Fig. 4

Network visualization of significant DE. The selectors on the upper left allow the user to select a network to display, and a specific experiment and timepoint to overlay. Each gene is a node, and links are defined by the type of network used. The 19F Metabolic (“Metab19F”) network has two genes linked, if their gene products participate in the same reaction, or subsequent reactions in the metabolism of 19F. In the Vancomycin experiment shown (at 120 min), significantly up- and down-regulated genes appear as red and blue nodes respectively. The selectors on the right help generate a scatter plot (lower right) that can relate network-related information (e.g. network degree) to metadata. In the example plot, degree is plotted against sequence diameter i.e. variability of homologous sequences across different strains of S. pneumoniae