Stochastic modelling of the MAPK signalling pathway

Date

2006-06-01

Author

Purutçuoğlu Gazi, Vilda

Metadata

Show full item record

Item Usage Stats

223
views

0
downloads

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. Because of its diverse functionality, it is also activated in a variety of hormone activation and many illnesses, which have multi-complex gene structure like cancer and heart diseases. In this study we describe the MAPK/ERK pathway via (quasi) biochemical reactions and then implement the pathway by a stochastic Markov process. We use two techniques, Gillespie algorithm and diffusion approximation, to simulate reactions and we compare their results. 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.

Subject Keywords

MAPK pathway, Stochastic simulation, Multiple parametrization

URI

https://hdl.handle.net/11511/87671
http://www.statmod.org/workshops_archive_proceedings_2006.htm

Conference Name

21st International Workshop on Statistical Modelling July 3–7 2006

Collections

Department of Statistics, Conference / Seminar

Suggestions

OpenMETU
Core

Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations' Results Purutçuoğlu Gazi, Vilda (2006-10-01) 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 ...
Bayesian inference for the MAPK/ERK pathway by considering the dependency of the kinetic parameters Purutçuoğlu Gazi, Vilda (Institute of Mathematical Statistics, 2008-01-01) 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 diff...
Automatic detection of mitochondria from electron microscope tomography images: a curve fitting approach Tasel, Serdar F.; HASSANPOUR, REZA; Mumcuoğlu, Ünal Erkan; Perkins, Guy; Martone, Maryann (2014-02-18) Mitochondria are sub-cellular components which are mainly responsible for synthesis of adenosine tri-phosphate (ATP) and involved in the regulation of several cellular activities such as apoptosis. The relation between some common diseases of aging and morphological structure of mitochondria is gaining strength by an increasing number of studies. Electron microscope tomography (EMT) provides high-resolution images of the 3D structure and internal arrangement of mitochondria. Studies that aim to reveal the c...
Inference of Gene Regulatory Networks Via Multiple Data Sources and a Recommendation Method Ozsoy, Makbule Gulcin; Polat, Faruk; Alhajj, Reda (2015-11-12) Gene regulatory networks (GRNs) are composed of biological components, including genes, proteins and metabolites, and their interactions. In general, computational methods are used to infer the connections among these components. However, computational methods should take into account the general features of the GRNs, which are sparseness, scale-free topology, modularity and structure of the inferred networks. In this work, observing the common aspects between recommendation systems and GRNs, we decided to ...
Visualization of interactions between fluorescently tagged g protein α11, α12/13 subtypes and adenosine 2a, dopamine 2 or homodimer adenosine 2a/2a receptors Kostromin, İrmak Begüm; Son, Çağdaş Devrim; Department of Biology (2018) G-Protein-coupled receptors (GPCRs) belong to one of the largest family of cell surface receptors, which transmit extracellular signals to intracellular responses by interacting with G- proteins. The G proteins are known as molecular switches that regulates different pathways via control of secondary messengers and signaling proteins. Adenosine 2A (A2A) and Dopamine 2 (D2) receptors belong to G-Protein-coupled receptors (GPCRs) family and are located mostly in striatopallidal γ-aminobutyric acid (GABA) cont...

Citation Formats

V. Purutçuoğlu Gazi, “Stochastic modelling of the MAPK signalling pathway,” Galway, Ireland, 2006, p. 431, Accessed: 00, 2021. [Online]. Available: https://hdl.handle.net/11511/87671.