BiclusterCard components II: Bicluster Motifs, Upstream Patterns, Plots.

Shown in the figure are, the expanded tab for Plots displaying a gene expression heatmap, the expanded tab for Bicluster Motifs, and an example of the upstream motif patterns for multi-species bicluster E. coli – S. Typhimurium bicluster 57. (A) Example plot of a gene expression heatmap for the bicluster genes and conditions in eco57 (left) and stm57 (right); upregulated expression (green) and downregulated expression (red). (B) Putative regulatory sequence motifs found in bicluster gene member promoters for eco57 (left) and stm57 (right). The table displays a row for each motif found and columns for the motif number, E-value, sequence logo, matches to any known motifs, and a link to motif pattern page. Eco57 motif #1 matches the known FNR binding sequence and motif #3 matches the known NarP binding sequence. (C) The promoter motif patterns for the motifs shown in (B) for eco57 (left) and stm57 (right). The location of the motifs are represented by colored rectangles on the promoter sequence (black line) and the colors correspond to the logo border colors seen in (B); motif #1 (red), motif #2 (green) motif #3 (blue). For the bicluster gene members shown, bicluster motifs #1 and #3 appear in the promoter regions of the eco57 members, whereas all three bicluster motifs appear in the promoters for the stm57 members. The identical motif pattern indicates MScM has determined them to be in an operon. It is known that narGHJI exist as an operon, but MScM has determined that yjjI is in an operon with yjjW (this is also predicted by [62]). However, yjjW is found only in the elaborated gene set of eco57 and it is not found in stm57.