Identifying coherent subnetworks in genome scale metabolic networks
dc.contributor.author | Verwoerd, W | |
dc.coverage.spatial | University of Canterbury | |
dc.date.accessioned | 2011-06-17T02:47:32Z | |
dc.date.issued | 2007-12 | |
dc.description.abstract | Constraint-based methods to analyse metabolic networks require the classification of metabolites into external compounds that are exchanged with the system environment, and internal ones that form intermediate steps on the metabolic pathways and which are therefore subject to stoichiometry constraints in the steady state. For eukaryotic cells it is not practical to analyse the complete cellular network, and so the subnetwork that describes the specific phenomena under study needs to be extracted. This study focuses on flavonoid production in the model plant Arabidopsis Thaliana. Software was developed to extract the full Arabidopsis metabolic network from the AraCyc database, in a format required by standard network analysis packages. Considerable processing is also required to reconcile information about reaction directions from different database tables and to classify metabolites as internal or external to the subnetwork. The paper outlines the strategies implemented in the software to address these issues. | |
dc.format.extent | pp.2013-2019 | |
dc.identifier | https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=elements_prod&SrcAuth=WosAPI&KeyUT=WOS:000290030702010&DestLinkType=FullRecord&DestApp=WOS_CPL | |
dc.identifier.isbn | 978-0-9758400-4-7 | |
dc.identifier.other | BUQ25 (isidoc) | |
dc.identifier.uri | https://hdl.handle.net/10182/3637 | |
dc.language.iso | en | |
dc.publisher | Modelling and Simulation Society of Australia and New Zealand Inc. | |
dc.relation | The original publication is available from Modelling and Simulation Society of Australia and New Zealand Inc. | |
dc.relation.isPartOf | MODSIM07 - Land, Water and Environmental Management: Integrated Systems for Sustainability, Proceedings | |
dc.rights | Copyright © The Authors. The responsibility for the contents of this paper rests upon the authors and not on the Modelling and Simulation Society of Australia and New Zealand Inc. | |
dc.source | Proceedings of the International Congress on Modelling and Simulation | |
dc.subject | flavonoids | |
dc.subject | constraints | |
dc.subject | biochemical pathway | |
dc.subject | subnet | |
dc.subject | metabolic network | |
dc.title | Identifying coherent subnetworks in genome scale metabolic networks | |
dc.type | Conference Contribution - published | |
lu.contributor.unit | LU | |
lu.contributor.unit | LU|Agriculture and Life Sciences | |
lu.contributor.unit | LU|Agriculture and Life Sciences|WFMB | |
lu.contributor.unit | LU|Research Management Office | |
lu.contributor.unit | LU|Research Management Office|OLD QE18 | |
lu.identifier.orcid | 0000-0001-8744-1578 | |
lu.subtype | Conference Paper | |
pubs.finish-date | 2007-12-13 | |
pubs.notes | Conference paper presented at the MODSIM07, International Congress on Modelling and Simulation, held December 2007, University of Canterbury, New Zealand. | |
pubs.publication-status | Published | |
pubs.start-date | 2007-12-10 |
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