title: Meta- and gene set analysis of stomach cancer gene expression data.
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/).
authors.affiliation: Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
authors.forename: Seon-Young
authors.initials: SY
authors.lastname: Kim
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Kim
authors.forename: Heun-Sik
authors.initials: HS
authors.lastname: Lee
authors.forename: Seung-Moo
authors.initials: SM
authors.lastname: Noh
authors.forename: Kyu-Sang
authors.initials: KS
authors.lastname: Song
authors.forename: June-Sik
authors.initials: JS
authors.lastname: Cho
authors.forename: Hyun-Yong
authors.initials: HY
authors.lastname: Jeong
authors.forename: Woo Ho
authors.initials: WH
authors.lastname: Kim
authors.forename: Young-Il
authors.initials: YI
authors.lastname: Yeom
authors.forename: Nam-Soon
authors.initials: NS
authors.lastname: Kim
authors.forename: Sangsoo
authors.initials: S
authors.lastname: Kim
authors.forename: Hyang-Sook
authors.initials: HS
authors.lastname: Yoo
authors.forename: Yong Sung
authors.initials: YS
authors.lastname: Kim
mesh_terms: D001665:Binding Sites; D002869:Chromosome Aberrations; D030541:Databases, Genetic; D050687:E2F1 Transcription Factor / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D006801:Humans; D046228:Microarray Analysis; D013274:Stomach Neoplasms / Q000235:genetics* / Q000473:pathology; D014157:Transcription Factors / Q000378:metabolism; D015854:Up-Regulation / Q000235:genetics
chemical_list: D050687:E2F1 Transcription Factor; D014157:Transcription Factors