Donaldson, R. and Calder, M. (2010) Modelling and analysis of biochemical signalling pathway cross-talk. Electronic Proceedings in Theoretical Computer Science, 19, pp. 40-54. (doi: 10.4204/EPTCS.19.3)
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Abstract
Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising) parallel composition of instances of generic modules (with internal and external labels). Pathways are then composed by (synchronising) parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways.
Item Type: | Articles |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Calder, Professor Muffy |
Authors: | Donaldson, R., and Calder, M. |
Subjects: | Q Science > QA Mathematics > QA75 Electronic computers. Computer science Q Science > QH Natural history > QH345 Biochemistry |
College/School: | College of Science and Engineering > School of Computing Science |
Journal Name: | Electronic Proceedings in Theoretical Computer Science |
Publisher: | Open Publishing Association |
ISSN: | 2075-2180 |
Published Online: | 01 January 2010 |
Copyright Holders: | Copyright © 2010 The Authors |
First Published: | First published in Electronic Proceedings in Theoretical Computer Science 19:40-54 |
Publisher Policy: | Reproduced with the permission of the authors |
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