Thiele2013 - Liver hepatocytes

  public model
Model Identifier
MODEL1310110014
Short description
Thiele2013 - Liver hepatocytes

The model of liver hepatocytes metabolism is derived from the community-driven global reconstruction of human metabolism (version 2.02, MODEL1109130000 ).

This model is described in the article:

Thiele I, et al .
Nature Biotechnology

Abstract:

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ~2x more reactions and ~1.7x more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.

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 (L2V4)
Related Publication
  • A community-driven global reconstruction of human metabolism.
  • Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating SM, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ
  • Nature biotechnology , 5/ 2013 , Volume 31 , pages: 419-425 , PubMed ID: 23455439
  • Center for Systems Biology, University of Iceland, Reykjavik, Iceland. ines.thiele@gmail.com
  • Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ∼2× more reactions and ∼1.7× more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.
Contributors
Camille Laibe

Metadata information

isDerivedFrom
BioModels Database MODEL1109130000
is
BioModels Database MODEL1310110014
isDescribedBy
PubMed 23455439
isVersionOf
occursIn
Brenda Tissue Ontology liver
Taxonomy Homo sapiens

Curation status
Non-curated

Original model(s)
http://www.nature.com/nbt/journal/v31/n5/extref/nbt.2488-S2.zip

Tags
Name Description Size Actions

Model files

MODEL1310110014_url.xml SBML L2V4 representation of Thiele2013 - Liver hepatocytes 10.83 MB Preview | Download

Additional files

MODEL1310110014.vcml Auto-generated VCML file 983.00 bytes Preview | Download
MODEL1310110014.png Auto-generated Reaction graph (PNG) 5.07 KB Preview | Download
MODEL1310110014.pdf Auto-generated PDF file 26.52 MB Preview | Download
MODEL1310110014.svg Auto-generated Reaction graph (SVG) 558.00 bytes Preview | Download
MODEL1310110014-biopax3.owl Auto-generated BioPAX (Level 3) 13.86 MB Preview | Download
MODEL1310110014-biopax2.owl Auto-generated BioPAX (Level 2) 8.47 MB Preview | Download
MODEL1310110014.sci Auto-generated Scilab file 167.00 bytes Preview | Download
MODEL1310110014_urn.xml Auto-generated SBML file with URNs 11.90 MB Preview | Download

  • Model originally submitted by : Camille Laibe
  • Submitted: 11-Oct-2013 17:32:11
  • Last Modified: 14-Oct-2013 19:34:44
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 14-Oct-2013 19:34:44
    • Submitted by: Camille Laibe
    • With comment: Current version of Thiele2013 - Liver hepatocytes
  • Version: 1 public model Download this version
    • Submitted on: 11-Oct-2013 17:32:11
    • Submitted by: Camille Laibe
    • With comment: Original import of Thiele2013 - Liver hepatocytes
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