Table 1.
Differential expression analyses of whole body and sex-specific organs in Drosophila pseudoobscura and D. ananassae.
| Comparison | Cuffdiff | edgeR | ||||||
|---|---|---|---|---|---|---|---|---|
| Total DEa | MBa | FBa | Total Tested | Total DEa | MBa | FBa | Total Tested | |
| D. pseudoobscurab | ||||||||
| whole body | 5269 | 2785 | 2484 | 13252 | 8284 | 3043 | 5242 | 12738 |
| testis-ovary | 7105 | 3184 | 3921 | 12575 | 8045 | 3292 | 4752 | 11946 |
| reproductive tract | 9067 | 4669 | 4398 | 11800 | 9228 | 3512 | 5716 | 11809 |
| Overlap (%)c | 4477 (85.0) |
2334 (83.8) |
2143 (86.3) |
11620 (92.4) |
5875 (73.0) |
2540 (83.5) |
3335 (70.2) |
11345 (95.0) |
| D. ananassaed | ||||||||
| whole body | 1791 | 1613 | 178 | 13786 | 3224 | 2138 | 1086 | 13081 |
| testis-ovary | 8997 | 4494 | 4503 | 13269 | 9429 | 3456 | 5973 | 11576 |
| Overlap (%)c | 1657 (92.5) |
1503 (93.2) |
154 (86.5) |
12538 (94.5) |
2593 (80.4) |
1835 (85.8) |
758 (69.8) |
11213 (96.9) |
a DE: differentially expressed at false discovery rate <0.01; MB: male-biased; FB: female-biased
b Annotated genes: 16,755
c Numbers and percentages (of smallest value) of genes overlapping between whole body and testis-ovary analyses
d Annotated genes: 16,225