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.

Evans BMC Genomics 2008 9:16   doi:10.1186/1471-2164-9-16

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