Protein interactions have been successfully used to infer functional links between proteins (25). In NCG, they are used to understand how the topological properties of the cancer proteins inside the protein–protein interaction network influence their role in cancer. NCG can be used to retrieve information on specific cancer genes, as well as to identify groups of cancer genes with identical properties, thus providing a flexible tool for investigating the complex landscape of cancer genetic determinants. In this paper, along with a general description of the features of NCG, we also provide a specific example of how NCG can be used by reporting the properties of PTEN, a tumor suppressor gene coding for a phosphatidylinositol phosphatase that is impaired in several cancer types.
