title: Identification of biomarkers for esophageal squamous cell carcinoma using feature selection and decision tree methods.
abstract: Esophageal squamous cell cancer (ESCC) is one of the most common fatal human cancers. The identification of biomarkers for early detection could be a promising strategy to decrease mortality. Previous studies utilized microarray techniques to identify more than one hundred genes; however, it is desirable to identify a small set of biomarkers for clinical use. This study proposes a sequential forward feature selection algorithm to design decision tree models for discriminating ESCC from normal tissues. Two potential biomarkers of RUVBL1 and CNIH were identified and validated based on two public available microarray datasets. To test the discrimination ability of the two biomarkers, 17 pairs of expression profiles of ESCC and normal tissues from Taiwanese male patients were measured by using microarray techniques. The classification accuracies of the two biomarkers in all three datasets were higher than 90%. Interpretable decision tree models were constructed to analyze expression patterns of the two biomarkers. RUVBL1 was consistently overexpressed in all three datasets, although we found inconsistent CNIH expression possibly affected by the diverse major risk factors for ESCC across different areas.
authors.affiliation: School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan ; Ph.D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
authors.forename: Chun-Wei
authors.initials: CW
authors.lastname: Tung
authors.affiliation: Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan ; Department of Public Health, Kaohsiung Medical University, Kaohsiung 80708, Taiwan ; Center of Environmental and Occupational Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung 812, Taiwan.
authors.forename: Ming-Tsang
authors.initials: MT
authors.lastname: Wu
authors.affiliation: Department of Food Science and Nutrition, Meiho University, Pingtung 91202, Taiwan.
authors.forename: Yu-Kuei
authors.initials: YK
authors.lastname: Chen
authors.affiliation: Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan.
authors.forename: Chun-Chieh
authors.initials: CC
authors.lastname: Wu
authors.affiliation: Division of Chest Surgery, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung 812, Taiwan.
authors.forename: Wei-Chung
authors.initials: WC
authors.lastname: Chen
authors.affiliation: Division of Chest Surgery, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung 812, Taiwan ; Division of Chest Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan.
authors.forename: Hsien-Pin
authors.initials: HP
authors.lastname: Li
authors.affiliation: Division of Chest Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan.
authors.forename: Shah-Hwa
authors.initials: SH
authors.lastname: Chou
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan ; Department of Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
authors.forename: Deng-Chyang
authors.initials: DC
authors.lastname: Wu
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan ; Department of Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
authors.forename: I-Chen
authors.initials: IC
authors.lastname: Wu
mesh_terms: D000074183:ATPases Associated with Diverse Cellular Activities; D000465:Algorithms; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000096:biosynthesis / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000737:chemistry* / Q000235:genetics; D002352:Carrier Proteins / Q000032:analysis* / Q000096:biosynthesis / Q000235:genetics; D004265:DNA Helicases / Q000032:analysis* / Q000096:biosynthesis / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D003663:Decision Trees; D055088:Early Detection of Cancer; D004527:Egg Proteins / Q000032:analysis* / Q000096:biosynthesis / Q000235:genetics; D004938:Esophageal Neoplasms / Q000737:chemistry* / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000032:analysis* / Q000096:biosynthesis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011237:Predictive Value of Tests; D012333:RNA, Messenger / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D014408:Biomarkers, Tumor; C118276:CNIH1 protein, human; D002352:Carrier Proteins; D018076:DNA, Complementary; D004527:Egg Proteins; D008565:Membrane Proteins; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D000074183:ATPases Associated with Diverse Cellular Activities; D004265:DNA Helicases; C486549:RUVBL1 protein, human