Dataset Information

Andersen2009 - Genome-scale metabolic network of Aspergillus niger (iMA871)

ABSTRACT: Andersen2009 - Genome-scale metabolic network of Aspergillus niger (iMA871) This model is described in the article: Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Andersen MR, Nielsen ML, Nielsen J. Mol. Syst. Biol. 2008; 4: 178 Abstract: The release of the genome sequences of two strains of Aspergillus niger has allowed systems-level investigations of this important microbial cell factory. To this end, tools for doing data integration of multi-ome data are necessary, and especially interesting in the context of metabolism. On the basis of an A. niger bibliome survey, we present the largest model reconstruction of a metabolic network reported for a fungal species. The reconstructed gapless metabolic network is based on the reportings of 371 articles and comprises 1190 biochemically unique reactions and 871 ORFs. Inclusion of isoenzymes increases the total number of reactions to 2240. A graphical map of the metabolic network is presented. All levels of the reconstruction process were based on manual curation. From the reconstructed metabolic network, a mathematical model was constructed and validated with data on yields, fluxes and transcription. The presented metabolic network and map are useful tools for examining systemwide data in a metabolic context. Results from the validated model show a great potential for expanding the use of A. niger as a high-yield production platform. This model is hosted on BioModels Database and identified by: MODEL1507180047. 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.

SUBMITTER: Nicolas Le Novère

PROVIDER: MODEL1507180047 | BioModels | 2015-07-30

REPOSITORIES: BioModels

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	MODEL1507180047?filename=MODEL1507180047-biopax2.owl	Owl
	MODEL1507180047?filename=MODEL1507180047-biopax3.owl	Owl
	MODEL1507180047?filename=MODEL1507180047.m	Other
	MODEL1507180047?filename=MODEL1507180047.pdf	Pdf
	MODEL1507180047?filename=MODEL1507180047.png	Other

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Publications

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger.

Andersen Mikael Rørdam MR Nielsen Michael Lynge ML Nielsen Jens J

Molecular systems biology 20080325

The release of the genome sequences of two strains of Aspergillus niger has allowed systems-level investigations of this important microbial cell factory. To this end, tools for doing data integration of multi-ome data are necessary, and especially interesting in the context of metabolism. On the basis of an A. niger bibliome survey, we present the largest model reconstruction of a metabolic network reported for a fungal species. The reconstructed gapless metabolic network is based on the report ...[more]

PMID: 18364712

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