Table 4 |
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|
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 |
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|
P(synergy/no. of TFBSs) |
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|
|
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|
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 |
- |
- |
- |
- |
- |
- |
- |
|
|
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|
*The number of genes whose promoters have at least two E2F1 binding sites. †PRF : positive rate from our function conservation approach. ‡FPRF: false positive rate from our function conservation approach. §PRPF: positive rate from phylogenetic footprinting approach. ¶FPRPF: false positive rate from phylogenetic footprinting approach. ¥PREEL: positive rate from EEL algorithm. #FPREEL: false positive rate from EEL algorithm. |
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|
Hu et al. Genome Biology 2007 8:R257 doi:10.1186/gb-2007-8-12-r257 |
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