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  Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

Saez-Rodriguez, J., Alexopoulos, L. G., Epperlein, J., Samaga, R., Lauffenburger, D. A., Klamt, S., et al. (2009). Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology, 5, 331. doi:10.1038/msb.2009.87.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-943F-7 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-8B57-E
Genre: Journal Article

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This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivativeworks is permitted but the resultingworkmay be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission.
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Saez-Rodriguez, J.1, 2, 3, Author              
Alexopoulos, L. G.1, 2, 3, Author
Epperlein, J.2, 3, Author
Samaga, R.4, Author              
Lauffenburger, D. A.1, 2, Author
Klamt, S.4, Author              
Sorger, P. K.1, 2, 3, Author
Affiliations:
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, ou_persistent22              
2Center for Cell Decision Processes, Boston, MA, USA, persistent:22              
3Department of Systems Biology, Harvard Medical School, Boston, MA, USA, persistent:22              
4Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, ou_1738139              

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 Abstract: Large-scale protein signalling networks are useful for exploring complex biochemical pathways but do not reveal how pathways respond to specific stimuli. Such specificity is critical for understanding disease and designing drugs. Here we describe a computational approach—implemented in the free CNO software—for turning signalling networks into logical models and calibrating the models against experimental data. When a literature-derived network of 82 proteins covering the immediate-early responses of human cells to seven cytokines was modelled, we found that training against experimental data dramatically increased predictive power, despite the crudeness of Boolean approximations, while significantly reducing the number of interactions. Thus, many interactions in literature-derived networks do not appear to be functional in the liver cells from which we collected our data. At the same time, CNO identified several new interactions that improved the match of model to data. Although missing from the starting network, these interactions have literature support. Our approach, therefore, represents a means to generate predictive, cell-type-specific models of mammalian signalling from generic protein signalling networks. This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission. [accessed February 5, 2010]

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Language(s): eng - English
 Dates: 2009
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1038/msb.2009.87
eDoc: 439656
Other: 34/09
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Title: Molecular Systems Biology
Source Genre: Journal
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Pages: - Volume / Issue: 5 Sequence Number: - Start / End Page: 331 Identifier: -