Figure 3
Heat map and dendrogram of protein spots with significant changes (ANOVA, p < 0.05). Panel A. A heat map depicts differences in protein expression from the SP-A knockout (KO). A line representing each numbered protein spot that was found to be significantly different by ANOVA is colored using a red to green scale with dark red indicating the greatest increases and dark green indicating the greatest decreases. Baseline KO is represented by the yellow column on the left. Each of the 234 significant protein spots is indicated by a colored bar. Proteins at levels higher than in the KO mice are in red (dark red > 25% increase; orange < 25% increase). Protein spots with levels lower than in the KO mice are indicated in green (dark green > 25% decrease; light green < 25% decrease). Map columns include: column 1, spot number (#); column 2, SP-A knockout (KO) (columns 3-5 are compared to this value); column 3, differences between KO vs. KO treated with SP-A for 6 hr (KO 6 hr SP-A); column 4, differences between KO vs. SP-A knockout treated with SP-A for 18 hr (KO 18 hr SP-A); and column 5, differences between KO vs. wild type (WT). Panel B. A dendrogram has been generated showing hierarchical clustering of protein spots based on expression profiles derived from the data depicted in the heat map. Each leaf or line on the left of the dendrogram corresponds to the adjacent bar in the heat map. On the dendrogram protein spots with similarities in their expression patterns are grouped together. The labeled groups indicate groups or protein spots that tended to be at their highest level in the indicated group (i.e the group labeled WT protein spots were at higher levels in WT than the other groups), although there were some exceptions (see results). Smaller distances between branches indicate a more similar expression profile. The clustering of the expression profiles of protein spots for this experiment can easily be seen by the division of the significant (ANOVA, p < 0.05) protein spots that are typically at their highest levels in the designated group.