Fig. 4

Normalized K cluster analysis demonstrates altered timing of expression caused by hypoxia. a K cluster groups shown as heat maps, in which gene expression is averaged across development, and deviations both from the developmental average, and hypoxia versus normoxia, are shown. Values in parentheses indicate the range of log2 fold change of genes in the cluster. b Expression analysis of three representative gene expression changes from hypoxia across development shown as lines; lighter shade indicates expression in hypoxia. X-axis developmental age, y-axis log₂FPKM. c Genes in clusters 5 and 11; transcription factors are disproportionately represented. d qRT-PCR of genes from cluster 5; error bars standard deviation; two-tailed t test; * p < 0.05; ** p < 0.01. e Pathway Commons Network analysis, displayed with PCViz, shows no shared paths between the genes in cluster 5 or 13. f KEGG analysis of K clusters. GO categories are only loosely organized into clusters, indicating that the effects of hypoxia on gene expression are not based on gene type/category