Figure 7

Examples of structure-based similarity and annotation-based similarity between functions in a hierarchy. Each circle represents a function, and each edge is a general-to-specific relationship between two functions. The depth of a function is the path length from the root to the function. The number close to each function represents the number of proteins annotated on the function. The structure-based similarity between two functions is calculated by the ratio of the depth of the most specific common function to the average depth of the functions of interest (Formula 13). The annotation-based similarity between two functions becomes the negative logarithm of the proportion of proteins annotated on the most specific common function (Formula 14). Some examples of the structure-based and the annotation-based similarity between two functions in the hierarchy are shown in the boxes.