Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor

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)

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