Understanding signalling networks as collections of signal transduction pathways

  • Authors:

  • Robin Donaldson;Carolyn Talcott;Merrill Knapp;Muffy Calder

  • Affiliations:

  • University of Glasgow, Glasgow, UK;SRI International, Menlo Park, CA;SRI International, Menlo Park, CA;University of Glasgow, Glasgow, UK

  • Venue:
  • Proceedings of the 8th International Conference on Computational Methods in Systems Biology
  • Year:
  • 2010

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Abstract

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, final 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.