Concentration-dependence of the transcriptome response to IL-3.

<p>Panel A: Slope of SIL3-51T gene set for a 24 hour culture at the concentrations shown. The data points for each of the concentrations were derived from different numbers of experiments (n = 2 for 0.06 ng/ml, and n = 4 for 0.2, 2.0 and 10.0 ng/ml) and the plots represent composites of the results from different experiments. The lines represent the comparison with the +IL-3 (●) dataset or the noIL3 dataset (○). The square symbols represent the slopes for an IL-5 at 10 ng/ml exposure (relative to the SIL3-51T test set) and open triangles, the slope for NGF at 10 ng/ml). Panel B: Fold changes in three groups of transcripts. Two groups were derived from SIL3-51T, those that increased with IL-3 (●, n = 34) and those that decreased with IL-3 (■, n = 17). The third group (○) are transcripts that increase greater than 5 fold at the 10 ng/ml IL-3 concentration. Panel C: value of the SIL3-51T relationship between concentrations of IL-3. The ordinate is the slope of the SIL3-51T relationship for IL-3 concentration(i) vs. concentration(i+1) where (i) is a chosen concentration and (i+1) the next higher concentration, for example, 0.06 ng/ml vs 0.2 ng/ml (or 0.2 vs. 2.0, 2.0 vs. 10). The two lines are the slopes for the noIL3 relationship (○) and the +IL3 relationship (●). Panel D: Concentration dependence for two subsets of transcripts chosen with a hierarchical clustering algorithm (see text), those that show similar changes at 2 vs. 10 ng/ml (●) and those that show significant differences at the two concentrations (○).