Macrophage Genome-Wide Control Biphasic acute-stochastic and collective modes of LPS response We analyzed the change (i.e., difference of expression) of response based on Pearson r of all genotypes by removing highest up- and down-regulated ORFs (one by one up to 300 ORFs) between 0 to 1 hr. For removing highest up-regulated ORFs, a biphasic (hyperbolic) phenomenon emerges in wildtype and single KOs but not in DKO (Figure 4A). The gradient of curves is steep up to the removal of about 80 ORFs in wildtype and 50 ORFs in both single KOs after which the slope gentles. In contrast, in DKO, only the gentle gradient exists (Figure 4B). As control, we next compared randomly removed ORFs in similar steps and found Pearson r (0–1 h) of all genotypes does not change noticeably (Figure 4C). This result points to a transition in the response: a small fraction of ‘acute’ responding ORFs, and the majority of ORFs responding ‘weakly’. Notably, for downregulat- ed ORFs, biphasic response is not observed for any genotype (Figure 4D). Figure 4. LPS induces biphasic acute-stochastic and collective modes of response in wildtype and single KOs but not DKO. A) Auto- correlation profiles of all genotypes when removing one by one up to 300 ORFs highest upregulated ORFs from 0 to 1 hr (in terms of expression change: Dx = x(1 h)2x(0 h)). B) Plot of average auto-correlations slopes of 0–1 h in A). Since DKO possesses only collective mode, we used average slope of DKO curve at N = 10 to distinguish biphasic transition (dotted gray line). Wildtype and single KO cross this slope at about N = 80 and N = 50 ORFs, respectively. This biphasic transition point further suggests collective mode. No biphasic behavior was found for C) randomly selected or D) downregulated ORFs. Confirmation of collective mode: E) Standard deviation (SD) of auto-correlation (0–1 h) of groups of randomly chosen ORFs in steps of 10 up to 300 from whole genome. Each point represents average SD of 30 groups, error bars represent highest and lowest SD. F) As in E) for 1–4 h auto-correlation. G) Auto-correlations of 80 highly expressed ORFs representing acute-stochastic mode in the wildtype. H) Average auto-correlations of 30 extractions of 80 randomly chosen ORFs in the wildtype collective mode. doi:10.1371/journal.pone.0004905.g004 PLoS ONE | www.plosone.org 5 March 2009 | Volume 4 | Issue 3 | e4905