FIG. 6.

Shotgun analysis of differential expression regardless of protein identification availability. Hierarchical clustering of (a) protein and (b) peptide isotope groups, with red and green corresponding to increased and decreased abundance, respectively, relative to that of time-matched, mock-infected primary CD4 cells. Features exhibiting differential expression (≥1.50-fold change, P < 0.01) were included in the analysis. The diagrams are visual representations of agglomerative clusters based on Euclidean distance correlation of protein and isotope group ratios.