Network-based Identification of Novel Cancer Genes
2010 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 9, no 4, 648-655 p.Article in journal (Refereed) Published
Genes involved in cancer susceptibility and progression can serve as templates for searching protein networks for novel cancer genes. To this end, we introduce a general network searching method, MaxLink, and apply it to find and rank cancer gene candidates by their connectivity to known cancer genes. Using a comprehensive protein interaction network, we searched for genes connected to known cancer genes. First, we compiled a new set of 812 genes involved in cancer, more than twice the number in the Cancer Gene Census. Their network neighbors were then extracted. This candidate list was refined by selecting genes with unexpectedly high levels of connectivity to cancer genes and without previous association to cancer. This produced a list of 1891 new cancer candidates with up to 55 connections to known cancer genes. We validated our method by cross-validation, Gene Ontology term bias, and differential expression in cancer versus normal tissue. An example novel cancer gene candidate is presented with detailed analysis of the local network and neighbor annotation. Our study provides a ranked list of high priority targets for further studies in cancer research. Supplemental material is included.
Place, publisher, year, edition, pages
2010. Vol. 9, no 4, 648-655 p.
Bioinformatics and Systems Biology
Research subject Biochemistry with Emphasis on Theoretical Chemistry
IdentifiersURN: urn:nbn:se:su:diva-49937DOI: 10.1074/mcp.M900227-MCP200ISI: 000276379400005OAI: oai:DiVA.org:su-49937DiVA: diva2:379935
authorCount :32010-12-202010-12-202013-02-28Bibliographically approved