Table 1.
Statistical analysis of ChIP-chip data
| Feature | All TBP + POL2 sites | Class I genes (p-value vs TBP + POL2) | Class II genes (p-value vs TBP + POL2) | p-value (Class I vs Class II) |
| Alternative promoters (average number) | 0.717 | 0.686 (0.008) | 0.934 (2.64 × 10−67) | 1.73 × 10−58 |
| Bidirectional promoters (percent) | 23.961 | 25.315 (0.005) | 28.186 (0.007) | 0.110 |
| Promoter occupancy (percent) | ||||
| H3K4me3 | 91.482 | 89.214 (8.72 × 10−05) | 82.721 (4.24 × 10−20) | 1.16 × 10−13 |
| OCT4 | 3.684 | 3.919 (0.728) | 3.064 (1.000) | 0.293 |
| NANOG | 12.438 | 13.448 (0.006) | 13.725 (0.698) | 0.861 |
| SOX2 | 10.243 | 11.471 (9.64 × 10−05) | 11.642 (0.474) | 0.901 |
| Promoter elements (percent) | ||||
| TATA box | 4.834 | 6.365 (5.15 × 10−15) | 7.353 (0.012) | 0.335 |
| BRE | 88.999 | 92.413 (6.27 × 10−24) | 92.892 (0.001) | 0.650 |
| Initiator | 99.608 | 99.928 (0.000) | 100.000 (1.000) | 0.402 |
| MTE | 0.679 | 0.611 (1.000) | 0.735 (1.000) | 0.626 |
| DCE | 99.843 | 99.964 (0.422) | 99.877 (1.000) | 0.402 |