Table 4 Significance of E2F1 synergy for different distance constraints and sensitivity/specificity for detecting synergistic E2F1 combinations by function conservation, phylogenetic footprinting, and EEL algorithm from experimentally proven E2F1 binding human promoters
From: Prediction of synergistic transcription factors by function conservation
| Â | P(synergy/no. of TFBSs) | Â | Â | Â | Â | Â | Â | Â | Â | |
|---|---|---|---|---|---|---|---|---|---|---|
Distance | Real sequences | Randomized sequences | P value | No. of genes* | PRF†| FPRF‡ | PRPF§ | FPRPF¶ | PREEL¥ | FPREEL# |
D10 | 0.039 | 0.027 | 1.6E-04 | 48 | 10.4% | 0.0% | 2.1% | 0.0% | 6.3% | 0.0% |
D20 | 0.077 | 0.041 | 3.0E-17 | 92 | 8.7% | 0.0% | 3.3% | 0.0% | 3.3% | 0.0% |
D30 | 0.109 | 0.064 | 1.1E-18 | 125 | 8.8% | 0.0% | 2.4% | 0.0% | 5.6% | 0.0% |
D40 | 0.139 | 0.084 | 2.2E-21 | 159 | 11.9% | 0.0% | 3.1% | 0.0% | 5.7% | 0.0% |
D50 | 0.171 | 0.098 | 1.6E-31 | 192 | 12.5% | 0.0% | 3.1% | 0.0% | 6.8% | 0.0% |
D60 | 0.186 | 0.119 | 2.4E-24 | 209 | 12.0% | 0.0% | 3.3% | 0.0% | 8.1% | 0.0% |
D70 | 0.215 | 0.141 | 6.0E-26 | 244 | 12.7% | 0.0% | 2.9% | 0.0% | 7.8% | 0.0% |
D80 | 0.243 | 0.154 | 6.0E-34 | 272 | 14.7% | 0.0% | 2.9% | 0.0% | 8.1% | 0.4% |
D90 | 0.265 | 0.167 | 7.1E-38 | 293 | 14.3% | 0.0% | 3.1% | 0.0% | 7.8% | 0.7% |
D100 | 0.280 | 0.177 | 4.6E-40 | 309 | 14.2% | 0.0% | 3.2% | 0.0% | 8.1% | 0.6% |
D200 | 0.400 | 0.312 | 1.2E-22 | 419 | 17.7% | 0.0% | 2.6% | 0.0% | 7.6% | 1.9% |
D300 | 0.477 | 0.393 | 2.6E-19 | 487 | 18.1% | 0.0% | 2.5% | 0.0% | 7.2% | 2.7% |
D400 | 0.524 | 0.459 | 4.9E-12 | 527 | 19.7% | 0.0% | 2.3% | 0.0% | 7.4% | 3.2% |
D500 | 0.559 | 0.505 | 5.3E-15 | 557 | 20.3% | 0.0% | 2.2% | 0.0% | 7.7% | 3.2% |
D600 | 0.579 | 0.547 | 5.0E-04 | 575 | 20.2% | 0.0% | 2.1% | 0.0% | 8.0% | 3.3% |
D700 | 0.600 | 0.578 | 1.1E-02 | - | - | - | - | - | - | - |
D800 | 0.612 | 0.604 | 1.9E-01 | - | - | - | - | - | - | - |
D900 | 0.618 | 0.617 | 4.9E-01 | - | - | - | - | - | - | - |
None | 0.618 | 0.619 | 5.2E-01 | - | - | - | - | - | - | - |