title: Stable Gene Signature Selection for Prediction of Breast Cancer Recurrence Using Joint Mutual Information.
abstract: In this experiment, a gene selection technique was proposed to select a robust gene signature from microarray data for prediction of breast cancer recurrence. In this regard, a hybrid scoring criterion was designed as linear combinations of the scores that were determined in the mutual information (MI) domain and protein-protein interactions network. Whereas, the MI-based score represents the complementary information between the selected genes for outcome prediction; and the number of connections in the PPI network between the selected genes builds the PPI-based score. All genes were scored by using the proposed function in a hybrid forward-backward gene-set selection process to select the optimum biomarker-set from the gene expression microarray data. The accuracy and stability of the finally selected biomarkers were evaluated by using five-fold cross-validation (CV) to classify available data on breast cancer patients into two cohorts of poor and good prognosis. The results showed an appealing improvement in the cross-dataset accuracy in comparison with similar studies whenever we applied a primary signature, which was selected from one dataset, to predict survival in other independent datasets. Moreover, the proposed method demonstrated 58-92 percent overlap between 50-genes signatures, which were selected from seven independent datasets individually.
authors.forename: Mohammadreza
authors.initials: M
authors.lastname: Sehhati
authors.forename: Alireza
authors.initials: A
authors.lastname: Mehridehnavi
authors.forename: Hossein
authors.initials: H
authors.lastname: Rabbani
authors.forename: Meraj
authors.initials: M
authors.lastname: Pourhossein
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000401:mortality*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D052138:Genes, Neoplasm / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000453:epidemiology / Q000235:genetics; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics*; D009364:Neoplasm Recurrence, Local / Q000175:diagnosis / Q000235:genetics* / Q000401:mortality*; D015995:Prevalence; D011379:Prognosis; D015203:Reproducibility of Results; D018570:Risk Assessment / Q000379:methods; D012680:Sensitivity and Specificity; D016019:Survival Analysis
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins