TABLE 1.
GENES DIFFERENTIATING BETWEEN HYPOXIC AND CONTROL SAMPLES
| True Hypoxia | Hypoxia Mimicry | ||||
|---|---|---|---|---|---|
| O2-Regulated Incubator 1 (n = 5) | O2-Regulated Incubator 2 (n = 5) | Billups-Rothenberg Chamber (n = 5) | |||
| 100 μM Cobalt Chloride (n = 4)* | 200 μM Cobalt Chloride (n = 4)* | ||||
| Twofold change | 169/70 | 168/46 | 123/147 | 236/713 | 311/705 |
| Fourfold change | 36/1 | 40/0 | 27/0 | 44/116 | 56/117 |
| FDR <5% (limma) | 781/1036 | 737/750 | 759/1427 | 1983/2116 | 2190/2286 |
| Twofold change (mean) | 145/56 | 196/667 | |||
| FDR <5% (Welch test) | 1016/1525 | 105/259† | |||
Probesets were selected by fold-change criterion (two- or fourfold, mean fold change was calculated either in each experiment separately or for three “true hypoxia” and two hypoxia mimicry experiments) or by statistical selection (limma, Bayesian moderated t-statistic for each experiment or classic Welch t-test for larger groups). False Discovery Rate (FDR) was estimated by Benjamini-Hochberg method. Numbers of probesets satisfying the criteria are given as “upregulated/downregulated.”
*
Two samples treated with 100 μM CoCl2 and two treated with 200 μM CoCl2 were compared to common controls (two samples).
†
Relatively low number of genes due to small number of samples compared.