Supplementary information
From the following article:
Integrating high-throughput and computational data elucidates bacterial networks
Markus W. Covert, Eric M. Knight, Jennifer L. Reed, Markus J. Herrgard and Bernhard O. Palsson
Nature 429, 92-96(6 May 2004)
doi:10.1038/nature02456
Suppplementary Notes
Text describing the contents of all the supplementary Excel files in more detail, together with a case-by-case study of inconsistent environments and strains from Figure 1 in the main text, and a completed MIAME checklist.
Supplementary Data 1
Regulatory Model Rules (iMC1010v1). A list of the genes accounted for by the model, together with the regulatory rules, if any.
Supplementary Data 2
Simulation Parameters. A detailed list of all parameters used to run the simulations described in the manuscript.
Supplementary Data 3
Regulatory Model Abbreviations. Abbreviations used in the model to represent metabolites or metabolic reactions.
Supplementary Data 4
Phenotype-Model Comparison. A more detailed version of the phenotype model comparison shown in Figure 1 of the main text.
Supplementary Data 5
Phenotype sensitivity analysis. Sensitivity analysis of the phenotype cutoff parameter.
Supplementary Data 6
Anaerobic-aerobic culture data. Growth, substrate uptake and by-product secretion of wild-type and 6 knockout E. coli strains under aerobic and anaerobic conditions.
Supplementary Data 7
Normalized Array Data. A table with all the dChip-normalized array data from our experiments.
Supplementary Data 8
Detailed hypothesis list. A detailed list of the regulatory interaction hypotheses generated by this study. Includes new regulatory rules implemented in iMC1010v2.
Supplementary Data 9
qPCR cross-validation. Results of qPCR validation of various changes in gene expression from the microarray data set.
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