Figure 1

Bacteriorhodopsin Halobacterium bicluster with known Bat-binding motif (UAS). A: expression ratios of the bicluster's genes, over all experimental conditions (conditions within the bicluster are to the left of the red dotted line). B: expression ratios over only the conditions within the bicluster. C: motif logos [74] and E-values [10] for motifs that were detected in the bicluster. D: network of associations between the bicluster's genes in the various association networks used by CMONKEY, including operons, KEGG [48] metabolic pathways ("met" – see Methods; only present in Figures 4 and 5), and Prolinks [23] associations. The nodes are color coded by COG [89] functional groupings. Genes labeled in red text encode known or putative transcriptional regulators. E: diagram of the upstream positions of the motifs, colored red, green and blue for motifs #1, 2 and 3, respectively. The genes' names are color-coded by COG functional annotation as in the network subfigure. The colors of the lines for each gene's sequence correspond to those in the expression ratio plots.