Table 2.
Number of differentially expressed genes located nearby transposable element (TE) insertions. d.f.: degrees of freedom (Additional file 9: Table S8A-D)
| Upregulated genes with TEs nearby | Chi-square test (post hoc test p value) | Downregulated genes with TEs nearby | Chi-square test (post hoc test p value) | Total number of DEGs with TEs nearby | Chi-square test | |
|---|---|---|---|---|---|---|
| All DEGs | 11 (9.7%) | 1.1543, df = 1, p-value = 0.2826 | 127 (9.8%) | 23.249, df = 1, p-value = 1.423e − 06, (1.22E − 04, depleted) | 138 (9.8%) | 18.895, df = 1, p-value = 1.381e − 05 (4.60E − 05, depleted) |
| Tolerant DEGs | 19 (13%) | 1.4124, df = 1, p-value = 0.2347 | 54 (7.5%) | 3.7558, df = 1, p-value = 0.05262 | 73 (8.5%) | 1.469, df = 1, p-value = 0.2255 |
| Sensitive DEGs | 1 (3%) | NA | 0 | NA | 1 (3%) | NA |
| Basal DEGs | 226 (14.3%) | 4.7876, df = 1, p-value = 0.02866 (depleted) | 189 (10%) | 3.7778, df = 1, p-value = 0.05194 | 415 (12%) | 10.144, df = 1, p-value = 0.001448 (5.23E − 03, depleted) |