Table 1.
Periodicity scores of selected genes
| Rank | Gene | Periodicity score | Max fold change | Avg. fold change |
|---|---|---|---|---|
| 1 | STK15 | 58.8 | 16 | 10 |
| 2 | PLK | 56.0 | 11 | 8.6 |
| 7 | CENPE | 42.6 | 11 | 6.8 |
| 17 | CKS2 | 35.1 | 11 | 5.5 |
| 25 | CCNA2 | 31.2 | 5.9 | 4.5 |
| 43 | CDC6 | 25.3 | 3.8 | 3.0 |
| 50 | CCNB1 | 24.3 | 7.3 | 4.1 |
| 54 | E2F1 | 23.0 | 4.9 | 3.9 |
| 95 | PCNA | 16.9 | 3.4 | 2.7 |
| 105 | CIT | 16.2 | 7.0 | 4.0 |
| 135 | GOLGIN-67 | 13.6 | 4.8 | 3.1 |
| 182 | ORC 1 | 11.2 | 3.7 | 2.2 |
| 355 | PRIM1 | 7.26 | 2.6 | 2.1 |
| 499 | VCL | 5.80 | 3.4 | 2.7 |
| 607 | BRCA1 | 5.17 | 2.5 | 2.1 |
| 618 | CCNE2 | 7.18 | 3.1 | 2.5 |
| 1127 | PSEN1 | 3.65 | 2.1 | 1.8 |
| 1333 | CDC42 | 3.29 | 2.3 | 2.0 |
| 1334 | cutoff | 3.286 | — | — |
| 1358 | ZNF162 | 3.25 | 1.9 | 1.8 |
| 1780 | YY1 | 2.75 | 3 | 2.3 |
Sample periodicity scores for representative cell cycle regulated genes. The cutoff for a cell cycle regulated gene was established by balancing the false positive and false negative rates. We used a cutoff that gave an estimated 0.15–0.75% false positive rate and 6.5% false negative rate, resulting in 1333 clones. The maximum fold change is the maximum amplitude observed in any of the five synchronizations. The average fold change is the average amplitude across all five synchronizations.