Analysis of signalling pathways using continuous time Markov chains

Muffy Calder, Vladislav Vyshemirsky, David Gilbert, Richard Orton

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable.
LanguageEnglish
Pages44-67
Number of pages24
JournalLecture Notes in Computer Science
Volume4220/2006
DOIs
Publication statusPublished - 2006

Fingerprint

Continuous-time Markov Chain
Signaling Pathways
Markov processes
Pathway
Signal transduction
Discrete Data
Signal Transduction
Reaction Rate
Quantitative Analysis
Ordinary differential equations
Reaction rates
Continuous Time
Simulation
Ordinary differential equation
Model
Logic
Proteins
Protein
Chemical analysis
Modeling

Keywords

  • systems biology
  • mathematical modelling
  • signalling pathways
  • Markov chain

Cite this

Calder, Muffy ; Vyshemirsky, Vladislav ; Gilbert, David ; Orton, Richard. / Analysis of signalling pathways using continuous time Markov chains. In: Lecture Notes in Computer Science. 2006 ; Vol. 4220/2006. pp. 44-67.
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Analysis of signalling pathways using continuous time Markov chains. / Calder, Muffy; Vyshemirsky, Vladislav; Gilbert, David; Orton, Richard.

In: Lecture Notes in Computer Science, Vol. 4220/2006, 2006, p. 44-67.

Research output: Contribution to journalArticle

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