Identification of differentially expressed genes between HIV controllers and noncontrollers by 2-way supervised comparisons. (A) By predefining controllers and noncontrollers on the basis of viral load, 2-way comparisons between the groups were conducted using SAM analysis to identify 30 genes at an FDR of 0% and 350 genes at an FDR of 5%. The graphs display the significantly different genes in red, with the x-axis value denoting the expected expression and the y-axis denoting the observed expression values. The threshold lines indicate the FDR cutoff rate of 0% and 5%. (B) The 20 patient samples were then reorganized using the expression values of either the 30 genes (FDR = 0%) or the 350 genes (FDR = 5%). Horizontal bars (in blue for controllers and red for noncontrollers) at the top of the figure indicate the clustering of controller and noncontroller samples.