title: Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray.
abstract: OBJECTIVE
  We evaluated the genome-wide gene expression profiles of various cancer cell lines to identify the gastrointestinal tract cancer cell-related genes.
  
  
  METHODS
  Gene expression profilings of 27 cancer cell lines and 9 tissues using 7.5K human cDNA microarrays in indirect design with Yonsei reference RNA composed of 11 cancer cell line RNAs were done. The significant genes were selected using significant analysis of microarray in various sets of data. The selected genes were validated using real-time PCR analysis.
  
  
  RESULTS
  After intensity-dependent, within-print-tip normalization by loess method, we observed that expression patterns of cell lines and tissues were substantially different, divided in two discrete clusters. Next, we selected 115 genes that discriminate gastrointestinal cancer cell lines from others using significant analysis of microarray. Among the expression profiles of five gastric cancer cell lines, 66 genes were identified as differentially expressed genes related to metastatic phenotype. YCC-16, which was established from the peripheral blood of one advanced gastric cancer patient, produced a unique gene expression pattern resembling the profiles of lymphoid cell lines. Quantitative real-time reverse transcription-PCR results of selected genes, including PXN, KRT8, and ITGB5, were correlated to microarray data and successfully discriminate the gastrointestinal tract cancer cell lines from hematologic malignant cell lines.
  
  
  CONCLUSIONS
  A gene expression database could serve as a useful source for the further investigation of cancer biology using the cell lines.
authors.affiliation: Cancer Metastasis Research Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea.
authors.forename: Tae Moon
authors.initials: TM
authors.lastname: Kim
authors.forename: Ha Jin
authors.initials: HJ
authors.lastname: Jeong
authors.forename: Min Young
authors.initials: MY
authors.lastname: Seo
authors.forename: Sang Chul
authors.initials: SC
authors.lastname: Kim
authors.forename: Gabee
authors.initials: G
authors.lastname: Cho
authors.forename: Chan Hee
authors.initials: CH
authors.lastname: Park
authors.forename: Tae Soo
authors.initials: TS
authors.lastname: Kim
authors.forename: Kyu Hyun
authors.initials: KH
authors.lastname: Park
authors.forename: Hyun Cheol
authors.initials: HC
authors.lastname: Chung
authors.forename: Sun Young
authors.initials: SY
authors.lastname: Rha
mesh_terms: D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000494:pharmacology; D005770:Gastrointestinal Neoplasms / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008954:Models, Biological; D005810:Multigene Family; D009362:Neoplasm Metastasis; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D005456:Fluorescent Dyes; D012313:RNA