Thiele2013 - Adrenal gland glandular cells

  public model
Short description
Thiele2013 - Adrenal gland glandular cells

The model of adrenal gland glandular cells 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
  • 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 MODEL1310110001
isDescribedBy
PubMed 23455439
occursIn
Taxonomy Homo sapiens
Brenda Tissue Ontology adrenal gland
isVersionOf

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

MODEL1310110001_url.xml SBML L2V4 representation of Thiele2013 - Adrenal gland glandular cells 11.77 MB Preview | Download

Additional files

MODEL1310110001-biopax3.owl Auto-generated BioPAX (Level 3) 14.61 MB Preview | Download
MODEL1310110001.png Auto-generated Reaction graph (PNG) 5.07 KB Preview | Download
MODEL1310110001.sci Auto-generated Scilab file 167.00 bytes Preview | Download
MODEL1310110001-biopax2.owl Auto-generated BioPAX (Level 2) 8.98 MB Preview | Download
MODEL1310110001.vcml Auto-generated VCML file 983.00 bytes Preview | Download
MODEL1310110001.svg Auto-generated Reaction graph (SVG) 558.00 bytes Preview | Download
MODEL1310110001_urn.xml Auto-generated SBML file with URNs 12.87 MB Preview | Download

  • Model originally submitted by : Camille Laibe
  • Submitted: Oct 11, 2013 4:43:07 PM
  • Last Modified: Oct 14, 2013 6:46:19 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Oct 14, 2013 6:46:19 PM
    • Submitted by: Camille Laibe
    • With comment: Current version of Thiele2013 - Adrenal gland glandular cells
  • Version: 1 public model Download this version
    • Submitted on: Oct 11, 2013 4:43:07 PM
    • Submitted by: Camille Laibe
    • With comment: Original import of Thiele2013 - Adrenal gland glandular cells