Cross-platform comparison of two pancreatic cancer phenotypes

Robert B. Scharpf, Christine A. Iacobuzio-Donahue, Leslie Cope, Ingo Ruczinski, Elizabeth Garrett-Mayer, Sindhu Lakkur, Domenico Campagna, Giovanni Parmigiani

Research output: Contribution to journalArticle

Abstract

Model-based approaches for combining gene expression data from multiple high throughput platforms can be sensitive to technological artifacts when the number of samples in each platform is small. This paper proposes simple tools for quantifying concordance in a small study of pancreatic cancer cells lines with an emphasis on visualizations that uncover intra- and inter-platform variation. Using this approach, we identify several transcripts from the integrative analysis whose over-or under-expression in pancreatic cancer cell lines was validated by qPCR.

Original languageEnglish (US)
Pages (from-to)257-264
Number of pages8
JournalCancer Informatics
Volume9
DOIs
StatePublished - Dec 30 2010

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Keywords

  • Cross-platform
  • Differential gene expression
  • Microarrays
  • Rank statistics

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Scharpf, R. B., Iacobuzio-Donahue, C. A., Cope, L., Ruczinski, I., Garrett-Mayer, E., Lakkur, S., Campagna, D., & Parmigiani, G. (2010). Cross-platform comparison of two pancreatic cancer phenotypes. Cancer Informatics, 9, 257-264. https://doi.org/10.4137/CIN.S5755