Nucleic Acids Research, 2008, Vol. 36, Database issue D635 Figure 1. Typical screenshots from Bacteriome.org. (A) Summary page of a typical search. Here we have identiﬁed 155 genes associated with the word ‘kinase’ that was entered in the wild search box on the home page. The user may select one of the three datasets to view interactions associated with these 155 genes. (B) Search results pages. These pages provide summary information on each gene identiﬁed by a search. One or more genes may be selected for either a more detailed view of each gene or for viewing within the context of an interaction network. An additional button is provided to view the network of all identiﬁed genes. (C) Network view. The embedded java applet provides an interactive view of the interactions associated with 100 selected genes (large nodes). In addition to switching between diﬀerent settings such as the interaction dataset and layers of neighbors to view, the Java applet features a graphical user interface to manipulate the network view. For example, the user could zoom into a section of the network, select and move groups or individual proteins and choose to view the nodes in terms of their PFAM domain architecture. (D) Alternatively, the user could also view the nodes in terms of their phylogenetic proﬁles. (E) The presented example shows the proﬁles for a group of chemotaxis related proteins that appear to form a functional module (left). Note how many of the proteins in this module appear to have homologs in a few restricted taxonomic groups including the various proteobacteria groups (diﬀerent shades of blue), spirochaetes (purple), ﬁrmicutes (green), cyanobacteria (yellow) and archaea (red) suggesting a degree of evolutionary modularity. (F) In addition to visualizing interactions between individual proteins, the Java applet has also been adapted to provide a view of predicted protein complexes/functional modules. This view shows a section of the interactions between the functional modules predicted for the functional interaction network. Each pie chart shows the proportion of proteins associated with each COG functional category. The size of the pie indicates the number of proteins associated with each complex/module. Placing the mouse over the pie provides details of constituent proteins which can be selected for a more detailed view.