Models

Dataset Information

104

Poolman2009_GS_Metabolism_Arabidopsis


ABSTRACT: This is the full scale model of the Arabidopsis metabolic network described in the article: A Genome-scale Metabolic Model of Arabidopsis thaliana and Some of its Properties. Poolman MG, Miguet L, Sweetlove LJ and Fell DA. Plant Physiol. 2009 Sep 15. [Epub ahead of print] PMID: 19755544 , doi: 10.1104/pp.109.141267 Abstract: We describe the construction and analysis of a genome-scale metabolic model of Arabidopsis thaliana primarily derived from the annotations in the Aracyc database. We used techniques based on Linear Programming to demonstrate that: 1) the model is capable of producing biomass components (amino-acids, nucleotides, lipid, starch and cellulose) in the proportion observed experimentally in a heterotrophic suspension culture ; 2) That, approximately, only 15 % of the available reactions are needed for this purpose and that the size of this network is comparable to estimates of minimal network size for other organisms ; 3) That reactions may be grouped according to the changes in flux resulting from a hypothetical stimulus (in this case demand for ATP), and that this allows the identification of potential metabolic modules ; 4) That total ATP demand for growth and maintenance can be inferred, and that this is consistent with previous estimates in prokaryotes and yeast. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

SUBMITTER: Mark Poolman  

PROVIDER: MODEL3618435756 | BioModels | 2005-01-01

REPOSITORIES: BioModels

altmetric image

Publications

A genome-scale metabolic model of Arabidopsis and some of its properties.

Poolman Mark G MG   Miguet Laurent L   Sweetlove Lee J LJ   Fell David A DA  

Plant physiology 20090915 3


We describe the construction and analysis of a genome-scale metabolic model of Arabidopsis (Arabidopsis thaliana) primarily derived from the annotations in the Aracyc database. We used techniques based on linear programming to demonstrate the following: (1) that the model is capable of producing biomass components (amino acids, nucleotides, lipid, starch, and cellulose) in the proportions observed experimentally in a heterotrophic suspension culture; (2) that approximately only 15% of the availa  ...[more]

Similar Datasets

2005-01-01 | MODEL3618487388 | BioModels
2019-05-15 | MODEL1801090001 | BioModels
2015-07-30 | MODEL1507180028 | BioModels
2012-04-10 | BIOMD0000000416 | BioModels
2015-07-30 | MODEL1507180011 | BioModels
2012-10-28 | E-GEOD-39753 | ArrayExpress
2011-04-29 | E-MEXP-2866 | ArrayExpress
2015-05-13 | E-GEOD-64463 | ArrayExpress
2011-03-28 | E-MEXP-3082 | ArrayExpress
| GSE22584 | GEO