Jerby2010_Liver_Metabolism

This is the genome-scale metabolic network described in the article:
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

Livnat Jerby, Tomer Shlomi, and Eytan Ruppin; Molecular Systems Biology 6:401, 2010; PmID: 20823844
, DOI: 10.1038/msb.2010.56

Abstract:
The computational study of human metabolism has been advanced with the advent of the first generic (non-tissue specific) stoichiometric model of human metabolism. In this study, we present a new algorithm for rapid reconstruction of tissue-specific genome-scale models of human metabolism. The algorithm generates a tissue-specific model from the generic human model by integrating a variety of tissue-specific molecular data sources, including literature-based knowledge, transcriptomic, proteomic, metabolomic and phenotypic data. Applying the algorithm, we constructed the first genome-scale stoichiometric model of hepatic metabolism. The model is verified using standard cross-validation procedures, and through its ability to carry out hepatic metabolic functions. The model's flux predictions correlate with flux measurements across a variety of hormonal and dietary conditions, and improve upon the predictive performance obtained using the original, generic human model (prediction accuracy of 0.67 versus 0.46). Finally, the model better predicts biomarker changes in genetic metabolic disorders than the generic human model (accuracy of 0.67 versus 0.59). The approach presented can be used to construct other human tissue-specific models, and be applied to other organisms.
The original SBML version was produced by COBRA_Toolbox and downloaded from the suplementary material of the article. To make this model SBML compliant, the unit for the FLUX_VALUE parameters had to be changed from mmole per gramm dry weight per hour to mmole per hr. To change the model back to its original form, either alter the unit definition of the unit mmol_per_hr accordingly or replace mmol_per_hr by mmol_per_gDW_per_hr in all reactions.
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