title: Classification of Non-Small Cell Lung Cancer Using Significance Analysis of Microarray-Gene Set Reduction Algorithm.
abstract: Among non-small cell lung cancer (NSCLC), adenocarcinoma (AC), and squamous cell carcinoma (SCC) are two major histology subtypes, accounting for roughly 40% and 30% of all lung cancer cases, respectively. Since AC and SCC differ in their cell of origin, location within the lung, and growth pattern, they are considered as distinct diseases. Gene expression signatures have been demonstrated to be an effective tool for distinguishing AC and SCC. Gene set analysis is regarded as irrelevant to the identification of gene expression signatures. Nevertheless, we found that one specific gene set analysis method, significance analysis of microarray-gene set reduction (SAMGSR), can be adopted directly to select relevant features and to construct gene expression signatures. In this study, we applied SAMGSR to a NSCLC gene expression dataset. When compared with several novel feature selection algorithms, for example, LASSO, SAMGSR has equivalent or better performance in terms of predictive ability and model parsimony. Therefore, SAMGSR is a feature selection algorithm, indeed. Additionally, we applied SAMGSR to AC and SCC subtypes separately to discriminate their respective stages, that is, stage II versus stage I. Few overlaps between these two resulting gene signatures illustrate that AC and SCC are technically distinct diseases. Therefore, stratified analyses on subtypes are recommended when diagnostic or prognostic signatures of these two NSCLC subtypes are constructed.
authors.affiliation: School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, China; Department of Neurology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, Jilin 130041, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, China.
authors.forename: Linlin
authors.initials: L
authors.lastname: Wang
authors.affiliation: School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, China.
authors.forename: Bochuan
authors.initials: B
authors.lastname: Du
authors.affiliation: School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, China.
authors.forename: Tianjiao
authors.initials: T
authors.lastname: Wang
authors.affiliation: School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, China.
authors.forename: Pu
authors.initials: P
authors.lastname: Tian
authors.affiliation: Division of Clinical Epidemiology, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, Jilin 130021, China; School of Mathematics, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, China.
authors.forename: Suyan
authors.identifier: 0000-0002-5942-1542
authors.initials: S
authors.lastname: Tian
mesh_terms: D000465:Algorithms; D002289:Carcinoma, Non-Small-Cell Lung / Q000145:classification / Q000175:diagnosis / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000145:classification / Q000175:diagnosis / Q000378:metabolism; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*