BackgroundFeature selection and gene set analysis are of increasing interest in the field of bioinformatics. While these two approaches have been developed for different purposes, we describe how some gene set analysis methods can be utilized to conduct feature selection.MethodsWe adopted a gene set analysis method, the significance analysis of microarray gene set reduction (SAMGSR) algorithm, to carry out feature selection for longitudinal gene expression data.ResultsUsing a real-world application and simulated data, it is demonstrated that the proposed SAMGSR extension outperforms other relevant methods. In this study, we illustrate that a gene's expression profiles over time can be regarded as a gene set and then a suitable gene set analysis method can be utilized directly to select relevant genes associated with the phenotype of interest over time.ConclusionsWe believe this work will motivate more research to bridge feature selection and gene set analysis, with the development of novel algorithms capable of carrying out feature selection for longitudinal gene expression data.
[1]Jilin Univ, Hosp 1, Div Clin Res, 71 Xinmin St, Changchun 130021, Jilin, Peoples R China.
[2]Univ Kentucky, Markey Canc Ctr, Dept Biostat, 800 Rose St, Lexington, KY 40536 USA.
[3]Emory Univ, Rollins Sch Publ Hlth, Dept Biostat & Bioinformat, 1518 Clifton Rd NE, Atlanta, GA 30322 USA.
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