Analysis Flow. A schematic sketch of the major steps in our analysis. Using two comprehensive mouse gene expression datasets, we partitioned the genes into distinct groups according to the subset of TLR stimulators to which they were responsive (A), and identified the TFs that control each response group by computational analysis of cis-regulatory promoter elements. We then characterized three kinetic patterns of the transcriptional network induced by LPS treatment (B), and again discovered the TFs that regulate each pattern. A similar analysis of two independent human datasets confirmed our main findings. Integrating the various sources of information points to novel putative targets of the studied TFs, adding new regulatory links to the transcriptional network of the innate immune system.