Global gene expression data were analyzed to search for the genes related to oxidative stress response, to examine the differences between hypoxia and anoxia, and to reveal new components of oxygen deprivation response escaped from the previous analyses. Gene Set Z-score (GSZ) was used to report gene ontology (GO) classes that showed significant regulation and also partial up-and downregulation in Arabidopsis anoxic and hypoxic microarray data sets. Under both anoxia and hypoxia significant upregulation was reported for anaerobic respiration, response to low oxygen levels, and response to hypoxia. Comparable high GSZ scores were shown for several oxidative stress-related GO classes and for functional groups of biological processes known to involve oxygen radical formation such as: cellular respiration, wounding, and response to high light and UV-B. Availability of oxygen in hypoxic experimental sets was marked by upregulation of several oxygenases, including ACC-oxidase responsible for ethylene synthesis. Consistent strong induction of several Fe-dependent ketoglutarate oxygenases (FeKGO) in the majority of hypoxic conditions analyzed suggests an important and yet unidentified function for these enzymes. Based on metabolic and gene expression studies we suggest that FeKGO may function in a bypass route for part of the TCA cycle (citrate-isocitrate) inhibited under hypoxia. This would incorporate 2-ketoglutarate supplied by activated GABA shunt and form succinate, a TCA cycle and mitochondrial electron transport chain substrate. FeKGO turnover is sustained by the putative route coupled to ascorbate-monodehydroascorbate cycling and hemoglobin-dependent NO elimination. The analysis strongly supports earlier findings that formation of activated oxygen and oxidative stress is an integral part of the response to oxygen deprivation. Several novel functional gene groups were highlighted by the analysis: upregulation of cysteamine dioxygenase activity and FeKGO and downregulation of circadian rhythm-related genes.