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Open Access Research article

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states

Aarash Bordbar, Neema Jamshidi and Bernhard O Palsson*

Author Affiliations

Department of Bioengineering, University of California San Diego, 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive, La Jolla, CA, 92093-0412, USA

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BMC Systems Biology 2011, 5:110  doi:10.1186/1752-0509-5-110

Published: 12 July 2011

Additional files

Additional file 1:

Comparison of iAB-RBC-283 and previous constraint-based model of human erythrocyte. iAB-RBC-283 was compared with the previous constraint-based model of the human erythrocyte. Topological analysis showed that iAB-RBC-283 is a much more expansive network that better describes human erythrocyte metabolism. In addition, we recapitulated the randomized sampling results of the previous network and showed that the new erythrocyte model is more accurate, capturing all the correct predictions of the previous model but also correcting its inaccurate predictions.

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Additional file 2:

Detected SNPs and FVA results for SNP perturbations. Tables containing the OMIM SNPs of enzymes that are in iAB-RBC-283 with known pathologies, symptoms, metabolic subsystem, and classification. In addition, exchange reactions determined by FVA to be different in SNP perturbations are provided.

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Additional file 3:

Detected drug targets and FVA results for drug effect perturbations. Tables containing the known drugs, from DrugBank, that have targets in enzymes that are in iAB-RBC-283. In addition, information is provided on the drug including name, description, and classification. The exchange reactions determined by FVA to be different in drug perturbations are also provided.

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Additional file 4:

iAB-RBC-283 Reconstruction (table format). The reconstruction is provided in a table format with reactions, metabolites, and gene-protein-reaction associations. In addition, information is provided on whether the reaction was detected in the proteomic or metabolomic data and citations are provided for reactions with existing experimental evidence, implicating the reactions presence in the human erythrocyte.

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Additional file 5:

iAB-RBC-283 Reconstruction (SBML format). The reconstruction is provided in the standardized SBML format. The XML file can be loaded in to COBRA toolbox to perform in silico simulations. A copy of the file is also available at the BioModels Database (id: MODEL1106080000).

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Additional file 6:

Citations for exchanges in the human erythrocyte. Table containing citations used to determine exchange rates of metabolites into the human erythrocyte.

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Additional file 7:

Parameter sensitivity of threshold for FVA simulations. Figure showing the average number of FVA-detected exchange reactions for each perturbation and different thresholds. Thresholds were tested from 5-60% at intervals of 5%. The average detected reactions were quite stable from 15-40% for both the SNP and drug perturbations. A final 40% threshold was used in the study.

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