Fig. 4

Identifying 8mers with regulatory potential. a Scoring all tested 8mers. An expression score was calculated for each 8mer by multiplying the RPM values in each GFP sub-population by a scaling factor (0–10 %: −2, 20–30 %: −1, 40–60 %: 0, 70–80 %: 1; 90–100 %: 2), then normalized by the summed RPM value. Each 8mer is plotted by rank (x-axis) and score (y-axis). The expression controls are marked in red. b The enrichment of each 8mer in each GFP sub-population was found by dividing its RPM values by the RPM values in GFP+ cells. The enrichment values are ordered by the expression score shown in A. c Candidate elements recapitulate their behavior observed in the primary screen. Each candidate was inserted into the IQGAP1 3′UTR-luciferase construct, and the luciferase activity of these reporter constructs were normalized to the geometric means of two expression controls with no regulatory effect (UUCCGUUA and UAAUGCCC). The relative luminescence values (y-axis) were plotted versus the expression score (x-axis) for each candidate sequence. Expression controls are indicated in red. Pearson r = 0.820, p < 10⁻⁵. d The 8mers with scores >1 were considered activating elements, and those scores < −1 were considered repressive elements. The enrichment for each category of sequences was determined for activating and repressive elements. Significance was assessed by two-sided Fisher exact tests; *p < 0.05, **p < 0.005, ***p < 0.0005