Open Access Highly Accessed Research article

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

Aarash Bordbar13, Adam M Feist13, Renata Usaite-Black12, Joseph Woodcock4, Bernhard O Palsson13 and Iman Famili12*

Author Affiliations

1 GT Life Sciences, 10520 Wateridge Circle, San Diego, CA 92121, USA

2 Current Affiliation: Intrexon Corporation, 1872 Pratt Dr., Blacksburg, VA 24060, USA

3 Current Affiliation: Department of Bioengineering, University of California San Diego, 417 Powell-Focht Bioengineering Hall, 9500 Gilman Dr., La Jolla, CA, 92093-0412, USA

4 Genomatica, 10520 Wateridge Circle, San Diego, CA 92121, USA

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BMC Systems Biology 2011, 5:180  doi:10.1186/1752-0509-5-180

Published: 31 October 2011

Additional files

Additional file 1:

Biomass Formulation. Supplementary information on sources and methods used to constract tissue-specific biomass functions.

Format: DOC Size: 1.5MB Download file

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Additional file 2:

Tissue specific models and multi-tissue model XLS (in compressed zip format). Metabolic models for adipocyte, hepatocyte, mycocyte, and multi-tissue network in XLS format

Format: ZIP Size: 337KB Download file

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Additional file 3:

Tissue specific models and multi-tissue model SBML (in compressed zip format). Metabolic models for adipocyte, hepatocyte, myocyte, and multi-tissue network in SBML format. The SBML format can be imported into Matlab and COBRA Toolbox for simulations

Format: ZIP Size: 251KB Download file

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Additional file 4:

QC/QA Tests and Futile Cycle Tests. Quality control tests to validate universal and tissue specific functionality and model consistency

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Additional file 5:

Unconstrained simulations of Cori and Alanine Cycles. Additional information on simulating the metabolic interaction between the liver and muscle based on sensitivity analysis of objectives (hepatic glucose and urea production)

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Additional file 6:

Reaction Activity Changes in Obese and Diabetic Obese Individuals. Differential metabolic reactions in simulations of obese and diabetic obese individuals determined by flux variability analysis

Format: XLS Size: 251KB Download file

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Additional file 7:

Liver metabolic network reconstruction comparison. Comparison of HM, Recon 1, and two existing liver metabolic networks in terms of metabolites and reactions.

Format: DOC Size: 119KB Download file

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Additional file 8:

Expression Data Sensitivity Analysis. Sensitivity analysis involving removing random permutations of patient samples from each group to determine robustness of expression data.

Format: XLSX Size: 14KB Download file

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