Table 1

Thresholds and total number of rules
Variables
 CF & Conf. threshold
 Support threshold
 Total number of rules
 FDR
Structural variables
 0.1
 0.01
 24
 0.093
Molecular Function & Structural variables
 0.4
 0.004
 20
 0.042
Biological Process & Structural variables
 0.5
 0.004
 7
 0.050
Cellular Component & Structural variables
 0.5
 0.004
 12
 0.011
Protein abundance & Responsiveness & TATA box
 0.1
 0.002
 15
 0.000
Protein abundance & Structural variables
 0.1
 0.002
 4
 0.040
Protein abundance & Molecular Function
 0.2
 0.002
 19
 0.109
Protein abundance & Biological Process
 0.4
 0.002
 21
 0.005
Protein abundance & Cellular Component
 0.3
 0.002
 14
 0.011
Responsiveness & Structural variables
 0.1
 0.002
 10
 0.044
Responsiveness & Molecular Function
 0.3
 0.002
 23
 0.069
Responsiveness & Biological Process
 0.6
 0.002
 19
 0.002
Responsiveness & Cellular Component
 0.4
 0.002
 19
 0.011
TATA box & Structural variables
 0.1
 0.002
 8
 0.098
TATA box & Molecular Function
 0.3
 0.002
 26
 0.213
TATA box & Biological Process
 0.5
 0.002
 15
 0.131
TATA box & Cellular Component
 0.3
 0.002
 12
 0.260
Cho et al. – EDA (grouping 1)
 0.4
 0.001
 23
 0.318
Cho et al. – EDA (grouping 2)
 0.4
 0.001
 6
 0.115
Cho et al. – G&S SHAVING (grouping 1)
 0.6
 0.002
 45
 0.006
Cho et al. – G&S SHAVING (grouping 2)
 0.6
 0.002
 36
 0.003
Gasch et al. – EDA (grouping 1)
 0.4
 0.001
 17
 0.005
Gasch et al. – EDA (grouping 2)
 0.4
 0.001
 21
 0.004
Gasch et al. – G&S SHAVING (grouping 1)
 0.6
 0.001
 56
 0.023
Gasch et al. – G&S SHAVING (grouping 2)
 0.7
 0.001
 35
 0.019

This table shows the CF, Confidence and Support thresholds set in each experiment as well as the total number of rules and the FDR obtained in each case.

Lopez et al. BMC Bioinformatics 2008 9:107   doi:10.1186/1471-2105-9-107