Hierarchical cluster analyses of differentially expressed genes in lung and liver of Gba1 mutant mice. The two-dimensional hierarchical clustering charts include 1171 genes differentially expressed in 9 V/null lung, and the corresponding genes in 9 V/null liver, and those in 4L or WT lung and liver at ages of 4-, 12-, 18-, or 28-wk (see Materials and Methods). The expression patterns of duplicate chip data are displayed in adjunct lanes for each transcript. The heat map (Pearson correlation) displays gene group correlation patterns across all time points. Each column represents the general expression profile of 1171 genes at a time point. Each row represents a single gene across all time points. The intensities (red to green scale bar) are the log ratios, log2(D/C), where D and C are the gene expression levels in the samples from Gba1 mutant mice and WT controls, respectively, and indicate up- or down-regulated RNA expression. Clustering was performed by distance measurements. In cluster 1 are the 407 genes down-regulated in 9 V/null and 4L lung compared to the corresponding genes in WT lung (genes listed in Additional file 2). In cluster 2 are the 647 genes had a variable degrees of up-regulation compared with WT controls. In cluster 3 (orange rectangle) is a group of 117 genes consistently up-regulated in the lung of 9 V/null mice at ages of 12- to 28-wk. These include 40 macrophage activation genes (see Figure 4).