Figure 3. The absence of natural clusters in protein abundance ratio data. (A) P. gingivalis proteomic data displayed as the log 2 of the spectral counts for internalized (y-axis) against control cells (x-axis). (B) As in (A), but displaying only points with at least a two-fold difference between internalized and control cells. (C) M. maripaludis proteomics data plotting the protein ratios of phosphate-limited/ammonia-limited samples (y-axis) against the ratios of phosphate-limited/H2-limited samples (x-axis). In this display, proteins regulated by phosphate limitation fall along the diagonal. (D) As in (C), but displaying only points with at least a 1.4-fold difference between conditions for both phosphate/ammonia limitation and phosphate/H2 limitation.