FIGURE 4 

The analysis of the gene ensemble that contains both the PAC and RRPE motifs. (A) Relative distance of PAC and RRPE to ATG is binned into three bins: [-150,ATG], [-300,-150], and [-1000,-300] bp, forming a total of nine PAC/RRPE-containing gene ensemble instances for nine combinations of promoter structures. Average motif strength is plotted against the position of PAC (along the x-axis) and RRPE (different curves). The black diamond curve represents motif strength averaged over all genes in three ensemble instances corresponding to three binned positions of RRPE (see Supplementary information 2 for motif strength averaged over all genes in three ensemble instances corresponding to three binned positions of PAC). In (B), predicted PAC and RRPE motif strengths are shown as a function of their relative order with respect to ATG (5'-RRPE-PAC-ATG and 5'-PAC-RRPE-ATG). For the 5'-RRPE-PAC-ATG ensemble instance, the magnitude of the PAC motif strength is about three times higher than the instance that contains these motifs in the reverse order, consistent with the corresponding degree of gene coexpression. Nevertheless, the motif strength of RRPE motif is insignificant regardless of motif order. In (C) and (D), the positions of PAC and RRPE motifs relative to ATG of gene promoters that contain them are presented. In (C), the location of each motif in RRPE-only (red), PAC-only (blue), and PAC/RRPE-only containing gene ensembles is represented by a filled circle of appropriate color located at a position it occurs in gene promoter relative to ATG. The choice of these 'only' ensembles is discussed in Supplementary information 2. Likewise, in (D), the positions of PAC and RRPE are plotted for PAC/RRPE gene ensemble with two different motif order arrangements. Data in (A) and (B) clearly indicate that there is no actual synergism between PAC and RRPE. This finding appears to contradict the appearance of PAC and RRPE synergic behaviors suggested in Supplementary information 2 and earlier work (Beer and Tavazoie, 2004). However, data shown in (C) and (D) and average pairwise expression correlation coefficient date in Table 1 not only confirm MED's prediction but also illustrate nature's use of geometry as another dimension for regulating transcription.