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. ^†PR_F : positive rate from our function conservation approach. ^‡FPR_F: false positive rate from our function conservation approach. ^§PR_PF: positive rate from phylogenetic footprinting approach. ^¶FPR_PF: false positive rate from phylogenetic footprinting approach. ^¥PR_EEL: positive rate from EEL algorithm. ^#FPR_EEL: false positive rate from EEL algorithm.