Table 3. Sizes of up-regulated and down-regulated differentially expressed gene signatures.
| Test Set Up | Upregulated Genes1 | Downregulated Genes | |||
|---|---|---|---|---|---|
| Stimulation | Group | p-value2 < 0.05 | FDR p-value (BH)3 < 0.05 | p-value < 0.05 | FDR p-value (BH) < 0.05 |
| EW | BER vs AC | 1248 | 138 | 1274 | 104 |
| BET vs AC | 1038 | 26 | 1096 | 24 | |
| BER vs BET | 709 | 0 | 944 | 0 | |
| M | BER vs AC | 959 | 16 | 1177 | 18 |
| BET vs AC | 979 | 2 | 752 | 2 | |
| BER vs BET | 485 | 0 | 952 | 1 | |
| EW vs M | BER | 2200 | 1340 | 2338 | 1270 |
| BET | 2008 | 1039 | 2553 | 1146 | |
| AC | 1642 | 488 | 1637 | 386 | |
| EW vs M | BER vs AC | 731 | 0 | 733 | 1 |
| BET vs AC | 1022 | 3 | 1105 | 2 | |
| BER vs BET | 568 | 0 | 364 | 0 | |
1From the total of 19959 tested genes
2p-value from a multivariate linear model from limma R package
3FDR rate from Benjamini–Hochberg adjustment of the p-values done in limma R package