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Modular modelling of signalling pathways and their cross-talk

Authors:

Robin Donaldson,

Muffy CalderAuthors Info & Claims

Theoretical Computer Science, Volume 456

Pages 30 - 50

https://doi.org/10.1016/j.tcs.2012.07.003

Published: 01 October 2012 Publication History

Abstract

Signalling pathways are well-known abstractions that explain the mechanisms whereby cells respond to signals. Collections of pathways form networks, and interactions between pathways in a network, known as cross-talk, enables further complex signalling behaviours. While there are several formal modelling approaches for signalling pathways, none make cross-talk explicit; the aim of this paper is to define and categorise cross-talk in a rigorous way. We define a modular approach to pathway and network modelling, based on the module construct in the PRISM modelling language, and a set of generic signalling modules. Five different types of cross-talk are defined according to various biologically meaningful combinations of variable sharing, synchronisation labels and reaction renaming. The approach is illustrated with a case-study analysis of cross-talk between the TGF-@b, WNT and MAPK pathways.

References

[1]

Danos, V., Feret, J., Fontana, W., Harmer, R. and Krivine, J., Rule-based modelling of cellular signalling, invited paper. In: Caires, L., Vasconcelos, V. (Eds.), Lecture Notes in Computer Science, vol. 4703. Springer, Berlin, Germany, Lisbon, Portugal. pp. 17-41.

[2]

Heiner, M., Gilbert, D. and Donaldson, R., Petri Nets in Systems and Synthetic Biology. In: LNCS, vol. 5016. Springer. pp. 215-264.

Digital Library

[3]

Calder, M., Gilmore, S. and Hillston, J., Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. Transactions on Computational Systems Biology VII. v4230. 1-23.

[4]

Calder, M., Vyshemirsky, V., Orton, R. and Gilbert, D., Analysis of signalling pathways using continuous time Markov chains. Transactions on Computational Systems Biology VI. v4220. 44-67.

[5]

Tymchyshyn, O. and Kwiatkowska, M., Combining intra- and inter-cellular dynamics to investigate intestinal homeostasis. In: LNCS, vol. 5054. Springer.

[6]

Degano, P., Prandi, D., Priami, C. and Quaglia, P., Beta-binders for biological quantitative experiments. Electronic Notes in Theoretical Computer Science. v164. 101-117.

[7]

Chabrier-rivier, N., Chiaverini, M., Danos, V., Fages, F. and Schächter, V., Modeling and querying biomolecular interaction networks. Theoretical Computer Science. v325. 25-44.

[8]

Taniguchi, C.M., Emanuelli, B. and Kahn, R.C., Critical nodes in signalling pathways: insights into insulin action. Nature Reviews Molecular Cell Biology. v7. 85-96.

[9]

Catt, I., Crosstalk (noise) in digital systems. Electronic Computers, IEEE Transactions on. vEC-16. 743-763.

[10]

Schwartz, M.A. and Ginsberg, M.H., Networks and crosstalk: integrin signalling spreads. Nature Cell Biology. v4. E65-E68.

[11]

Hatakeyama, M., Kimura, S., Naka, T., Kawasaki, T., Yumoto, N., Ichikawa, M., Kim, J., Saito, K., Saeki, M., Shirouzu, M., Yokoyama, S. and Konagaya, A., A computational model on the modulation of Mitogen-Activated Protein Kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochemical Journal. v373 Pt. 2. 451-463.

[12]

Sreenath, S.N., Soebiyanto, R., Mesarovic, M.D. and Wolkenhauer, O., Coordination of crosstalk between MAPK-PKC pathways: an exploratory study. Systems Biology, IET. v1. 33-40.

[13]

McClean, M.N.N., Mody, A., Broach, J.R.R. and Ramanathan, S., Cross-talk and decision making in MAP kinase pathways. Nature Genetics.

[14]

Heiner, M., Koch, I. and Will, J., Model validation of biological pathways using Petri nets***demonstrated for apoptosis. Journal BioSystems. v75. 15-28.

