Selvarasu2009 - Genome-scale metabolic network of Mus Musculus (iSS724)

  public model
Model Identifier
MODEL1507180042
Short description
Selvarasu2009 - Genome-scale metabolic network of Mus Musculus (iSS724)

This model is described in the article:

Selvarasu S, Karimi IA, Ghim GH, Lee DY.
Mol Biosyst 2010 Jan; 6(1): 152-161

Abstract:

Genome-scale metabolic modeling has been successfully applied to a multitude of microbial systems, thus improving our understanding of their cellular metabolisms. Nevertheless, only a handful of works have been done for describing mammalian cells, particularly mouse, which is one of the important model organisms, providing various opportunities for both biomedical research and biotechnological applications. Presented herein is a genome-scale mouse metabolic model that was systematically reconstructed by improving and expanding the previous generic model based on integrated biochemical and genomic data of Mus musculus. The key features of the updated model include additional information on gene-protein-reaction association, and improved network connectivity through lipid, amino acid, carbohydrate and nucleotide biosynthetic pathways. After examining the model predictability both quantitatively and qualitatively using constraints-based flux analysis, the structural and functional characteristics of the mouse metabolism were investigated by evaluating network statistics/centrality, gene/metabolite essentiality and their correlation. The results revealed that overall mouse metabolic network is topologically dominated by highly connected and bridging metabolites, and functionally by lipid metabolism that most of essential genes and metabolites are from. The current in silico mouse model can be exploited for understanding and characterizing the cellular physiology, identifying potential cell engineering targets for the enhanced production of recombinant proteins and developing diseased state models for drug targeting.

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.

Format
SBML (L3V1)
Related Publication
  • Genome-scale modeling and in silico analysis of mouse cell metabolic network.
  • Selvarasu S, Karimi IA, Ghim GH, Lee DY
  • Molecular bioSystems , 1/ 2010 , Volume 6 , pages: 152-161 , PubMed ID: 20024077
  • Department of Chemical and Biomolecular Engineering, National University of Singapore, Engineering Drive 4, Singapore. cheld@nus.edu.sg
  • Genome-scale metabolic modeling has been successfully applied to a multitude of microbial systems, thus improving our understanding of their cellular metabolisms. Nevertheless, only a handful of works have been done for describing mammalian cells, particularly mouse, which is one of the important model organisms, providing various opportunities for both biomedical research and biotechnological applications. Presented herein is a genome-scale mouse metabolic model that was systematically reconstructed by improving and expanding the previous generic model based on integrated biochemical and genomic data of Mus musculus. The key features of the updated model include additional information on gene-protein-reaction association, and improved network connectivity through lipid, amino acid, carbohydrate and nucleotide biosynthetic pathways. After examining the model predictability both quantitatively and qualitatively using constraints-based flux analysis, the structural and functional characteristics of the mouse metabolism were investigated by evaluating network statistics/centrality, gene/metabolite essentiality and their correlation. The results revealed that overall mouse metabolic network is topologically dominated by highly connected and bridging metabolites, and functionally by lipid metabolism that most of essential genes and metabolites are from. The current in silico mouse model can be exploited for understanding and characterizing the cellular physiology, identifying potential cell engineering targets for the enhanced production of recombinant proteins and developing diseased state models for drug targeting.
Contributors
Nicolas Le Novère

Metadata information

is
BioModels Database MODEL1507180042
hasProperty
Mathematical Modelling Ontology Constraint-based model

Curation status
Non-curated

Modelling approach(es)

Original model(s)
https://github.com/opencobra/m_model_collection/tree/master/sbml3

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Model files

MODEL1507180042_url.xml SBML L3V1 representation of Selvarasu2009 - Genome-scale metabolic network of Mus Musculus (iSS724) 1.49 MB Preview | Download

Additional files

MODEL1507180042.vcml Auto-generated VCML file 944.00 bytes Preview | Download
MODEL1507180042-biopax3.owl Auto-generated BioPAX (Level 3) 4.78 MB Preview | Download
MODEL1507180042-biopax2.owl Auto-generated BioPAX (Level 2) 2.52 MB Preview | Download
MODEL1507180042_urn.xml Auto-generated SBML file with URNs 1.49 MB Preview | Download
MODEL1507180042.m Auto-generated Octave file 747.00 bytes Preview | Download
MODEL1507180042.sci Auto-generated Scilab file 380.00 bytes Preview | Download
MODEL1507180042.pdf Auto-generated PDF file 8.16 MB Preview | Download
MODEL1507180042.xpp Auto-generated XPP file 369.00 bytes Preview | Download
MODEL1507180042.png Auto-generated Reaction graph (PNG) 5.07 KB Preview | Download
MODEL1507180042.svg Auto-generated Reaction graph (SVG) 558.00 bytes Preview | Download

  • Model originally submitted by : Nicolas Le Novère
  • Submitted: 18-Jul-2015 15:28:50
  • Last Modified: 28-Jul-2015 21:52:14
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 28-Jul-2015 21:52:14
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Selvarasu2009 - Genome-scale metabolic network of Mus Musculus (iSS724)
  • Version: 1 public model Download this version
    • Submitted on: 18-Jul-2015 15:28:50
    • Submitted by: Nicolas Le Novère
    • With comment: Original import of MODEL1507180042.xml.origin
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