TABLE 4.
ONTOLOGY CLASSES REGULATED BY TRUE HYPOXIA
| Gene Ontology ID | Name | Number of Probesets | p-Value |
|---|---|---|---|
| Upregulated genes | |||
| GO:0006096 | glycolysis | 9 | 1.52E-08 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 13 | 4.65E-08 |
| GO:0019320 | hexose catabolism | 9 | 1.01E-07 |
| GO:0042981 | regulation of apoptosis | 12 | 0.0001 |
| GO:0006915 | apoptosis | 15 | 0.0006 |
| GO:0019883 | antigen presentation, endogenous antigen | 3 | 0.001 |
| GO:0043066 | negative regulation of apoptosis | 6 | 0.001 |
| GO:0018401 | peptidyl-proline hydroxylation to 4-hydroxy-L-proline | 2 | 0.001 |
| GO:0018193 | peptidyl-amino acid modification | 5 | 0.003 |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | 10 | 0.003 |
| GO:0048511 | rhythmic process | 4 | 0.004 |
| GO:0046777 | autophosphorylation | 3 | 0.004 |
| GO:0016540 | protein autoprocessing | 3 | 0.004 |
| Downregulated genes | |||
| GO:0009069 | serine family amino acid metabolism | 5 | 1.53E-05 |
| GO:000625 | DNA metabolism | 21 | 4.77E-05 |
| GO:0006220 | pyrimidine nucleotide metabolism | 5 | 4.85E-05 |
| GO:0006260 | DNA replication | 10 | 6.83E-05 |
| GO:0044237 | cellular metabolism | 120 | 7.06E-05 |
| GO:0006396 | RNA processing | 15 | 7.57E-05 |
| GO:0000398 | nuclear mRNA splicing, via spliceosome | 10 | 0.0001 |
| GO:0006461 | protein complex assembly | 8 | 0.0002 |
| GO:0006544 | glycine metabolism | 3 | 0.0004 |
| GO:0016070 | RNA metabolism | 16 | 0.0004 |
| GO:0006519 | amino acid and derivative metabolism | 13 | 0.0004 |
| GO:0009063 | amino acid catabolism | 5 | 0.0005 |
| GO:0006397 | mRNA processing | 11 | 0.0006 |
| GO:0006281 | DNA repair | 9 | 0.001 |
| GO:0008295 | spermidine biosynthesis | 2 | 0.002 |
| GO:0016478 | negative regulation of translation | 2 | 0.002 |
| GO:0009058 | biosynthesis | 30 | 0.003 |
| GO:0019752 | carboxylic acid metabolism | 15 | 0.003 |
| GO:0006974 | response to DNA damage stimulus | 9 | 0.004 |
| GO:0045454 | cell redox homeostasis | 2 | 0.004 |
| GO:0007098 | centrosome cycle | 2 | 0.004 |
| GO:0009071 | serine family amino acid catabolism | 2 | 0.004 |
Gene ontology analysis of transcripts differentiating “true hypoxia” samples from control ones (454 genes with FWER < 0.05). Only chosen ontology groups are presented from among all significantly upregulated or downregulated classes (p < 0.005, see Materials and Methods).