During topological analysis the interaction signature of the input gene set is compared to the signatures of pathways and processes in the reference database. The signature is a vector of 5 topological properties of the interaction network formed by a set of genes, such as network density, centrality of nodes in the network and nodes tendency to form clusters.
The Euclidean distance between two vectors is used to compare the signatures. The smaller the distance, the more similar the pathway interactions topology is to the iteractions topology of the input gene set.