Fig. 2.

Genome-wide hypoxia differential expression. (A) log₂ hypoxia induction vs. log₁₀ average intensity scatterplot (MA plot) showing the effect of hypoxia on the expression of all 37,157 transcripts measured. Y-axis shows a relatively uniform degree of hypoxia induction for transcripts at all hybridization intensities. Horizontal red lines indicate 2-fold induction and repression. (B) Volcano scatterplot of all transcripts showing statistical significance on Y-axis as determined by empirical Bayesian method and x-axis demonstrating fold hypoxia induction. Orange triangles; 100 most downregulated genes; blue triangles: 100 most upregulated genes; red circles: 100 most statistically significant differentially expressed genes. Vertical red lines indicate 2-fold induction and repression. Horizontal red line indicates p < 0.01. These figure panels are complementary or modified presentations, respectively, of the data presented in Fig. 2A of the primary hypoxia study [1].