<abstract xml:lang="en" xmlns="http://www.w3.org/1999/xhtml"><p>The paper is concerned with application of mathematical modeling to the analysis of signaling pathways. Two issues, deterministic modeling of gene transcription and model-driven discovery of regulatory elements, are dealt with. First, the biological background is given and the importance of the stochastic nature of biological processes is addressed. The assumptions underlying deterministic modeling are presented. Special emphasis is put on describing gene transcription. A framework for including unknown processes activating gene transcription by means of first-order lag elements is introduced and discussed. Then, a particular interferon-β induced pathway is introduced, limited to early events that precede activation of gene transcription. It is shown how to simplify the system description based on the goals of modeling. Further, a computational analysis is presented, facilitating better understanding of the mechanisms underlying regulation of key components in the pathway. The analysis is illustrated by a comparison of simulation and experimental data.</p></abstract>

The paper is concerned with application of mathematical modeling to the analysis of signaling pathways. Two issues, deterministic modeling of gene transcription and model-driven discovery of regulatory elements, are dealt with. First, the biological background is given and the importance of the stochastic nature of biological processes is addressed. The assumptions underlying deterministic modeling are presented. Special emphasis is put on describing gene transcription. A framework for including unknown processes activating gene transcription by means of first-order lag elements is introduced and discussed. Then, a particular interferon-β induced pathway is introduced, limited to early events that precede activation of gene transcription. It is shown how to simplify the system description based on the goals of modeling. Further, a computational analysis is presented, facilitating better understanding of the mechanisms underlying regulation of key components in the pathway. The analysis is illustrated by a comparison of simulation and experimental data.

Model Based Analysis of Signaling Pathways

Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland

International Journal of Applied Mathematics and Computer Science

{"article-title":"Model Based Analysis of Signaling Pathways"}

The paper is concerned with application of mathematical modeling to the analysis of signaling pathways. Two issues, deterministic modeling of gene...

Model Based Analysis of Signaling Pathways

Published Online: Jun 16, 2008

Page range: 139 - 145

DOI: https://doi.org/10.2478/v10006-008-0013-z

Keywords
Signaling pathways, dynamical systems, systems biology, interferon-beta

This content is open access.

Model Based Analysis of Signaling Pathways

Published Online: Jun 16, 2008

Page range: 139 - 145

DOI: https://doi.org/10.2478/v10006-008-0013-z

KeywordsSignaling pathways, dynamical systems, systems biology, interferon-beta

This content is open access.

Keywords
Signaling pathways, dynamical systems, systems biology, interferon-beta