Microarray analysis of the in vivo sequence preferences of a minor groove binding drug

BMC Genomics

Table 8 Analysis of A/T heteropolymeric sequence occurrences

A/T Heteropolymeric Sequences		5-mers		6-mers
		Direct	Indirect	Direct	Indirect
AT, TA	observed	0.500	0.294	0.533	0.214
	yeast	0.180	0.180	0.180	0.180
	p-value	< .0001	0.007	< .0001	0.228
ATA, TAT	observed	0.359	0.157	0.396	0.125
	yeast	0.065	0.065	0.065	0.065
	p-value	< .0001	0.004	< .0001	0.033
ATAT, TATA	observed	0.192	0.029	0.222	0.071
	yeast	0.024	0.024	0.024	0.024
	p-value	< .0001	0.418	< .0001	0.022
ATATA, TATAT	observed	0.154	0.000	0.167	0.036
	yeast	0.010	0.010	0.010	0.010
	p-value	< .0001	0.662	< .0001	0.090
ATATAT, TATATA	observed	-	-	0.083	0.000
	yeast	-	-	0.010	0.010
	p-value	-	-	< .0001	0.579

The rate of occurrence (observed) of 2–6 nt A/T heteropolymeric sequences in the unique 5-mer and 6-mer sequences listed in Tables 4-7 for the direct and indirect gene categories was compared to the rate of occurrence (yeast) in the 200 nt upstream region of 5869 yeast genes using a 1-sided Z-test. Highly significant p-values are shown in bold.

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