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Figure 3. Graphical approach to illustrating degree of differential expression in two genetic backgrounds. The degree of differential expression [log (wild-type/o2)] of transcripts likely to be differentially expressed (those with low P-values) is plotted as XY data, with each axis representing the degree of differential expression for an o2 vs. wild-type comparison in one genetic background. Ellipses indicate the regions where transcripts would be expected to cluster given the following hypotheses to explain differences in phenotypic severity in different genetic backgrounds. A. Hypothesis 1. The degree of differential expression hypothesis suggests one set of transcripts will be uniformly and differentially regulated, more so in one genetic background than the other. This difference in transcript levels causes the difference in phenotypic severity. B. Hypothesis 2. The genotype-specific differential expression hypothesis suggests certain transcripts will be differentially expressed in one genetic background while others will be differentially expressed in the other genetic background. The difference in phenotypic severity is determined by the specific transcripts that are differentially expressed in each genetic background.
