Figure 2: Hierarchical clustering of genes determined to be significantly altered in mice at 12 hours and 48 hours in response to WT Y. pestis CO92 infection (a) and in the livers (b), lungs (c), and spleens (d) of mice infected for 48 hours with a lpp mutant of Y. pestis CO92, compared to WT Y. pestis. Clustering was performed using Genespring GX 10.0 on normalized and log transformed signal ratios. The three replicate samples representing the three experimental conditions (uninfected animals and mice infected with WT Y. pestis CO92 or its lpp mutant) are labeled as control, WT, and mutant, respectively. Note that mice infected for 48 hours with WT Y. pestis CO92 exhibited a collection of altered gene expressions that were common to all three tissues examined (panel a). Most notably, the three replicates representing tissue (liver, lung, or spleen) infected with the mutant clustered together, and mutant-infected samples clustered apart from uninfected controls and mice infected with WT Y. pestis for each tissue examined (panels b–d). The vertical dendrograms indicate relative similarity between samples (columns), while the horizontal dendrograms indicate clusters for genes (rows). Bright red indicates the highest normalized intensity value, bright blue the lowest, and yellow represents median values.