Understanding signalling networks as collections of signal transduction pathways

Donaldson, R., Tallcott, C., Knapp, M. and Calder, M. (2010) Understanding signalling networks as collections of signal transduction pathways. In: Conference on Computational Methods in Systems Biology (CMSB 2010), Trento, Italy, 29 Sep - 1 Oct 2010, pp. 86-95. ISBN 9781450300681 (doi: 10.1145/1839764.1839775)

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A signalling network is a network of reactions that govern how a cell responds to its environment. A pathway is a dynamic flow of "signal" through the network (signal transduction), for example from a receptor to a transcription factor that enables expression of a gene. In this paper we introduce a method to compute all pathways in a signalling network that satisfy a simple property constraining initial, signal and intermediate states. This method, concerned with signal transduction, is compared to the steady state view underlying Petri net place/transition invariants and flux balance analysis. We apply the method to the signalling network model being developed in the Pathway Logic project and identify knockout/inhibition targets and common (pathway) events. This approach also allows us to better understand and formalise the interaction between pathways in a network, for example to identifying pathway inhibition targets that limit the effect on unrelated pathways.

Item Type:Conference Proceedings
Keywords:Signalling Networks, Pathways, Reaction Minimal Paths, T Invariants
Glasgow Author(s) Enlighten ID:Donaldson, Mr Robin and Calder, Professor Muffy
Authors: Donaldson, R., Tallcott, C., Knapp, M., and Calder, M.
College/School:College of Science and Engineering > School of Computing Science
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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
436881The molecular noseAndrew PittEngineering & Physical Sciences Research Council (EPSRC)EP/E032745/2RI MOLECULAR CELL & SYSTEMS BIOLOGY