Abstract
In the course of understanding biological regulatory networks (BRN), scientists usually start by studying small BRNs that they believe to be of particular importance to represent a biological function, and then, embed them in the whole network. Such a reduction can lead to neglect relevant regulations and to study a network whose properties can be very different from the properties of this network viewed as a part of the whole. In this paper we study, from a logical point of view, the preservation of properties inherited from small BRNs. The signature of BRN, constituted by a graph, is one of the distinctive features on which embeddings can be defined which leads us to give a first condition on the subgraphs ensuring the preservation of properties of the embedded graphs.
This work is performed within the European project GENNETEC (GENetic NeTworks: Emergence and Complexity) STREP 34952.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Aiguier, M., Le Gall, P., Mabrouki, M.: A formal denotation of complex systems: how to use algebraic refinement to deal with complexity of systems, Tech. report (2008), http://www.epigenomique.genopole.fr/~aiguier
Bernot, G., Comet, J.-P., Richard, A., Guespin, J.: Application of formal methods to biological regulatory networks: Extending Thomas’ asynchronous logical approach with temporal logic. Journal of Theoretical Biology 229(3), 339–347 (2004)
de Jong, H.: Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9(1), 67–103 (2002)
de Jong, H., Geiselmann, J., Hernandez, C., Page, M.: Genetic network analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 19(3), 336–344 (2003)
de Jong, H., Gouzé, J.-L., Hernandez, C., Page, M., Sari, T., Geiselmann, J.: Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bulletin of Mathematical Biology 66(2), 301–340 (2004)
Emerson, E.A.: Temporal and modal logic. In: Handbook of theoretical computer science formal models and semantics, vol. b, pp. 995–1072. MIT Press, Cambridge (1990)
Glass, L., Kauffman, S.A.: The logical analysis of continuous non-linear biochemical control networks. J. Theor. Biol. 39, 103–129 (1973)
Goguen, J.A., Burstall, R.-M.: Institutions: Abstract model theory for specification and programming. Journal of the ACM 39(1), 95–146 (1992)
Mateus, D., Gallois, J.-P., Comet, J.-P., Le Gall, P.: Symbolic modeling of genetic regulatory networks. Journal of Bioinformatics and Computational Biology (2007)
De Nicola, R., Vaandrager, F.: Three logics for branching bisimulation. J. ACM 42(2), 458–487 (1995)
Thieffry, D., Thomas, R.: Dynamical behaviour of biological regulatory networks - ii. immunity control in bacteriophage lambda. Bull. Math. Biol. 57(2), 277–297 (1995)
Thomas, R.: Logical analysis of systems comprising feedback loops. J. Theor. Biol. 73(4), 631–656 (1978)
Thomas, R., d’Ari, R.: Biological feedback. CRC Press, Boca Raton (1990)
van Glabbeck, R., Weijland, W.P.: Refinement in branching time semantics. In: Proc. IFIP Conference, pp. 613–618 (1989)
Wehrheim, H.: Inheritance of temporal logic properties. In: Najm, E., Nestmann, U., Stevens, P. (eds.) FMOODS 2003. LNCS, vol. 2884, pp. 79–93. Springer, Heidelberg (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Mabrouki, M., Aiguier, M., Comet, JP., Le Gall, P. (2008). Property Preservation along Embedding of Biological Regulatory Networks. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds) Algebraic Biology. AB 2008. Lecture Notes in Computer Science, vol 5147. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85101-1_10
Download citation
DOI: https://doi.org/10.1007/978-3-540-85101-1_10
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85100-4
Online ISBN: 978-3-540-85101-1
eBook Packages: Computer ScienceComputer Science (R0)