HIF-dependent and HIF-independent hypoxic response genes.

(A–B) Gene ontology (GO) analysis was performed on HIF-independent (HI) and HIF-dependent (HD) gene sets that were derived from microarray analysis of H- or N-treated control (w¹¹¹⁸) animals or sima mutants collected at the partial clear-gut late-L3 time. See Figure S1 for the analysis scheme. GO categories are listed in order of statistical significance. The numbers of H-regulated genes affected are shown along with the total number of genes in each category. All transcripts are up- or downregulated at least 1.5-fold and have a false discovery rate (FDR) of <1%. (C) A heat map was created to illustrate the similarity or dissimilarity of hypoxic responses for major GO categories impacted by H-treatment in control animals and sima mutants. Red (upregulated), green (downregulated), or white (no significant change) values represent hypoxic responses observed in the backgrounds indicated. For this analysis, FDR stringency was <1%, unless otherwise noted with * for a particular genotype, where a relaxed gate was used (1–5%).