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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

  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 - - - - - - -
  1. *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.