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Analysis of matched mRNA measurements from two different microarray technologies.

Winston Patrick Kuo1, Tor-Kristian Jenssen, Atul J Butte

  • 1Children's Hospital Informatics Program and Division of Endocrinology, Department of Medicine, Children's Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. wpkuo@mit.edu

Bioinformatics (Oxford, England)
|April 6, 2002
PubMed
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Gene expression measurements from different microarray technologies show poor agreement. Factors like GC-content and probe specificity limit cross-platform data utilization, hindering reproducible research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Multiple gene expression measurement technologies exist, necessitating cross-technology agreement for data integration.
  • Utilizing data across different platforms can reduce experimental redundancy but requires comparable measurements.

Purpose of the Study:

  • To assess the agreement between measurements from two high-throughput DNA microarray technologies.
  • To identify factors influencing the comparability of gene expression data across platforms.

Main Methods:

  • Compared mRNA measurements for 2895 genes across 56 National Cancer Institute (NCI 60) cell lines.
  • Calculated correlation between matched measurements and concordance of gene/cell line clusters from Stanford cDNA and Affymetrix oligonucleotide microarrays.

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Main Results:

  • Measurements from the two microarray platforms exhibited poor correlation and discordant clustering.
  • Gene expression relationships within platforms were not preserved across technologies.
  • Probe-specific factors (GC-content, length, intensity, cross-hybridization) influenced measurement agreement.

Conclusions:

  • Broad utilization of gene expression data across different microarray platforms is challenging due to poor cross-technology agreement.
  • Probe-specific characteristics significantly impact measurement comparability, limiting the integration of data from diverse platforms.