Table 6. The total number of root differentially expressed genes at each expression category for each analysis method and the percentage of these DEGs associated with the total number enriched gene ontology (GO) for that expression category.
|
AR /TC Expression category1 |
J1 | J3 | DESeq2 | edgeR | limma-voom | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DEGs | GO terms | DEGs | GO terms | DEGs | GO terms | DEGs | GO terms | DEGs | GO terms | |||||||
| Total | % | Total | % | Total | % | Total | % | Total | % | |||||||
| AR | ns_up | 314 | 70 | 9 | 0 | - | - | 314 | 70 | 9 | 0 | - | - | 0 | - | - |
| ns_down | 528 | 88 | 26 | 1 | - | - | 528 | 88 | 26 | 0 | - | - | 1 | - | - | |
| up_ns | 3 | - | - | 0 | - | - | 3 | - | - | 0 | - | - | 0 | - | - | |
| up_up | 2 | 0 | - | - | 2 | 0 | - | - | 0 | - | - | |||||
| ns_down_down | 330 | 89 | 35 | 0 | - | - | 329 | 89 | 34 | 0 | - | - | 1 | - | 0 | |
| ns_down_ns | 195 | 70 | 16 | 0 | - | - | 197 | 70 | 16 | 0 | - | - | 0 | - | - | |
| ns_ns_down | 1761 | 89 | 79 | 1376 | 85 | 69 | 1624 | 90 | 84 | 1478 | 84 | 68 | 1493 | 84 | 65 | |
| ns_ns_up | 1805 | 45 | 11 | 1527 | 68 | 15 | 1556 | 66 | 14 | 1614 | 50 | 13 | 1861 | 45 | 11 | |
| ns_up_up | 156 | 53 | 8 | 0 | - | - | 154 | 53 | 9 | 0 | - | - | 0 | - | - | |
| ns_up_down | 8 | - | 0 | 0 | - | - | 8 | - | 0 | 0 | - | - | 0 | - | - | |
| ns_down_up | 3 | - | 0 | 0 | - | - | 2 | - | 0 | 0 | - | - | 0 | - | - | |
| ns_up_ns | 150 | 67 | 5 | 0 | - | - | 152 | 68 | 5 | 0 | - | - | 0 | - | - | |
| up_ns_ns | 3 | - | 0 | 0 | - | - | 3 | - | 0 | 0 | - | - | 0 | - | - | |
| up_up_ns | 2 | - | 0 | 0 | - | - | 2 | - | 0 | 0 | - | - | 0 | - | - | |
| TC | ns_up | 43 | - | - | 0 | - | - | 43 | - | - | 2 | - | - | 0 | - | - |
| ns_down | 144 | 83 | 24 | 1 | - | - | 144 | 83 | 24 | 3 | - | - | 1 | - | - | |
| up_ns | 5 | - | - | 0 | - | - | 5 | - | - | 0 | - | - | 0 | - | - | |
| ns_down_down | 21 | 29 | 1 | 0 | - | - | 21 | 29 | 1 | 0 | - | - | 0 | - | - | |
| ns_down_ns | 120 | 86 | 30 | 0 | - | - | 120 | 86 | 30 | 3 | - | 0 | 0 | - | - | |
| ns_ns_down | 1625 | 90 | 67 | 942 | 85 | 50 | 1514 | 90 | 65 | 1275 | 89 | 62 | 1048 | 84 | 49 | |
| ns_ns_up | 1274 | 48 | 12 | 845 | 51 | 12 | 1071 | 54 | 15 | 920 | 50 | 13 | 1141 | 44 | 9 | |
| ns_up_up | 9 | - | 0 | 0 | - | - | 8 | - | 0 | 0 | - | - | 0 | - | - | |
| ns_up_down | 6 | - | 0 | 0 | - | - | 6 | - | 0 | 1 | - | 0 | 0 | - | - | |
| ns_down_up | 2 | - | 0 | 0 | - | - | 2 | - | 0 | 0 | - | - | 0 | - | - | |
| ns_up_ns | 28 | - | 0 | 0 | - | - | 29 | - | 0 | 0 | - | - | 0 | - | - | |
| up_ns_ns | 5 | - | 0 | 0 | - | - | 5 | - | 0 | 0 | - | - | 0 | - | - | |
1Expression categories which contained 0 DEGs have been omitted for clarity.