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Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

Evan S Snitkin1, Aimée M Dudley2, Daniel M Janse3, Kaisheen Wong, George M Church4 and Daniel Segrè15*

Author Affiliations

1 Bioinformatics graduate Program, Boston University, Boston, MA 02215, USA

2 Institute for Systems Biology, Seattle, WA 98103, USA

3 McKinsey & Company, London, SW1Y 4UH, UK

4 Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA

5 Departments of Biology and Biomedical Engineering, Boston University, Boston, MA, 02215, USA

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Genome Biology 2008, 9:R140  doi:10.1186/gb-2008-9-9-r140

Published: 22 September 2008

Additional files

Additional data file 1:

Figure S1a-c are heatmaps representing the concordance between the experimental gene deletion phenotypes and the corresponding predictions made by each of the three yeast models. Figure S2a, b are comparisons of the experimental data generated in the current study with similar data generated in previous studies using different experimental approaches.

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Additional data file 2:

Table S1 contains the original experimental phenotype measurements for 465 gene deletion strains under the 16 different conditions. Table S2 contains the changes made to the experimental data based on the re-checking of mutants whose original phenotype disagreed with iFF708 model predictions. Table S3 contains the refined experimental data. Table S4 contains the upper bounds used for the three yeast models in order to model the 16 experimental conditions. Table S5 contains a list of changes made to the three models used in the current study. Table S6 contains a list of mutants that were predicted to be discordant by the iFF708 model, and therefore submitted to experimental verification. Table S7 contains guidelines for interpreting patterns of discordance between experimentally generated mutant phenotypes and corresponding model predictions. Table S8 contains a list of all discordances that remained after the experimental refinement, and our interpretation of them, based on the guidelines laid out in Table S7.

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