Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

Abstract

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer. With the constant delivery of results from the mutational screenings of cancer genomes, NCG represents a versatile resource for retrieving detailed information on particular cancer genes, as well as for identifying common properties of precompiled lists of cancer genes. NCG is freely available at: http://bio.ifom-ieo-campus.it/ncg.

Figure 1.

Cancer genes collected in NCG. Venn diagrams of the different lists of cancer genes stored in NCG. The Cancer Gene Census provides information on the cancer type (A) and on the phenotypic effect of the mutation (B). The CAN-genes reported so far refer to four cancer types (C). The overlap among the different data sources used in this study is overall very poor (D).

Figure 2.

Duplicability, orthology and network properties of the tumor suppressor gene PTEN. (A) Using the PTEN protein sequence as a query, three hits are found on the human genome. The best hit corresponds to genomic locus of PTEN, while the two additional hits account for a recent duplication transcribing for the processed pseudogene PTENP1, and to a short region of identity lying in the intron of ANKFN1, respectively. (B) The orthology ratio reflects the co-orthology relationships of human PTEN at different branching points of the tree of life. The only inparalogs of PTEN in eukaryotes are found in A. thaliana and D. rerio, indicating that this gene maintained a strict singleton status during eukaryotic evolution. (C) PTEN interacts with 35 other human proteins, four of which are cancer proteins and 22 are hubs. This makes PTEN a central node of the human protein-protein interaction network.