Table 5

Comparison of active promoter predictions.

untreated cella


Active promoters

Inactive promoters


Total Prediction

Expression Supported Prediction

PPV


Heintzman et al. [15]b

197

127

64.47%

31


229

127

55.46%

32


HMM (c1 = 1.95)

197

128

64.97%

25


HMM (c1 = 1.6)

229

135

58.95%

31


HMM (c1 = 0.5)

309

143

46.28%

40


treated cella


Active promoters

Inactive promoters


Total Prediction

Expression Supported Prediction

PPV


Heintzman et al. [15]

204

128

62.75%

23


213

128

60.09%

23


HMM (c1 = 1.853)

204

128

62.75%

19


HMM (c1 = 1.367)

247

139

56.27%

22


HMM (c1 = 0.5)

328

145

44.21%

30


aThe total numbers of predictions in Table 5 are slightly different from Table 4 because when multiple predicted sites were supported by the same TSS or any enhancer evidence, we merged these predictions (see Methods).

bThe number of correctly predicted active promoters did not change using a lower cut-off in the profile-based method.

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

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