Meta- and Gene Set Analysis of Stomach Cancer Gene Expression Data

  • Kim, Seon-Young (Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Jeong-Hwan (Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Heun-Sik (Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Noh, Seung-Moo (Department of General Surgery, College of Medicine, Chungnam National University) ;
  • Song, Kyu-Sang (Department of Pathology, College of Medicine, Chungnam National University) ;
  • Cho, June-Sik (Department of Diagnostic Radiology, College of Medicine, Chungnam National University) ;
  • Jeong, Hyun-Yong (Department of Internal Medicine, College of Medicine, Chungnam National University) ;
  • Kim, Woo Ho (Department of Pathology, Seoul National University College of Medicine) ;
  • Yeom, Young-Il (Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Nam-Soon (Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Sangsoo (National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Yoo, Hyang-Sook (The Center for Functional Analysis of Human Genome, 21st Century Frontier R&D Program, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Yong Sung (Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2007.01.30
  • Accepted : 2007.05.07
  • Published : 2007.10.31

Abstract

We generated gene expression data from the tissues of 50 gastric cancer patients, and applied meta-analysis and gene set analysis to this data and three other stomach cancer gene expression data sets to define the gene expression changes in gastric tumors. By meta-analysis we identified genes consistently changed in gastric carcinomas, while gene set analysis revealed consistently changed biological themes. Genes and gene sets involved in digestion, fatty acid metabolism, and ion transport were consistently down-regulated in gastric carcinomas, while those involved in cellular proliferation, cell cycle, and DNA replication were consistently up-regulated. We also found significant differences between the genes and gene sets expressed in diffuse and intestinal type gastric carcinoma. By gene set analysis of cytogenetic bands, we identified many chromosomal regions with possible gross chromosomal changes (amplifications or deletions). Similar analysis of transcription factor binding sites (TFBSs), revealed transcription factors that may have caused the observed gene expression changes in gastric carcinomas, and we confirmed the overexpression of one of these, E2F1, in many gastric carcinomas by tissue array and immunohistochemistry. We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/).

Keywords

Database;Gastric Cancer;Gene Set;Meta-Analysis;Microarray

Acknowledgement

Supported by : Ministry of Science and Technology in Korea

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