Sigurdsson2010 - Genome-scale metabolic model of Mus Musculus (iMM1415)

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Model Identifier
MODEL1507180055
Short description
Sigurdsson2010 - Genome-scale metabolic model of Mus Musculus (iMM1415)

This model is described in the article:

Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ.
BMC Syst Biol 2010; 4: 140

Abstract:

BACKGROUND: Well-curated and validated network reconstructions are extremely valuable tools in systems biology. Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms. RESULTS: We mapped the published, detailed reconstruction of human metabolism (Recon 1) to other mammals. By searching for genes homologous to Recon 1 genes within mammalian genomes, we were able to create draft metabolic reconstructions of five mammals, including the mouse. Each draft reconstruction was created in compartmentalized and non-compartmentalized version via two different approaches. Using gap-filling algorithms, we were able to produce all cellular components with three out of four versions of the mouse metabolic reconstruction. We finalized a functional model by iterative testing until it passed a predefined set of 260 validation tests. The reconstruction is the largest, most comprehensive mouse reconstruction to-date, accounting for 1,415 genes coding for 2,212 gene-associated reactions and 1,514 non-gene-associated reactions.We tested the mouse model for phenotype prediction capabilities. The majority of predicted essential genes were also essential in vivo. However, our non-tissue specific model was unable to predict gene essentiality for many of the metabolic genes shown to be essential in vivo. Our knockout simulation of the lipoprotein lipase gene correlated well with experimental results, suggesting that softer phenotypes can also be simulated. CONCLUSIONS: We have created a high-quality mouse genome-scale metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes). We demonstrate that the mouse model can be used to perform phenotype simulations, similar to models of microbe metabolism. Since the mouse is an important experimental organism, this model should become an essential tool for studying metabolic phenotypes in mice, including outcomes from drug screening.

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
  • A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.
  • Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ
  • BMC systems biology , 0/ 2010 , Volume 4 , pages: 140 , PubMed ID: 20959003
  • Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
  • BACKGROUND: Well-curated and validated network reconstructions are extremely valuable tools in systems biology. Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms. RESULTS: We mapped the published, detailed reconstruction of human metabolism (Recon 1) to other mammals. By searching for genes homologous to Recon 1 genes within mammalian genomes, we were able to create draft metabolic reconstructions of five mammals, including the mouse. Each draft reconstruction was created in compartmentalized and non-compartmentalized version via two different approaches. Using gap-filling algorithms, we were able to produce all cellular components with three out of four versions of the mouse metabolic reconstruction. We finalized a functional model by iterative testing until it passed a predefined set of 260 validation tests. The reconstruction is the largest, most comprehensive mouse reconstruction to-date, accounting for 1,415 genes coding for 2,212 gene-associated reactions and 1,514 non-gene-associated reactions.We tested the mouse model for phenotype prediction capabilities. The majority of predicted essential genes were also essential in vivo. However, our non-tissue specific model was unable to predict gene essentiality for many of the metabolic genes shown to be essential in vivo. Our knockout simulation of the lipoprotein lipase gene correlated well with experimental results, suggesting that softer phenotypes can also be simulated. CONCLUSIONS: We have created a high-quality mouse genome-scale metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes). We demonstrate that the mouse model can be used to perform phenotype simulations, similar to models of microbe metabolism. Since the mouse is an important experimental organism, this model should become an essential tool for studying metabolic phenotypes in mice, including outcomes from drug screening.
Contributors
Nicolas Le Novère

Metadata information

is
BioModels Database MODEL1507180055
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

MODEL1507180055_url.xml SBML L3V1 representation of Sigurdsson2010 - Genome-scale metabolic model of Mus Musculus (iMM1415) 5.51 MB Preview | Download

Additional files

MODEL1507180055.sci Auto-generated Scilab file 380.00 bytes Preview | Download
MODEL1507180055.m Auto-generated Octave file 747.00 bytes Preview | Download
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MODEL1507180055-biopax2.owl Auto-generated BioPAX (Level 2) 6.06 MB Preview | Download
MODEL1507180055.vcml Auto-generated VCML file 944.00 bytes Preview | Download
MODEL1507180055.pdf Auto-generated PDF file 19.36 MB Preview | Download
MODEL1507180055-biopax3.owl Auto-generated BioPAX (Level 3) 11.56 MB Preview | Download
MODEL1507180055.xpp Auto-generated XPP file 369.00 bytes Preview | Download
MODEL1507180055.png Auto-generated Reaction graph (PNG) 5.07 KB Preview | Download
MODEL1507180055_urn.xml Auto-generated SBML file with URNs 5.51 MB Preview | Download

  • Model originally submitted by : Nicolas Le Novère
  • Submitted: 18-Jul-2015 15:34:09
  • Last Modified: 28-Jul-2015 21:53:56
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 28-Jul-2015 21:53:56
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Sigurdsson2010 - Genome-scale metabolic model of Mus Musculus (iMM1415)
  • Version: 1 public model Download this version
    • Submitted on: 18-Jul-2015 15:34:09
    • Submitted by: Nicolas Le Novère
    • With comment: Original import of MODEL1507180055.xml.origin
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