Figure 3

Genome-wide changes in expression upon perturbation of the TBP regulatory network. We grouped 2,903 ORFs (rows) that changed expression by at least 1.5-fold in at least one of the 63 conditions (columns) examined into 10 clusters using the K-means algorithm [63]. Clusters 1-10 contained the following number of ORFs, respectively: 338, 333, 225, 330, 344, 359, 259, 282, 127, 306; 3,323 ORFs did not meet the filtering criteria. Changes are relative to a galactose-induced null TBP in a wild-type TBP background. Red, green, and black denote increased, decreased, and no change in gene expression. Gray denotes no data. Color intensity reflects the magnitude of change on a log₂ scale. Columns were arranged by hierarchical clustering [63]. Color boxes above each column indicate the relevant strain genotypes. All mutations are located on TBP except where designated 'spt3Δ', and 'ΔTAND', which signify deletion of SPT3 and the TAF1 TAND domain. Boxes with dashed outlines indicate null TBP. All strains harbor a chromosomal copy of the endogenous wild-type TBP gene (SPT15).