[15]

Fisher, J., Piterman, N., Hajnal, A. and Henzinger, T.A., Predictive modeling of signaling crosstalk during C. Elegans vulval development. PLoS Computational Biology. v3. e92+

[16]

Donaldson, R. and Calder, M., Modelling and analysis of biochemical signalling pathway cross-talk. In: EPTCS 19, pp. 40-54.

[17]

Calder, M. and Hillston, J., Process algebra modelling styles for biomolecular processes. Transactions on Computational Systems Biology XI, LNBI. v5750. 1-25.

[18]

Ciocchetta, F., Degasperi, A., Hillston, J. and Calder, M., Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA. Electronic Notes in Theoretical Computer Science. v229. 145-163.

[19]

Alur, R. and Henzinger, T., Reactive modules. Formal Methods in System Design. v15. 7-48.

[20]

PRISM Website, PRISM *** Probabilistic Symbolic Model Checker, 2011. http://www.prismmodelchecker.org.

[21]

Guo, X. and Wang, X.-F., Signaling cross-talk between TGF-β/BMP and other pathways. Cell Research. v19. 71-88.

[22]

NIH, Insulin signaling and receptor cross-talk program announcement PA-07-058, 2006.

[23]

Katzenellenbogen, B., Estrogen receptors: bioactivities and interactions with cell signaling pathways. Biology of Reproduction. v54. 287-293.

[24]

Bosscher, K.D., Berghe, W.V. and Haegeman, G., Cross-talk between nuclear receptors and nuclear factor ***b. Oncogene. v25. 6868-6886.

[25]

R. Breitling, Private correspondence, 2009.

[26]

Calder, M. and Miller, A., Feature interaction detection by pairwise analysis of LTL properties. Formal Methods in System Design. v28. 213-261.

[27]

Plath, M. and Ryan, M., The feature construct for SMV: Semantics. Feature Interactions in Telecommunications and Software Systems VI. 129-144.

Cited By

Vogelsang A(2020)Feature dependencies in automotive software systemsJournal of Systems and Software10.1016/j.jss.2019.110458160:COnline publication date: 1-Feb-2020
https://dl.acm.org/doi/10.1016/j.jss.2019.110458
Colvin R(2016)Modelling and analysing neural networks using a hybrid process algebraTheoretical Computer Science10.1016/j.tcs.2015.08.019623:C(15-64)Online publication date: 11-Apr-2016
https://dl.acm.org/doi/10.1016/j.tcs.2015.08.019
Apel SKolesnikov SSiegmund NKästner CGarvin BClassen ASiegmund N(2013)Exploring feature interactions in the wildProceedings of the 5th International Workshop on Feature-Oriented Software Development10.1145/2528265.2528267(1-8)Online publication date: 26-Oct-2013
https://dl.acm.org/doi/10.1145/2528265.2528267

Modular modelling of signalling pathways and their cross-talk

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Published In

cover image Theoretical Computer Science

Theoretical Computer Science Volume 456, Issue

October, 2012

117 pages

ISSN:0304-3975

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Copyright © Elsevier B.V. © 2012.

Publisher

Elsevier Science Publishers Ltd.

United Kingdom

Publication History

Published: 01 October 2012

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Cited By

Vogelsang A(2020)Feature dependencies in automotive software systemsJournal of Systems and Software10.1016/j.jss.2019.110458160:COnline publication date: 1-Feb-2020
https://dl.acm.org/doi/10.1016/j.jss.2019.110458
Colvin R(2016)Modelling and analysing neural networks using a hybrid process algebraTheoretical Computer Science10.1016/j.tcs.2015.08.019623:C(15-64)Online publication date: 11-Apr-2016
https://dl.acm.org/doi/10.1016/j.tcs.2015.08.019
Apel SKolesnikov SSiegmund NKästner CGarvin BClassen ASiegmund N(2013)Exploring feature interactions in the wildProceedings of the 5th International Workshop on Feature-Oriented Software Development10.1145/2528265.2528267(1-8)Online publication date: 26-Oct-2013
https://dl.acm.org/doi/10.1145/2528265.2528267

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