Gene expression in response to PQ exposure in the Δ ura3 parent vs. Δ VNG0258H mutant strains. Line graphs represent mean expression profiles for each cluster of genes. Colors are as in Figure 5. The dotted line on each graph represents the time of PQ addition to each culture. (A) Genes requiring VNG0258H for repression regardless of PQ addition. (B) Genes requiring VNG0258H for repression in the absence of PQ and up-reguation in the presence of PQ. (C) Genes requiring VNG0258H for activation in the absence of PQ. (D) Genes induced in response to PQ but independent of VNG0258H. (E) Genes repressed in response to PQ but independent of VNG0258H. Gene expression profiles for individual genes in each cluster are shown in Additional file 9: Figure S4. Annotation details for genes in each cluster are listed in Additional file 5: Table S3.