Perturbation avalanches and criticality in gene regulatory networks

Journal of Theoretical Biology

Volumn 242, Issue 1, 2006, Pages 164-170

  Ramo P ^a   Kesseli, J ^a   Yli Harja, O ^a  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

Author keywords

Boolean network; Branching process; Criticality; Gene regulatory network; Perturbation avalanche

Indexed keywords

AVALANCHE; PERTURBATION; SIZE DISTRIBUTION;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHAOTIC DYNAMICS; CONCEPTUAL FRAMEWORK; DNA MICROARRAY; GENE CONTROL; GENETIC ALGORITHM; GENETIC STABILITY; MOLECULAR DYNAMICS; PHASE TRANSITION; PRIORITY JOURNAL; THEORETICAL MODEL;

ANIMALS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SILENCING; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747118681     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2006.02.011     Document Type: Article

References (33)

1. Albert R., and Barabasi A. Statistical mechanics of complex networks. Rev. Mod. Phys. 47 (2002) 47-97
2. 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 (2003) 1-18
3. Aldana M., Coppersmith S., and Kadanoff L.P. Boolean dynamics with random couplings (2003), Springer Applied Mathematical Sciences Series. Springer, New York
4. Athreya K., and Ney P. Branching Processes (1972), Dover, New York
5. Bagley R.J., and Glass L. Counting and classifying attractors in high dimensional dynamical systems. J. Theor. Biol. 183 (1996) 269-284
6. Bastolla U., and Parisi G. A numerical study of the critical line of Kauffman networks. J. Theor. Biol. 187 (1997) 117-133
7. Bornholdt S. Less is more in modeling large genetic networks. Science 310 (2005) 449-451
8. Drossel B., Mihaljev T., and Greil F. On the number of attractors in random boolean networks. Phys. Rev. Lett. 94 (2005) 088701
9. Goh K.I., Lee D.S., and Kim D. Sandpile on scale-free networks. Phys. Rev. Lett. 91 (2003) 148701
10. Greil F., and Drossel B. The dynamics of critical Kauffman networks under asynchronous stochastic update. Phys. Rev. Lett. 95 (2005) 048701
11. Harris S., Sawhill B., Wuenche A., and Kauffman S. A model of transcriptional regulatory networks based on biases in the observed regulation rules. Complexity 7 4 (2001) 23-40
12. Harris, T.E., 1963. The Theory of Branching Processes, vol. 119 Die Grundlehren Der Mathematischen Wissenschaften. Springer, Berlin.
13. Huang S., and Ingber D.E. Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp. Cell Res. 261 (2000) 91-103
14. Hughes T.R., et al. Functional discovery via a compendium of expression profiles. Cell 102 (2000) 109-126
15. Jensen H.J. Self-Organized Criticality: Emergent Complex Behaviour in Physical and Biological Systems (1998), Cambridge University Press, Cambridge, MA
16. Just W., Shmulevich I., and Konvalina J. The number and probability of canalizing functions. Physica D 197 (2004) 211-221
17. Kauffman S. The Origins of Order (1993), Oxford University Press, New York
18. Kauffman S. A proposal for using the ensemble approach to understand genetic regulatory networks. J. Theor. Biol. 230 (2004) 581-590
19. Kauffman S., Peterson C., Samuelsson B., and Troein C. Random boolean network models and the yeast transcriptional network. Proc. Natl Acad. Sci. USA 100 (2003) 14796-14799
20. Kesseli J., Rämö P., and Yli-Harja O. On spectral techniques in analysis of boolean networks. Physica D 206 1-2 (2005) 49-61
21. Klemm, K., Bornholdt, S., 2004. Stable and unstable attractors in boolean networks. eprint arXiv:cond-mat/0411102.
22. Lee T., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 5594 (2002) 799-804
23. Li F., Long T., Lu Y., Ouyang Q., and Tang C. The yeast cell-cycle network is robustly designed. Proc. Natl Acad. Sci. USA 101 14 (2004) 4781
24. Lynch, J.F., 2001. Critical points for random boolean networks. eprint arXiv:nlin/0110036.
25. Mendoza L., and Alvarez-Buylla E.R. Dynamics of the genetic regulatory network for Arabidopsis thalianaflower morphogenesis. J. Theor. Biol. 193 2 (1998) 307-319
26. Newman M. Power laws, pareto distributions and zipf's law. Contemp. Phys. 46 (2005) 323-351
27. Otter R. The multiplicative process. Ann. Math. Statist. 20 (1949) 206-224
28. Rämö P., Kesseli J., and Yli-Harja O. Stability of functions in gene regulatory networks. Chaos 15 (2005) 034101
29. Samuelsson B., and Troein C. Random maps and attractors in random boolean networks. Phys. Rev. E 72 (2005) 046112
30. Serra R., Villani M., and Semeria A. Genetic networks models and statistical properties of gene extression data in knock-out experiments. J. Theor. Biol. 227 (2004) 149-157
31. Shmulevich I., Kauffman S., and Aldana M. Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc. Natl Acad. Sci. USA 102 38 (2005) 13439-13444
32. Wagner, A., 2001. Estimating coarse gene network structure from large-scale gene perturbation data. Santa Fe Institute Working Paper 01-09-051.
33. Wuensche, A., 1998. Discrete dynamical networks and their attractor basins. Santa Fe Institute Working Paper 98-11-101.