Systematic variation in gene expression patterns in human cancer cell lines

Douglas T. Ross, Uwe Scherf, Michael B. Eisen, Charles M. Perou, Christian Rees, Paul Spellman, Vishwanath Iyer, Stefanie S. Jeffrey, Matt Van De Rijn, Mark Waltham, Alexander Pergamenschikov, Jeffrey C F Lee, Deval Lashkari, Dari Shalon, Timothy G. Myers, John N. Weinstein, David Botstein, Patrick O. Brown

Research output: Contribution to journalArticle

1719 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)227-235
Number of pages9
JournalNature Genetics
Volume24
Issue number3
DOIs
StatePublished - Mar 2000
Externally publishedYes

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Gene Expression
Cell Line
Neoplasms
Tumor Cell Line
Antitumor Drug Screening Assays
National Cancer Institute (U.S.)
Oligonucleotide Array Sequence Analysis
Interferons
Breast
Breast Neoplasms
Pharmaceutical Preparations
Genes

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., ... Brown, P. O. (2000). Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics, 24(3), 227-235. https://doi.org/10.1038/73432

Systematic variation in gene expression patterns in human cancer cell lines. / Ross, Douglas T.; Scherf, Uwe; Eisen, Michael B.; Perou, Charles M.; Rees, Christian; Spellman, Paul; Iyer, Vishwanath; Jeffrey, Stefanie S.; Van De Rijn, Matt; Waltham, Mark; Pergamenschikov, Alexander; Lee, Jeffrey C F; Lashkari, Deval; Shalon, Dari; Myers, Timothy G.; Weinstein, John N.; Botstein, David; Brown, Patrick O.

In: Nature Genetics, Vol. 24, No. 3, 03.2000, p. 227-235.

Research output: Contribution to journalArticle

Ross, DT, Scherf, U, Eisen, MB, Perou, CM, Rees, C, Spellman, P, Iyer, V, Jeffrey, SS, Van De Rijn, M, Waltham, M, Pergamenschikov, A, Lee, JCF, Lashkari, D, Shalon, D, Myers, TG, Weinstein, JN, Botstein, D & Brown, PO 2000, 'Systematic variation in gene expression patterns in human cancer cell lines', Nature Genetics, vol. 24, no. 3, pp. 227-235. https://doi.org/10.1038/73432
Ross, Douglas T. ; Scherf, Uwe ; Eisen, Michael B. ; Perou, Charles M. ; Rees, Christian ; Spellman, Paul ; Iyer, Vishwanath ; Jeffrey, Stefanie S. ; Van De Rijn, Matt ; Waltham, Mark ; Pergamenschikov, Alexander ; Lee, Jeffrey C F ; Lashkari, Deval ; Shalon, Dari ; Myers, Timothy G. ; Weinstein, John N. ; Botstein, David ; Brown, Patrick O. / Systematic variation in gene expression patterns in human cancer cell lines. In: Nature Genetics. 2000 ; Vol. 24, No. 3. pp. 227-235.
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