Supplementary Data for:
Functional Profiling of the Saccharomyces cerevisiae genome

Analysis Methods

The details of the procedures and algorithms used to analyze the data can be found [here].

Data Files

The list of fitness profiling data for defined environmental conditions along with the data for standard conditions can be found [here].(Note: This link opens a window to a different site) Plots and statistics comparing Fitness Scores and Expression Data from Church and Young Labs can be found [here]

Function Classification

Figure S1. Distribution of slow growing yeast strains by functional category. The percent of genes in each major functional category [MIPS](Note: This opens a window to a different site) relative to the whole genome is plotted along the x-axis in blue. The percent of genes in each major functional category relative to the total number of slow growing strains is plotted along the x-axis in yellow.

Table S1: Relationship of average intensity ratio to growth rate

average ratio after ~ 10 generations approximate % of wildtype growth 3X 80% 10X 65% 20X 50%

Table S2: List of slow growing homozygous strains in standard conditions (YPD)

Table S2

Comparison to Expression Results

Condition Measured Genes Significantly Up-Regulated Significantly Down-Regulated % with Significant Upregulation & Significant for Fitness Defect % with Significant Downregulation & Significant for Fitness Defect Galactose 4682 99 84 6.06 0.00 Alkali 4711 434 464 3.00 3.23 1M NaCl 4711 679 1047 0.88 1.15 1.5M Sorbitol 4711 588 1024 0.34 0.0   Figure 4c: Comparison of expression and fitness profiling data for pH 8. If a gene exhibits a significant increase in expression and is required to be expressed for survival in that condition, the corresponding deletion strain should also exhibit a decrease in fitness. Accordingly, (and for the sake of clarity) only those genes designated as sensitive by the fitness defect score were plotted. Red triangles represent genes with significant fitness defect scores (above the horizontal blue line) plotted as a function of their corresponding log ratio expression values. Black triangles represent genes with significant log ratio expression (outside of the two vertical blue lines) plotted with their corresponding fitness defect scores. The value of the fitness defect scores plotted is the minimum score from two experiments. In the galactose case, 6.1 % of the genes significantly up regulated also exhibited a significant decrease in fitness, while only 3.0 %, 0.88% and 0.34% of the genes significantly up regulated also exhibited a significant decrease in fitness for pH 8.0, 1M NaCl and 1.5M sorbitol, respectively. See table above.