title: Prediction of core cancer genes using multi-task classification framework.
abstract: Cancer is deemed as a highly heterogeneous disease specific to cell type and tissue origin. All cancers, however, share a common pathogenesis. Therefore, it is widely believed that cancers may share common mechanisms. In this study, we introduce a novel strategy based on multi-tasking learning methods to predict core cancer genes shared by multiple cancers in the hope of elucidating common cancer mechanisms. Our strategy uses two multi-tasking learning algorithms, one for feature selection and the other for validation of selected features. The combined use of two methods results in more robust classifiers and reliable selected features. The top 73 significant features, mapped to 72 genes, are selected as core cancer genes. The effectiveness of the 73 features is further demonstrated in a blind test conducted on an independent test data. The biological significance of these genes is evaluated using systems biology analyses. Extensive functional, pathway and network analysis confirms findings in previous studies and brings new insights into common cancer mechanisms. Our strategy can be used as a general method to find important genes from large gene expression datasets on the genomic level. The selected genes can be used to predict cancers.
authors.affiliation: Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA.
authors.forename: Shan
authors.initials: S
authors.lastname: Gao
authors.forename: Shuo
authors.initials: S
authors.lastname: Xu
authors.forename: Yaping
authors.initials: Y
authors.lastname: Fang
authors.forename: Jianwen
authors.initials: J
authors.lastname: Fang
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks / Q000235:genetics; D052138:Genes, Neoplasm / Q000235:genetics*; D006801:Humans; D015203:Reproducibility of Results; D060388:Support Vector Machine