Figure 7. Gene Expression Profiling of puf3 Mutants.

Distribution of average Cy5/Cy3 fluorescence ratios from three independent microarray hybridizations comparing mRNA levels of puf3Δ with wild-type cells grown in minimal media with glycerol. The left frequency axis refers to all genes (black line); the axis to the right refers to Puf3p and Puf4p (control) targets, shown as red and blue lines, respectively. Relative expression levels of the 220 Puf3p mRNA targets in puf3Δ cells were selectively increased compared to all other mRNAs analyzed (p < 10⁻³⁴), whereas Puf4p targets were not (p > 0.05). Thirty-nine genes involved in aerobic respiration (according to GO annotation and SGD), but not bound by Puf3p, were similarly enriched (p < 5 × 10⁻⁵) in the puf3 mutant as random sets of 39 Puf3p targets (p < 10⁻⁶). Likewise, 220 randomly selected mRNAs coding for mitochondrial proteins that were not associated with Puf3p in the experiments herein were weakly enriched in the mutant (p < 10⁻⁸).