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Number of genes declared differentially expressed for triple-target and two-color experiments Number of differentially expressed genes (FDR = 5%).
| Comparison | Triple-target experiments | Two-color experiments | Common |
| C1 versus C2 | 3353 | 2188 | 1925 |
| C1 versus C3 | 3986 | 3384 | 2737 |
| C2 versus C3 | 4519 | 3465 | 2928 |
