Topological analysis

Topological signature

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.

Pathway similarity

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.

Steps of analysis

  1. select interaction network
    (large but biased due to small-scale experiments or small but derived from genome-scale studies)
  2. select the identifier format of your gene set
  3. select a reference database of pathways and cellular processes
  4. enter a list of genes/proteins and click "use gene list" button or select nodes from the current network view and click "use selected nodes" button