Table 3

Performance comparison of various prediction algorithms for ER binding using the independent dataset shown in Table 2

Prediction algorithm

Sensitivity

Specificity

Harmonic mean

Fisher's exact test P value

Consensus ERE with ≤2 mismatches

94.74%

30%

45.57%

0.104838

Consensus ERE with ≤3 mismatches

94.74%

0%

0.00%

1

Dragon ERE finder v2.0

68.42%

40%

50.49%

0.477589

TFAC 8.1 (min FP)

31.57%

100%

47.99%

0.057117

TFAC 8.1 (min FN)

78.94%

40%

53.10%

0.255439

h-ERE (stringent)

42.10%

90%

57.37%

0.084693

h-ERE (medium)

68.42%

70%

69.20%

0.056272

h-ERE (relaxed)

73.68%

70%

71.79%

0.03043

h-ERE (loose)

84.21%

70%

76.45%

0.006199

h-ERE outperformed the other algorithms. ERE, estrogen response element.

Vega et al. Genome Biology 2006 7:R82   doi:10.1186/gb-2006-7-9-r82