Clustering of transcripts based on patterns of differential expression. Differentially expressed transcripts were clustered using pair-wise average linkage with un-centered correlation distance (A) or pair-wise average linkage with absolute un-centered correlation distance (B). Each column of the left represents a comparison as described in Figure 3. Red bars represent up-regulated transcripts and green bars represent down-regulated transcripts. Intensity of color is directly related to magnitude of differential expression. The presence of a computationally derived regulatory motif upstream of the transcript containing the probes for the differentially expressed gene is denoted on the right for the regulators Fur (blue), PvdS (yellow), HrpL (orange), and RpoD (purple). Roman numerals represent transcript clusters highlighted in the discussion section.