Table 7

Predicted active and inactive promoters in the mouse genome.

Active Promotera


Cell lines

Active Gene

Total Prediction

Refseq Supported PPV

Predicted promoters not present in the expression measurement

Expression Supported PPV


ES

7887

13853

81.4%

7191

88.6%


MEF

8092

11913

88.1%

5480

92.3%


NPC

7413

12700

84.1%

6259

89.0%


Inactive Promoterb


Cell lines

Inactive Gene

Total Prediction

Refseq Supported PPV

Predicted promoters not present in the expression measurement

Expression Supported PPV


ES

4753

2862

77.0%

1806

79.2%


MEF

4248

4301

66.1%

3061

74.6%


NPC

5259

422

73.2%

267

94.8%


a Active promoter supported by gene expression and Refseq: TP is the number of active genes prediction as active and FP is the number of inactive genes predicted as active. b Inactive promoter supported by gene expression: TP is the number of inactive genes predicted as inactive and FP is the number of active genes predicted as inactive. In both cases, we only considered predictions located within 2.5 Kb to annotated genes and the total number of predictions is thus usually larger than the sum of TPs and FPs. Refseq supported PPV shows how much percent of the total active/inactive promoter predictions are supported by Refseq.

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

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