Macrophage Genome-Wide Control Figure 2. Genome-wide invariance between wildtype, single and double KOs. Highly correlated gene expressions between genotypes, and between time points. A) Left panel: wildtype 0 h (x-axis) vs. wildtype 1 h (y-axis), right panel: wildtype 1 h (x-axis) vs. DKO 1 h (y-axis). Other combinations of genotype and time points also show similar correlations (data not shown). Each point in the plot represents the expression of a single ORF. B) Whole genome Pearson correlations between samples. doi:10.1371/journal.pone.0004905.g002 Figure 3. Temporal Pearson correlation reveals genotype differences. A) Auto- and B) cross-correlations for whole genome (22690 ORFs). C) Auto- and D) cross-correlations for immune-related genes. See maintext for details. Immune-related genes constitute 157 well-known genes induced during immune and inflammatory response (obtained from GenMAPP [20]). doi:10.1371/journal.pone.0004905.g003 PLoS ONE | www.plosone.org 4 March 2009 | Volume 4 | Issue 3 | e4905