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

P(synergy/no. of TFBSs)


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

-

-

-

-

-

-

-


*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.

Hu et al. Genome Biology 2007 8:R257   doi:10.1186/gb-2007-8-12-r257

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