Figure 1.

The entire Regulatory Overview for E. coli after selecting the command Tools→Regulatory Overview. In this case, zoom level 2 was automatically selected as the best zoom level given the size of the browser window. The names of the genes are displayed for the inner-most ellipse, but not for the other two ellipses as not enough space is available for the names. This display uses the `nested ellipses' layout. The outer most ellipse has all the genes that do not regulate any gene but are regulated by at least one gene. Genes that are regulated by the same set of genes are grouped together, forming a leaf shape. The two inner ellipses contains the regulator genes. The inner-most ellipse has the genes that regulate the largest numbers of genes. They are displayed in ascending alphabetical order starting from the right side. This layout is not based on the locations of the genes on the genome. Each circle, square, minus, or plus icon represents a gene. A square represents a sigma factor, a plus represents a gene for which all its regulators are activators, a minus represents a gene for which all its regulators are inhibitors, and a circle represents a gene that has activators and inhibitors. No regulation relationships are shown in the diagram below. Relationship arrows can be added with the searching and highlighting operations.