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

BMC Genomics

Table 6 Difference criterion sequences in indirect gene category

5-mer	Indirectly Affected	Difference	6-mer	Indirectly Affected	Difference
acctc	50%	48%	ctgaaa	42%	38%
aatct	58	42	taagga	42	38
ctaat	58	40	atataa	58	33
ctcac	50	37	aaacaa	50	32
cttat	50	37	aaacca	42	31
gatta	50	37	aataca	42	31
aacaa	67	36	tctttc	42	31
ataca	67	36	ataaat	50	30
aaagc	50	35	acacat	33	30
acaca	58	35	ctcacc	33	30

Sequences found to be most overrepresented in the upstream regions of genes hypothesized to be indirectly affected by berenil compared to unaffected genes. The percentage of affected genes and difference in percentage between affected and unaffected genes having each sequence is listed. Bolded sequences are shared with Table 7.

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