research-article

Understanding signalling networks as collections of signal transduction pathways

Authors:

Robin Donaldson,

Carolyn Talcott,

Muffy CalderAuthors Info & Claims

CMSB '10: Proceedings of the 8th International Conference on Computational Methods in Systems Biology

Pages 86 - 95

https://doi.org/10.1145/1839764.1839775

Published: 29 September 2010 Publication History

Abstract

A signalling network is a network of reactions that govern how a cell responds to its environment. A pathway is a dynamic flow of "signal" through the network (signal transduction), for example from a receptor to a transcription factor that enables expression of a gene. In this paper we introduce a method to compute all pathways in a signalling network that satisfy a simple property constraining initial, final and intermediate states. This method, concerned with signal transduction, is compared to the steady state view underlying Petri net place/transition invariants and flux balance analysis. We apply the method to the signalling network model being developed in the Pathway Logic project and identify knockout/inhibition targets and common (pathway) events. This approach also allows us to better understand and formalise the interaction between pathways in a network, for example to identifying pathway inhibition targets that limit the effect on unrelated pathways.

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Cited By

Knapp MLaderoute KTalcott C(2022)Pathway Logic: Curation and Analysis of Experiment‐Based Signaling Response NetworksSystems Biology Modelling and Analysis10.1002/9781119716600.ch5(127-171)Online publication date: 18-Nov-2022
https://doi.org/10.1002/9781119716600.ch5
Santos-Buitrago BRiesco AKnapp MAlcantud JSantos-Garcia GTalcott C(2019)Soft Set Theory for Decision Making in Computational Biology Under Incomplete InformationIEEE Access10.1109/ACCESS.2019.28969477(18183-18193)Online publication date: 2019
https://doi.org/10.1109/ACCESS.2019.2896947
Talcott CKnapp M(2017)Explaining Response to Drugs Using Pathway LogicComputational Methods in Systems Biology10.1007/978-3-319-67471-1_15(249-264)Online publication date: 1-Sep-2017
https://doi.org/10.1007/978-3-319-67471-1_15
Show More Cited By

Index Terms

Understanding signalling networks as collections of signal transduction pathways
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis
      1. Model verification and validation

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cover image ACM Other conferences

CMSB '10: Proceedings of the 8th International Conference on Computational Methods in Systems Biology

September 2010

119 pages

ISBN:9781450300681

DOI:10.1145/1839764

Conference Chair:
Paola Quaglia
CoSBi and University of Trento, Italy

Copyright © 2010 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 29 September 2010

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September 29 - October 1, 2010

Trento, Italy

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Cited By

Knapp MLaderoute KTalcott C(2022)Pathway Logic: Curation and Analysis of Experiment‐Based Signaling Response NetworksSystems Biology Modelling and Analysis10.1002/9781119716600.ch5(127-171)Online publication date: 18-Nov-2022
https://doi.org/10.1002/9781119716600.ch5
Santos-Buitrago BRiesco AKnapp MAlcantud JSantos-Garcia GTalcott C(2019)Soft Set Theory for Decision Making in Computational Biology Under Incomplete InformationIEEE Access10.1109/ACCESS.2019.28969477(18183-18193)Online publication date: 2019
https://doi.org/10.1109/ACCESS.2019.2896947
Talcott CKnapp M(2017)Explaining Response to Drugs Using Pathway LogicComputational Methods in Systems Biology10.1007/978-3-319-67471-1_15(249-264)Online publication date: 1-Sep-2017
https://doi.org/10.1007/978-3-319-67471-1_15
Talcott C(2016)The Pathway Logic formal modeling system: Diverse views of a formal representation of signal transduction2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2016.7822740(1468-1476)Online publication date: Dec-2016
https://doi.org/10.1109/BIBM.2016.7822740
Santos-García GTalcott CRiesco ASantos-Buitrago BDe Las Rivas J(2016)Role of Nerve Growth Factor Signaling in Cancer Cell Proliferation and Survival Using a Reachability Analysis Approach10th International Conference on Practical Applications of Computational Biology & Bioinformatics10.1007/978-3-319-40126-3_18(173-181)Online publication date: 1-Jun-2016
https://doi.org/10.1007/978-3-319-40126-3_18
Santos-García GTalcott CDe Las Rivas J(2016)Analysis of Cellular Proliferation and Survival Signaling by Using Two Ligand/Receptor Systems Modeled by Pathway LogicHybrid Systems Biology10.1007/978-3-319-26916-0_13(226-245)Online publication date: 10-Jan-2016
https://doi.org/10.1007/978-3-319-26916-0_13

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