HIF-dependent and HIF-independent hypoxic response genes.

<p>(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 (<i>w<sup>1118</sup></i>) animals or <i>sima</i> mutants collected at the partial clear-gut late-L3 time. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003230#pgen.1003230.s001" target="_blank">Figure S1</a> 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 <i>sima</i> 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%).</p>