Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Table 4 Motif similarity between the first and second promoters of the same gene^a

	Similar^b			Intermediate^b			Different^b			# of used pairs			# of omitted pairs
	all^c	high quality^d	cap^e	all	high quality	cap	all	high quality	cap	all	high quality	cap	all	high quality	cap
Observed value (shared motifs allowed)	34.07	31.52	36.04	17.70	16.30	23.42	48.23	52.17	40.54	226	92	111	1182	445	278
Observed value (shared motifs not allowed)	12.65	11.59	15.19	15.66	15.94	21.52	71.69	72.46	63.29	166	69	79	1242	468	310
Random mean^f	9.50	8.34	8.67	10.83	12.51	14.31	79.66	79.15	77.03	226	92	111	1182	445	278
p-value^g (random >= observed value, shared motifs allowed)	0	0	0	2e-04	0.1399	0.0021	1	1	1	--	--	--	--	--	--
p-value^g (random <= observed value, shared motifs allowed)	1	1	1	1	0.9227	0.9991	0	0	0	--	--	--	--	--	--
p-value^g (random >= observed value, shared motifs not allowed)	0.0438	0.1286	0.0078	0.0041	0.1399	0.0108	0.9991	0.9622	1	--	--	--	--	--	--
p-value^g (random <= observed value, shared motifs not allowed)	0.9562	0.8714	0.9922	0.9959	0.8601	0.9892	9e-04	0.0378	0	--	--	--	--	--	--

^agenes with exactly two alternative promoters. Similar results were obtained for genes with multiple alternative promoters (data not shown).
^bpercentage of the alternative promoter pairs defined as similar, intermediate, and different (see Methods).
^cThe promoter set contains all promoters from Drosophila genome annotation release 5.5.
^dThe promoter set contains only high quality promoters in fly genome; see Methods.
^eThe promoter set contains only cap-supported promoters in fly genome; see Methods.
^fmean of 10,000 randomizations.
^gempirical p-value calculated as the proportion of sampled randomizations where the percentage of the promoter pairs in each of the three similarity levels was no less than/no greater than the observed values

ISSN: 1471-2164