Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression

BMC Genomics

Table 3 Number of genes – comparisons with hybrid genome – third quarter comparison

	Genome	Number of TSSs Quarters 1,2 4	Number of TSSs Quarter 3	Total	Proportion
	i	ii	iii	iv = ii + iii	v = iii/iv
A	real	8803	6968	15771	44.2%
B	hybrid	5939	3924	9863	39.8%
C	A – B	2864	3044	5908	51.5% (X)
D	real (random)	9362	4386	13748	31.9% (Y)

Quarter 3 is the region up to 50 kb downstream of the A+/T+ boundary. Quarters 1,2, 4 are the other parts of the region between 100 kb upstream and 100 kb downstream of this boundary. Row D refers to the control analysis in which TSSs are replaced by an equal number of random positions (the red line of Figure 9a). The figure of 51.5% (X) is significantly different from the figure 31.9% (Y) using a binomial distribution approximated by the normal distribution and a t-type test, p < 10^-50, n1 = 5908, n2 = 13478, z = 25, one tailed test.

ISSN: 1471-2164