Each node represents the features of a single taxonomic group, or organism. The nodes are arranged hierarchically in concentric rings. The parent taxon, located in the centre, leads recursively outwards towards its children. The name of the taxonomic group, and the mean number of domains per organism are displayed alongside the taxonomic nodes.
There are 5 types of node: Overall, Domain, Kingdom, Subkingdom and Species. The "Overall" node displays the mean number of domains per organism across the tree of life. The Overall node is surrounded by the three "Domain" (or superkingdom) nodes: eukaryota, bacteria and archaea. The Domain nodes are surrounded by the "Kingdom" nodes, for example metazoa from the eukaryota Kingdom. The largest Kingdoms (in terms of fully sequenced organisms), contain "Subkingdom" nodes. The largest Kingdoms include metazoa, euryarchaeota, proteobacteria, actinobacteria and firmicutes. The remaining Kingdoms, and the Subkingdoms, contain "Species" nodes. Note that the Species nodes do not include any of the organisms we have classified as strains. An example may help illustrate the hierarchy of taxonomic groups. The Homo sapiens (human) species occurs within the mammalia Subkingdom, metazoa Kingdom and eukaryota Domain.
The organisms within a taxonomic group can be viewed by selecting the outer taxonomic group node. The name of the organism, and the number of proteins in the organism which contain the domain are displayed alongside the organism nodes. From here, you can view the domain assignment details of each organism by clicking on an organism node.
Minimum/maximum domain occurrence
By selecting the minimum or maximum node, you can also view the organisms with the smallest and largest number of domains respectively. The minimum/maximum domain occurrence always applies to all organisms.
The model organism link displays a selection of chosen model organisms used frequently in genetic research.
There is often a wide variation in occurrence of domains in different taxonomic groups. In order to display both large and small nodes, it is necessary to use a logarithmic scale for node size. For taxonomic groups, the radius of the node is equal to the logarithm of the mean domain occurrence found per organism in the taxonomic group. For organisms, the radius of the node is equal to the logarithm of the number of domains occurring in the organism. There is one exception. The radius is set to half of log 2 when the mean domain occurrence, or number of domains in the organism, equals 1.
The colour of the node represents the superkingdom to which it belongs, and is detailed in the legend on the graphic.