Figure 4.

Gene expression signatures of all viable SAGA deletion mutants. (A, B) Hierarchical cluster analyses of 3502 genes varying in expression over 1.5-fold in at least one mutant with columns representing the different mutants indicated and rows representing genes. The mRNA levels in each mutant relative to the levels in wild-type cells are colour coded as indicated at lower right, with missing data in white. The three classes discussed in the main text are indicated at the bottom. (A) All viable SAGA deletion mutants were clustered using the Change correlation. (B) The tra1Δ, spt7Δ, and ada1Δ mutants were re-clustered using the Smooth correlation. (C, D) Venn diagrams show the degree of overlap between the three different classes of SAGA mutants. Classes were identified from the hierarchical clustering shown in (A): Class 1 consists of spt7Δ and ada1Δ mutants; Class 2 consists of ada2Δ, ada3Δ, and gcn5Δ mutants; Class 3 consists of sgf11Δ, spt20Δ, spt8Δ, and sus1Δ mutants. The total number of genes affected >1.5-fold for each data set is indicated in parenthesis. The significance of overlaps between different gene lists was calculated in GeneSpring GX7 (Agilent) by using a standard Fisher's exact test.