Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1A - Assessment of microarray reproducibility. (A) Scatter plot of control versus control. Spots with absent, marginal, or present detection signals are displayed in yellow, blue, or red, respectively. (B) Plot of log₂ average versus log₂ difference from two control normalized replicates, suggesting that scalar normalization is appropriate. Results from all other possible pairwise comparisons with normalized control data yielded plots with very similar appearance (not shown).
• Supplemental Figure 1B
• Supplemental Figure 2 and 3 - Supplemental Figure 2. Determination of false discovery rate (FDR) comparing treatment versus control for p <= 0.001. The FDR was calculated using the software Q (Storey and Tibshirani, 2003). π₀ is an estimate for the overall proportion of truly null values for p less than or equal to a selected threshold t using tuning parameter λ = 1, and q is the minimum FDR attainable when calling an event significant. Like p, q is used to determine the proportion of events likely to give a false event rather than the probability that an event is false. (A) FDR determination for 3% glc versus control. (B) FDR for 60 mM N versus control. (C) FDR for 3% glc and 60 mM N versus control. (D) FDR for 3% 3-O-methylglucose versus control. Supplemental Figure 3. FDR determination for treatments containing CHX. (A) 3% glc & CHX versus CHX control. (B) 60 mM N & CHX versus CHX control. (C) 3% glc, 60 mM N, & CHX versus CHX control. (D) 3% 3-O-methylglucose & CHX versus CHX control.
• Supplemental Table 1 - Expression level of genes described in Figure 1.
• Supplemental Table 2 - Glucose-regulated genes described in Figure 4.
• Supplemental Table 3 - Genes associated with carbohydrate metabolism described in Figure 6.
• Supplemental Table 4A - Expression data for genes described in Figures 8A through 8D.
• Supplemental Table 4B
• Supplemental Table 4C
• Supplemental Table 4D
• Supplemental Table 5 - Transport-associated genes described in Figure 8.
• Supplemental Table 6 - Summary of nitrogen metabolism genes described in Figure 11.