title: Gene expression profiling of colorectal tumors and normal mucosa by microarrays meta-analysis using prediction analysis of microarray, artificial neural network, classification, and regression trees.
abstract: BACKGROUND
  Microarray technology shows great potential but previous studies were limited by small number of samples in the colorectal cancer (CRC) research. The aims of this study are to investigate gene expression profile of CRCs by pooling cDNA microarrays using PAM, ANN, and decision trees (CART and C5.0).
  
  
  METHODS
  Pooled 16 datasets contained 88 normal mucosal tissues and 1186 CRCs. PAM was performed to identify significant expressed genes in CRCs and models of PAM, ANN, CART, and C5.0 were constructed for screening candidate genes via ranking gene order of significances.
  
  
  RESULTS
  The first screening identified 55 genes. The test accuracy of each model was over 0.97 averagely. Less than eight genes achieve excellent classification accuracy. Combining the results of four models, we found the top eight differential genes in CRCs; suppressor genes, CA7, SPIB, GUCA2B, AQP8, IL6R and CWH43; oncogenes, SPP1 and TCN1. Genes of higher significances showed lower variation in rank ordering by different methods.
  
  
  CONCLUSIONS
  We adopted a two-tier genetic screen, which not only reduced the number of candidate genes but also yielded good accuracy (nearly 100%). This method can be applied to future studies. Among the top eight genes, CA7, TCN1, and CWH43 have not been reported to be related to CRC.
authors: Division of Bioinformatics and Statistics, School of Public Health, National Defense Medical Center, Taipei 114, Taiwan.
authors: Chi-Ming
authors: CM
authors: Chu
authors: Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan.
authors: Chung-Tay
authors: CT
authors: Yao
authors: Division of Bioinformatics and Statistics, School of Public Health, National Defense Medical Center, Taipei 114, Taiwan.
authors: Yu-Tien
authors: YT
authors: Chang
authors: Department of Nursing, Oriental Institute of Technology and Far Eastern Memorial Hospital, New Taipei City 220, Taiwan.
authors: Hsiu-Ling
authors: HL
authors: Chou
authors: Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei 114, Taiwan.
authors: Yu-Ching
authors: YC
authors: Chou
authors: Department of Nursing, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.
authors: Kang-Hua
authors: KH
authors: Chen
authors: Advpharma, Inc., New Taipei City 221, Taiwan.
authors: Harn-Jing
authors: HJ
authors: Terng
authors: Division of Colorectal Surgery, Cheng Hsin Rehabilitation Medical Center, Taipei 112, Taiwan.
authors: Chi-Shuan
authors: CS
authors: Huang
authors: Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, Taipei 114, Taiwan.
authors: Chia-Cheng
authors: CC
authors: Lee
authors: Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei 114, Taiwan.
authors: Sui-Lun
authors: SL
authors: Su
authors: Division of Surgery, Tri-Service General Hospital, Taipei 114, Taiwan.
authors: Yao-Chi
authors: YC
authors: Liu
authors: Department of Epidemiology, School of Public Health, National Defense Medical Center, Taipei 114, Taiwan.
authors: Fu-Gong
authors: FG
authors: Lin
authors: Department of Medical Informatics, Faculty of Medicine, University of Heidelberg, Heidelberg 69120, Germany.
authors: Thomas
authors: T
authors: Wetter
authors: Department of Nursing, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.
authors: Chi-Wen
authors: CW
authors: Chang
mesh_terms: D003106:Colon / Q000378:metabolism* / Q000473:pathology; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism*; D016571:Neural Networks, Computer; D020411:Oligonucleotide Array Sequence Analysis; D012044:Regression Analysis; D059467:Transcriptome