Table 4

Comparison of PPV = TP/(TP+FP) in promoter predictions using the annotated TSS sites.

Untreated


Total Prediction (TP+FP)

TP

PPV

p-value


Heintzman et al.

198

181

91.41%

< 1.0 × 10-16


HMM(c1 = 2.205)

198

189

95.45%

< 1.0 × 10-16


HMM (c1 = 1.6)

256

234

91.41%

< 1.0 × 10-16


HMM (c1 = 0.5)

337

264

78.34%

< 1.0 × 10-16


Treated


Total Prediction (TP+FP)

TP

PPV

p-value


Heintzman et al.

207

183

88.41%

< 1.0 × 10-16


HMM (c1 = 2.1)

207

196

94.69%

< 1.0 × 10-16


HMM (c1 = 1.367)

279

247

88.50%

2.8 × 10-3


HMM (c1 = 0.5)

362

278

76.80%

< 1.0 × 10-16


We calculated p value by generating random predictions on the ENCODE regions.

Won et al. BMC Bioinformatics 2008 9:547   doi:10.1186/1471-2105-9-547

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