Table 1

Coverage of inverted repeats in E. coli footprint data

Mismatches allowed

Random average coverage %

Footprint coverage %

Z-score

Associated p-value


Activators

0

55

44

-2.4

0.008

1

82

74

-1.92

0.03

2

82

75

-2.54

0.006

Dual

0

68

79

4.84

6.61E-07

1

96

96

1.54

0.06

2

96

97

0.09

0.46

Repressors

0

66

84

6.43

0

1

90

91

0.36

0.36

2

91

91

-0.01

0.49

All regulators

0

65

77

6.51

0

1

93

92

0.30

0.38

2

93

93

-1.09

0.14


Coverage of known sites and random sites (after 500 shuffle simulations) considering different mismatch tolerances is shown with associated Z-score and p-values for each regulator type. Coverage is defined as the percentage of sites (out of 341 dual regulators, 77 activators and 211 repressors) that are identified as being palindromic when allowing 0, 1 or 2 mismatches. The average coverage of 500 simulations is shown for the random data set (matched to the same number of examples for each respective TFBS set)

Laing et al. BMC Genomics 2008 9:79   doi:10.1186/1471-2164-9-79

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