title: Identification of gene markers in the development of smoking-induced lung cancer.
abstract: Lung cancer is a malignant tumor with high mortality in both women and men. To study the mechanisms of smoking-induced lung cancer, we analyzed microarray of GSE4115. GSE4115 was downloaded from Gene Expression Omnibus including 78 and 85 bronchial epithelium tissue samples separately from smokers with and without lung cancer. Limma package in R was used to screen differentially expressed genes (DEGs). Hierarchical cluster analysis for DEGs was conducted using orange software and visualized by distance map. Using DAVID software, functional and pathway enrichment analyses separately were conducted for the DEGs. And protein-protein interaction (PPI) network was constructed using Cytoscape software. Then, the pathscores of enriched pathways were calculated. Besides, functional features were screened and optimized using the recursive feature elimination (RFE) method. Additionally, the support vector machine (SVM) method was used to train model. Total 1923 DEGs were identified between the two groups. Hierarchical cluster analysis indicated that there were differences in gene level between the two groups. And SVM analysis indicated that the five features had potential diagnostic value. Importantly, MAPK1 (degree=30), SRC (degree=29), SMAD4 (degree=23), EEF1A1 (degree=21), TRAF2 (degree=21) and PLCG1 (degree=20) had higher degrees in the PPI network of the DEGs. They might be involved in smoking-induced lung cancer by interacting with each other (e.g. MAPK1-SMAD4, SMAD4-EEF1A1 and SRC-PLCG1). MAPK1, SRC, SMAD4, EEF1A1, TRAF2 and PLCG1 might be responsible for the development of smoking-induced lung cancer.
authors.affiliation: Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030; Department of Respiratory and Critical Care Medicine, Ningxia People's Hospital, Yinchuan, China, 750011.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Department of Respiratory and Critical Care Medicine, Ningxia People's Hospital, Yinchuan, China, 750011.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhuan
authors.affiliation: Department of Respiratory and Critical Care Medicine, Ningxia People's Hospital, Yinchuan, China, 750011.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yan
authors.affiliation: Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030.
authors.forename: Simin
authors.initials: S
authors.lastname: Jiang
authors.affiliation: Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030. Electronic address: taowangtww@163.com.
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
mesh_terms: D020869:Gene Expression Profiling; D005819:Genetic Markers; D006801:Humans; D016015:Logistic Models; D008175:Lung Neoplasms / Q000209:etiology / Q000235:genetics*; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D012907:Smoking / Q000009:adverse effects*; D060388:Support Vector Machine
chemical_list: D005819:Genetic Markers
keywords: Differentially expressed genes; Enrichment analysis; Lung cancer; Protein–protein interaction network; Support vector machine method