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Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations Results

Purutcuoglu, Vilda ; Wit, Ernst

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
The MAPK (mitogen-activated protein kinase) or its synonymous ERK (extracellular signal regulated kinase) pathway whose components are Ras, Raf, and MEK proteins with many biochemical links, is one of the major signalling systems involved in cellular growth control of eukaryotes including cell proliferation, transformation, differentiation, and apoptosis. In this study we describe the MAPK/ERK pathway via (quasi) biochemical reactions and then implement the pathway by a stochastic Markov process. A novelty of our approach is to use multiple parametrizations in order to deal with molecules for which localization in the cell is an intricate part of the dynamic process and to describe the protein using different binding sites and various phosphorylations. We simulate the system by exact and different approximate simulations via the Poisson t-leap, the Binomial t-leap and the diffusion methods, in which we introduce a new updating plan for the dependent columns of the diffusion matrix. Finally we compare the results of different algorithms by the current biological knowledge and find out new relations about this complex system.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Purutcuoglu, Vilda ; Wit, Ernst  (2006)  Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations Results. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 3(2), 2006. Special Issue: 3rd Integrative Bioinformatics Workshop, Harpenden, United Kingdom, 2

Online-Journal: http://journal.imbio.de/index.php?paper_id=38
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2007/219

Also published by Shaker:
Ralf Hofestädt, Thoralf Töpel (eds.). Integrative Bioinformatics -
Yearbook 2006. Shaker, 2007.


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