title: GTA: a game theoretic approach to identifying cancer subnetwork markers.
abstract: The identification of genetic markers (e.g. genes, pathways and subnetworks) for cancer has been one of the most challenging research areas in recent years. A subset of these studies attempt to analyze genome-wide expression profiles to identify markers with high reliability and reusability across independent whole-transcriptome microarray datasets. Therefore, the functional relationships of genes are integrated with their expression data. However, for a more accurate representation of the functional relationships among genes, utilization of the protein-protein interaction network (PPIN) seems to be necessary. Herein, a novel game theoretic approach (GTA) is proposed for the identification of cancer subnetwork markers by integrating genome-wide expression profiles and PPIN. The GTA method was applied to three distinct whole-transcriptome breast cancer datasets to identify the subnetwork markers associated with metastasis. To evaluate the performance of our approach, the identified subnetwork markers were compared with gene-based, pathway-based and network-based markers. We show that GTA is not only capable of identifying robust metastatic markers, it also provides a higher classification performance. In addition, based on these GTA-based subnetworks, we identified a new bonafide candidate gene for breast cancer susceptibility.
authors.affiliation: Research Laboratory of Computational Biology, Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran.
authors.forename: S
authors.initials: S
authors.lastname: Farahmand
authors.forename: S
authors.initials: S
authors.lastname: Goliaei
authors.forename: N
authors.initials: N
authors.lastname: Ansari-Pour
authors.forename: Z
authors.initials: Z
authors.lastname: Razaghi-Moghadam
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D030541:Databases, Genetic; D005716:Game Theory; D053263:Gene Regulatory Networks; D006801:Humans; D009369:Neoplasms / Q000235:genetics*