Predominance of gene sets associated with EGF in cycling samples subjected to hypoxia, especially in ovarian and prostate cancer cells. Since the EGF pathway is generally involved in establishing and maintaining the malignant WY 14643 phenotype, our results suggest that this pathway may contribute to cycling hypoxia-related adverse effects. GSEA also confirmed that exposition to hypoxia and reoxygenation affected the NFkB and AP1 signaling pathways, which have been previously shown to be involved in cellular response to transient/acute hypoxia. The other group of genes induced by cycling hypoxia in SK-OV-3 cells comprised transcripts of proinflammatory cytokines such as IL8, IL6, and IL1A and chemokine such as CXCL2. CXCL2 was also slightly more induced by cycling hypoxia than by chronic hypoxia in PC-3 cells. In contrast, in melanoma cells, its expression was significantly suppressed under cycling hypoxia. All these genes are known to play a role in cancer biology. The predominance of the regulation of immune response genes by cycling hypoxia in melanoma and ovarian cancer cells was also evidenced by GSEA. Moreover, in ovarian cancer cells, sets of genes regulating adhesion, migration, and invasion as well as proliferation and cell cycle proved to be more responsive to cycling than to chronic hypoxia. However, the flow cytometry analysis did not show any differences in cell cycle either in samples subjected to chronic or cycling hypoxia compared to control samples. In contrast to SK-OV-3 and PC-3 cells, the melanoma cell line appeared to be the least responsive to cycling hypoxia. Gene expression was rather suppressed than stimulated in these cells. The fold changes were also relatively low. Moreover, out of the six validated genes, qRT-PCR only allowed us to confirm the differential expression of EPHA2 and CXCL2. EPHA2 has a significant role in melanoma biology as an oncogene and promalignant protein, while CXCL2 is a neutrophil attractant. CXCL2 down-regulation is related to inhibition of neutrophil accumulation and their survival. Thus, EPHA2 and CXCL2 potential role in cycling hypoxia-induced melanoma progression is worth further investigation. In conclusion, our global gene expression analysis of three tumor cell lines exposed to cycling and chronic hypoxia revealed substantial similarities in the molecular profiles induced by these two different experimental hypoxic conditions. Additionally, we have selected genes and indicated processes, which seem to be preferentially regulated by cycling hypoxia and reoxygenation.