Table 3. The numbers of differentially expressed genes with a p-value less than 0.05 are shown for each comparison.

See S1–S4 Tables for full lists of significant differentially expressed genes.

Test Sample (#)	vs.	Control Sample (#)	Partek Genes p<0.05 (Total: # up, # down)	DESeq2 Genes p<0.05 (Total: # up, # down)	Both Methods Genes p<0.05 (Total: # up, # down)
OD/MS, normoxia (4)	vs.	Control, normoxia (3)	470: 75 ↑, 395 ↓	273: 176 ↑, 97 ↓	58: 25 ↑, 33 ↓
OD/MS, hypoxia (3)	vs.	Control, hypoxia (3)	640: 253 ↑, 387 ↓	196: 80 ↑, 116 ↓	28: 10 ↑, 18 ↓
OD/MS, hypoxia (3)	vs.	OD/MS, normoxia (3)	1319: 239 ↑, 1080 ↓	1172: 642 ↑, 530 ↓	363: 195 ↑, 168 ↓
Control, hypoxia (3)	vs.	Control, normoxia (3)	1492: 160 ↑, 1332 ↓	441: 302 ↑, 139 ↓	154: 95 ↑, 59 ↓