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December 2008 Bayesian inference for the {MAPK}/{ERK} pathway by considering the dependency of the kinetic parameters
Vilda Purutçuoğlu, Ernst Wit
Bayesian Anal. 3(4): 851-886 (December 2008). DOI: 10.1214/08-BA332


The MAPK/ERK pathway is one of the major signal transduction systems which regulates the cellular growth control of all eukaryotes like the cell proliferation and the apoptosis. Because of its importance in cellular lifecycle, it has been studied intensively, resulting in a number of qualitative descriptions of this regulatory mechanism. In this study we describe the MAPK/ERK pathway as an explicit set of reactions by combining different sources. Our reaction set takes into account the localization and different binding sites of the molecules in the cell by implementing the multiple parametrization. Then we estimate the model parameters of the network in a Bayesian setting via MCMC and data augmentation schemes. In the estimation we apply the Euler approximation, which is the discretized version of the diffusion technique. Additionally in inference of such a realistic and complex system we consider all possible kinds of dependencies coming from distinct stages of updates. To test the inference method we use the simulated data generated by the Gillespie algorithm. From the analysis it is clear that the sampler mixes well and partially is able to identify the dynamics of the MAPK/ERK pathway.


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Vilda Purutçuoğlu. Ernst Wit. "Bayesian inference for the {MAPK}/{ERK} pathway by considering the dependency of the kinetic parameters." Bayesian Anal. 3 (4) 851 - 886, December 2008.


Published: December 2008
First available in Project Euclid: 22 June 2012

zbMATH: 1330.62405
MathSciNet: MR2469802
Digital Object Identifier: 10.1214/08-BA332

Keywords: Data augmentation , dependency in diffusion matrix , diffusion approximation , MAPK/ERK pathway , MCMC

Rights: Copyright © 2008 International Society for Bayesian Analysis


Vol.3 • No. 4 • December 2008
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