FIGURE 3 

Four classes of transcriptional regulatory principles in S. cerevisiae. These graphs illustrate the dependency of motif strength on motif geometric constraints for the PAC (A, blue curve), RRPE (A, red curve), MCB (C), and the RAP1 (E) motifs. The position of the start codon is indicated by 'ATG'. To form instances of a gene ensemble containing each of these motifs (see Materials and methods section), the motif distance relative to ATG is binned with a bin size of 150 bp, except the last bin with a bin size of 250 bp. The average motif strength of each of these motif-containing gene ensemble instances (see Supplementary information 3 for the distribution of correlation coefficients) is plotted in the middle of each bin, with the error bar indicating the standard error of the average. Panels (B), (D), and (F) show the degree of gene coexpression, as measured by the average pairwise expression correlation, for the corresponding motif-containing gene ensemble instances for panels (A), (C), and (E). For MCB and RAP1 motifs, their orientational effects (5' represented in red, 3' represented in blue) on gene expression are also presented in addition to their geometric constraint.