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Open Access Highly Accessed Methodology article

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

Yuliang Wang12, James A Eddy13 and Nathan D Price12*

Author Affiliations

1 Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA

2 Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, 61801, USA

3 Department of Bioengineering, University of Illinois, Urbana, IL, 61801, USA

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BMC Systems Biology 2012, 6:153  doi:10.1186/1752-0509-6-153

Published: 13 December 2012

Additional files

Additional file 1:

Codes and input data to run mCADRE in a zipped file.

Format: ZIP Size: 1.4MB Download file

Open Data

Additional file 2:

All 126 TSEM metabolic model files in a zipped file.

Format: ZIP Size: 9.3MB Download file

Open Data

Additional file 3: Table S1:

Includes a list of universally important metabolites that must be produced from glucose. Table S2. Includes a sensitivity analysis of the inactivated core to non-core ratio. Table S3. Includes GEO accession numbers for microarray samples used to build liverCADRE. Table S4. Includes the coverage and functionality comparison of liverCADRE, the original liver, MBA model, and the new liver MBA model (based on the same training data as liverCADRE). Table S5. Includes the GEO accession numbers for microarray samples used in independent comparison of liverCADRE and liverMBA. Table S6. Includes the Human Protein Atlas staining data for 560 metabolic genes. Tables S7-S9. Include the detail results of liver metabolic function tests. Table S10. Includes the biomass composition. Table S11. Includes the RPMI-1640 medium. Table S12. Includes the enrichment of pathways listed in Table 3 and Table 4 in brain and tumor tissues based on gene expression data alone. Table S13. Includes comparison of protein staining evidence for unique gene associated reactions in kidneyReduced and kidneyTSEM. Table S14. Includes kidneyTSEM simulation results of 41 renal metabolic functions. Table S15. Includes kidneyTSEM simulation of effects of genetic perturbations on renal metabolic functions.

Format: XLSX Size: 44KB Download file

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Additional file 4:

Inconsistent reactions in each of the 126 TSEM models.

Format: ZIP Size: 744KB Download file

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Additional file 5:

liverCADRE in SBML format.

Format: XML Size: 2.7MB Download file

Open Data