Table 2 Results of using different distance criterion to define cis regulators
3 Mb | 10 Mb | 20 Mb | ||||
|---|---|---|---|---|---|---|
Parameter | cis (<) | trans (≥) | cis (<) | trans (≥) | cis (<) | trans (≥) |
No. tests | 9,699 | 3,845,729 | 29,827 | 3,825,601 | 52,853 | 3,802,575 |
(%) | 87.68 | 95.05 | 89.32 | 95.08 | 89.62 | 95.11 |
Framework I, α = 0.0001 | ||||||
No. rejections | 69 | 7,974 | 204 | 7,839 | 302 | 7,741 |
(%) | 1.23 | 4.58 | 1.31 | 4.64 | 1.57 | 4.67 |
E [No. false positives] | 1 | 365 | 3 | 363 | 5 | 361 |
Framework II, γ = 0.05 | ||||||
No. rejections | 200 | 8,398 | 519 | 8,113 | 761 | 7,927 |
E [No. true positives] | 190 | 7,978 | 493 | 7,707 | 723 | 7,531 |
Framework III, R = 2,000 | ||||||
Rejection without stratification | 29 | 1971 | 90 | 1,910 | 127 | 1,873 |
Rejection with stratification | 67 | 1933 | 184 | 1,816 | 222 | 1,778 |
Overall (%) | 2.03 | 1.99 | 1.99 | |||