Figure 1

Fold change versus AC test probability plot. This plot was obtained using PatternLab's ACFold algorithm and displays the results obtained with the multi-surfactant shotgun proteomic approach when comparing the A172 cell lines before and after the treatment with perillyl alcohol. Each protein (represented as a dot) was mapped according to its log₂(fold change) on the ordinate (y) axis and -log₂(1-(AC test p-value)) on the abscissa (x) axis. A total of 104 proteins (blue dots) were selected as differentially expressed because they satisfied both the AC test and the FDR q-value specified cutoffs. 23 proteins (orange dots) did not meet the fold change cutoff but were indicated as statistically differentially expressed, therefore deserving further analysis. 267 proteins (green dots) met the fold change cutoff, but the AC test indicated that this happened by chance. 2293 proteins (red dots) were pinpointed as not differentially expressed between classes because they failed both the AC test and the fold change cutoffs. The number of dots does not match the number of identified proteins due to the many overlaps.