Table 3.
Significant transcription factor (TF)-binding sites in genes having differential-expression at P < 0.05 and absolute fold-change >2; TF-binding site enrichment by Pscana.
| TF Nameb | Matrix ID | Z Score | P-value | Bonferroni P-value |
|---|---|---|---|---|
| UP-REGULATED IN YOLK SAC | ||||
| Plag1 | MA0163.1 | 5.12465 | 1.42E-07 | 9.00E-05 |
| Arnt::Hif1a | MA0259.1 | 5.09355 | 1.67E-07 | 0.000105754 |
| Znf423 | MA0116.1 | 4.17542 | 1.43E-05 | 0.009050338 |
| Klf13 | MA0657.1 | 4.16993 | 1.45E-05 | 0.009184069 |
| Sp1 | MA0079.3 | 4.04080 | 2.60E-05 | 0.016508603 |
| Glis3 | MA0737.1 | 3.69324 | 0.000107782 | 0.06844157c |
| DOWN-REGULATED IN YOLK SAC | ||||
| Gata4 | MA0482.1 | 4.80921 | 7.39E-07 | 0.000469005 |
| Gata1 | MA0035.3 | 4.57615 | 2.31E-06 | 0.001464596 |
| Gata1 | MA0035.2 | 4.12192 | 1.84E-05 | 0.011684635 |
| Gata2 | MA0036.2 | 3.84142 | 5.99E-05 | 0.03805663 |
| UP-REGULATED IN KIDNEY | ||||
| Prdm1 | MA0508.1 | 3.81093 | 6.77507E-05 | 0.04302169 |
| DOWN-REGULATED IN LUNG | ||||
| Hnf4a | MA0114.2 | 5.94132 | 1.30E-09 | 8.25E-07 |
| Hnf4g | MA0484.1 | 5.47657 | 2.01E-08 | 1.28E-05 |
| Foxa2 | MA0047.1 | 5.37203 | 3.64E-08 | 2.31E-05 |
| Hnf4a | MA0114.3 | 5.29283 | 5.63E-08 | 3.57E-05 |
| Hnf1b | MA0153.1 | 5.20468 | 9.09E-08 | 5.77E-05 |
| Hnf1a | MA0046.1 | 4.93196 | 3.75E-07 | 0.000238357 |
| Foxa1 | MA0148.1 | 4.85155 | 5.82E-07 | 0.000369529 |
| Foxa1 | MA0148.2 | 4.83018 | 6.48E-07 | 0.000411578 |
| Hnf1b | MA0153.2 | 4.7235 | 1.09E-06 | 0.000694766 |
| Hnf4a | MA0114.1 | 4.64095 | 1.64E-06 | 0.001038854 |
| Hnf1a | MA0046.2 | 4.51127 | 3.06E-06 | 0.00194136 |
| Cux1 | MA0754.1 | 4.01251 | 2.88E-05 | 0.018313464 |
| Cux2 | MA0755.1 | 3.9537 | 3.70E-05 | 0.02347703 |
| Foxa2 | MA0047.2 | 3.85396 | 5.64E-05 | 0.035813048 |
| Foxa1 | MA0148.3 | 3.72288 | 9.58E-05 | 0.060801885c |
| Cebpe | MA0837.1 | 3.677 | 0.00011437 | 0.072621775c |
| Bhlha15 | MA0607.1 | 3.60496 | 0.00015141 | 0.09614281c |
| Rxrg | MA0856.1 | 3.60157 | 0.00015358 | 0.097521395c |
| UP-REGULATED IN HEART | ||||
| Ebf1 | MA0154.2 | 3.90828 | 4.56688E-05 | 0.02899969 |
aUsing this rigorous method of analysis, we found no significant TF-binding sites in placenta, liver or cerebellum.
bTF name denotes the TF-binding site(s) enriched by Pscan.
cAlthough 30 enriched TF-binding sites are listed, these five are not statistically significant (i.e. P > 0.05 when the Bonferroni-corrected P-value is taken into account).