robust development module. Nature (London) 406 6792 (2000) 188-192
43. Wagner A. Does evolutionary plasticity evolve?. Evolution 50 3 (1996) 1008-1023
44. Wagner A. Robustness against mutations in genetic networks of yeast. Nature Genetics 24 4 (2000) 355-361
45. Wagner A. Robustness and Evolvability in Living Systems (2005), Princeton University Press, Princeton, NJ