Systematic variation in gene expression patterns in human cancer cell lines

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  • Ross, Douglas T.
    • Other Affiliation: Departments of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
  • Scherf, Uwe
    • Other Affiliation: Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  • Eisen, Michael B.
    • Other Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
  • Perou, Charles M.
  • Rees, Christian
    • Other Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
  • Spellman, Paul
    • Other Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
  • Iyer, Vishwanath
    • Other Affiliation: Departments of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
  • Jeffrey, Stefanie S.
    • Other Affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
  • Van de Rijn, Matt
    • Other Affiliation: Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
  • Waltham, Mark
    • Other Affiliation: Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  • Pergamenschikov, Alexander
    • Other Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
  • Lee, Jeffrey C.F.
    • Other Affiliation: Incyte Pharmaceuticals, Fremont, California, USA
  • Lashkari, Deval
    • Other Affiliation: Genometrix Inc., The Woodlands, Texas, USA
  • Shalon, Dari
    • Other Affiliation: Incyte Pharmaceuticals, Fremont, California, USA
  • Myers, Timothy G.
    • Other Affiliation: Information Technology Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
  • Weinstein, John N.
    • Other Affiliation: Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  • Botstein, David
    • Other Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
  • Brown, Patrick O.
    • Other Affiliation: Departments of Biochemistry, Stanford University School of Medicine, Stanford, California, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
Abstract
  • We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens revealed features of the expression patterns in the tumours that had recognizable counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumours in vivo.
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  • Article
Rights statement
  • In Copyright
Journal title
  • Nature Genetics
Journal volume
  • 24
Journal issue
  • 3
Page start
  • 227
Page end
  • 235
Language
  • English
Version
  • Postprint
ISSN
  • 1061-4036

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