Serial Gene Expression Profiling of Neural Stem Cells Shows Transcriptome Switch by Long-Term Physioxia from Metabolic Adaption to Cell Signaling Profile

Figure 3

Global comparison of PANTHER gene categories “biological process” in midbrain NSC cultures. Displayed are percentages of hits from oxygen-regulated genes to specific categories according to the PANTHER domain “biological process.” The PANTHER classification includes the total up-/downregulated genes (lower number in the inner circle) with at least a twofold difference for short- and long-term cultures. The grey circles indicate all analysed genes without a change of expression due to O₂ treatment. After 2 days of culture (2 d), no gene was downregulated in hypoxic cells, but 9 genes from different categories were upregulated, which formed a total of 31 hits. 3 genes and 14 hits of them were also upregulated in hypoxic prolonged cultures, while the other 6 genes did not undergo any O₂ change in prolonged cultures. In total, 226 genes were upregulated and formed 529 hits, and 112 genes with 272 hits were downregulated after 13 days of hypoxic culture (13 d). The hits result from the multiple biological functions of a gene. Since a gene can also have multiple functions, one gene also often results in multiple hits. Also shown are the percentages of individual hits in the various biological functions (categories) to the total hits of the regulated genes.