Table 3.
Enriched TF PWMs in Promoters of Cell-Cycle-Regulated Genes A.
| TF | Number of promoters with hits | Number of hits | Analytical score | Rank relative to abundance in random sets |
| NF-Y | 152 | 203 | 1.2 × 10−11 | 1 |
| E2F | 78 | 92 | 1.2 × 10−8 | 1 |
| NRF-1 | 127 | 234 | 3.3 × 10−6 | 1 |
| Sp1 | 223 | 365 | 1.3 × 10−4 | 1 |
| ATF | 113 | 162 | 5.3 × 10−4 | 2 |
| CREB | 91 | 117 | 9.3 × 10−4 | 2 (1) |
| B. | |||||
| TF | Number of promoters with hits | Number of hits | Cell cycle phase | Analytical score | Rank relative to abundance in random sets |
| Arnt | 33 | 37 | G1/S | 5.1 × 10−4 | 5 (4) |
| YY1 | 20 | 25 | M/G1 | 8.1 × 10−4 | 5 (3) |
(A) A set of 568 promoters of cell cycle-regulated genes scanned for overrepresented TF PWMs, disclosing six significantly enriched PWMs. Information for each PWM is as in Table 1.
(B) Whitfield et al. (Whitfield et al. 2002) partitioned the cell cycle-regulated genes according to their expression periodicity patterns into five clusters corresponding to different phases of the cell cycle. When the promoter sequences of these clusters were scanned for enriched PWMs, two PWMs were enriched in a specific phase cluster, but not in the 568 set as a whole. Full lists of genes whose promoters were found to contain high scoring sites for the enriched TFs are provided in Supplemental Tables B1–B8 (available online at www.genome.org.)