Dataset Information

E-GEOD-123583

ABSTRACT: Functional relationship of Arabidopsis thaliana GUN1 and FUG1 in plastid proteostasis

PROVIDER: E-GEOD-123583 | ExpressionAtlas | 2020-04-17

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-123583-analysis-methods.tsv	Tabular
	E-GEOD-123583-analytics.tsv	Tabular
	E-GEOD-123583-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-123583-configuration.xml	Xml
	E-GEOD-123583-g4_g1-mvaPlot.png	Other

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Project description:deOliveiraDalMolin2010 - Genome-scale metabolic network of Arabidopsis thaliana (AraGEM) This model is described in the article: AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK. Plant Physiol. 2010 Feb; 152(2): 579-589 Abstract: Genome-scale metabolic network models have been successfully used to describe metabolism in a variety of microbial organisms as well as specific mammalian cell types and organelles. This systems-based framework enables the exploration of global phenotypic effects of gene knockouts, gene insertion, and up-regulation of gene expression. We have developed a genome-scale metabolic network model (AraGEM) covering primary metabolism for a compartmentalized plant cell based on the Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association entries, and 1,567 unique reactions compartmentalized into the cytoplasm, mitochondrion, plastid, peroxisome, and vacuole. The curation process identified 75 essential reactions with respective enzyme associations not assigned to any particular gene in the Kyoto Encyclopedia of Genes and Genomes or AraCyc. With the addition of these reactions, AraGEM describes a functional primary metabolism of Arabidopsis. The reconstructed network was transformed into an in silico metabolic flux model of plant metabolism and validated through the simulation of plant metabolic functions inferred from the literature. Using efficient resource utilization as the optimality criterion, AraGEM predicted the classical photorespiratory cycle as well as known key differences between redox metabolism in photosynthetic and nonphotosynthetic plant cells. AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism. This model is hosted on BioModels Database and identified by: MODEL1507180028. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. 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.

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E-GEOD-123583

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