Kinetics of the LPS-induced transcriptional response. (A) Genes that were induced by LPS (by at least 1.8-fold) were divided into three kinetic sets according to the time their expression was first induced and the time it peaked. The 'EE' set contains the early induction, early peak genes; the 'ED' set contains early induction, delayed peak genes; and the 'DD' set contains delayed induction, delayed peak genes. The figure displays the mean expression patterns of the genes assigned to the three kinetic sets in the MmBMM dataset (y-axis is log2 of induction fold). (B) Mean expression of induced genes that encode for TFs: ATF/CREB (Atf3, Fos, Jun, Junb), NF-κB (Nfkb1, Nfkb2, Rel, Relb), and ISRE (Irf1, Irf2, Irf7, Stat1, Stat2, Stat3, Stat5a). The expression pattern of each TF is highly correlated with that of the kinetic wave, in which the computational promoter analysis found an over-representation of its BSs (compare the kinetic expression of the TF genes (B) and the induced waves (A)).