TLR-induced transcriptional programs. (A) Genes that were induced by at least one of the six examined TLR stimulators (induction of at least 1.8-fold at any time point) were partitioned into distinct sets according to their agent-induction pattern. Taking into account sets that contained at least 40 genes, only two complex induction patterns were identified in addition to the six agent-specific patterns: universal and LPS-PIC patterns. Selected genes are shown in the heat-map for each set (a complete list of genes is provided in Additional File 1). The maximum induction of the gene over the examined time points per stimulator is depicted in the heat-map. (B) Enriched GO functional categories were identified in the universal and LPS-PIC sets (p-values in parentheses are corrected for multiple testing using a bootstrap procedure on 1,000 randomly chosen gene sets of the same size as the true sets). (C) Highly significant over-represented cis-regulatory elements were identified in the promoters of the universal and LPS-PIC sets, pointing to a pivotal role for NF-κB and ISRE in the induction of these two components of the TLR-induced transcriptional program.