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Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium

Figure 5

Co-clustering of genes showing similar patterns of regulation.

The expression profiles for all genes were input to SEBINI [18] and analyzed using the CLR algorithm [19]. The results shown in the figure use a force-directed network layout algorithm where genes (shown as small colored circles) are generally closer together when their statistical association, and thus degree of predicted co-regulation, is stronger (the cutoff for the genes shown is 5 standard deviations from the mean or greater; p<.0001). The results were visualized as a network of similarity relationships using Cytoscape [57]. Insert cluster shows the same analysis but on a different data set derived from the NIH sponsored gene expression omnibus GEO (cutoff score 5). Co-clustered genes are described in Table 2.

Figure 5

doi: https://doi.org/10.1371/journal.ppat.1000306.g005