A framework for mapping, visualisation and automatic model creation of signal‐transduction networks
Abstract Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal‐transduction networks that avoids the combinatorial...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2012-04-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2012.12 |
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| _version_ | 1850179326998216704 |
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| author | Carl‐Fredrik Tiger Falko Krause Gunnar Cedersund Robert Palmér Edda Klipp Stefan Hohmann Hiroaki Kitano Marcus Krantz |
| author_facet | Carl‐Fredrik Tiger Falko Krause Gunnar Cedersund Robert Palmér Edda Klipp Stefan Hohmann Hiroaki Kitano Marcus Krantz |
| author_sort | Carl‐Fredrik Tiger |
| collection | DOAJ |
| description | Abstract Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal‐transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system. |
| format | Article |
| id | doaj-art-7469b0e7c62d4355ba289a0e218b9f33 |
| institution | OA Journals |
| issn | 1744-4292 |
| language | English |
| publishDate | 2012-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-7469b0e7c62d4355ba289a0e218b9f332025-08-20T02:18:32ZengSpringer NatureMolecular Systems Biology1744-42922012-04-018112010.1038/msb.2012.12A framework for mapping, visualisation and automatic model creation of signal‐transduction networksCarl‐Fredrik Tiger0Falko Krause1Gunnar Cedersund2Robert Palmér3Edda Klipp4Stefan Hohmann5Hiroaki Kitano6Marcus Krantz7Department of Cell and Molecular Biology, University of GothenburgTheoretical Biophysics, Humboldt‐Universität zu BerlinDepartment of Cell and Molecular Biology, University of GothenburgDepartment of Clinical and Experimental Medicine, Diabetes and Integrative Systems Biology, Linköping UniversityTheoretical Biophysics, Humboldt‐Universität zu BerlinDepartment of Cell and Molecular Biology, University of GothenburgDepartment of Clinical and Experimental Medicine, Diabetes and Integrative Systems Biology, Linköping UniversityDepartment of Cell and Molecular Biology, University of GothenburgAbstract Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal‐transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.https://doi.org/10.1038/msb.2012.12combinatorial complexitymathematical modellingnetwork mappingsignal transductionvisualisation |
| spellingShingle | Carl‐Fredrik Tiger Falko Krause Gunnar Cedersund Robert Palmér Edda Klipp Stefan Hohmann Hiroaki Kitano Marcus Krantz A framework for mapping, visualisation and automatic model creation of signal‐transduction networks Molecular Systems Biology combinatorial complexity mathematical modelling network mapping signal transduction visualisation |
| title | A framework for mapping, visualisation and automatic model creation of signal‐transduction networks |
| title_full | A framework for mapping, visualisation and automatic model creation of signal‐transduction networks |
| title_fullStr | A framework for mapping, visualisation and automatic model creation of signal‐transduction networks |
| title_full_unstemmed | A framework for mapping, visualisation and automatic model creation of signal‐transduction networks |
| title_short | A framework for mapping, visualisation and automatic model creation of signal‐transduction networks |
| title_sort | framework for mapping visualisation and automatic model creation of signal transduction networks |
| topic | combinatorial complexity mathematical modelling network mapping signal transduction visualisation |
| url | https://doi.org/10.1038/msb.2012.12 |
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