The methodology used to measure differential gene expression affects the outcome

Yongzeng Ding, Li Xu, Borko D. Jovanovic, Irene B. Helenowski, David Lee Kelly, William J. Catalona, Ximing J. Yang, Michael Pins, Raymond C. Bergan

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Confirmation of gene expression by a second methodology is critical in order to detect false-positive findings associated with microarrays. However, the impact of methodology upon the measurement of gene expression has not been rigorously evaluated. In the current study, we compared differential gene expression between PC3 and PC3-M human prostate cancer cell lines using three separate methods: microarray, quantitative RT/PCR (qRT/PCR), and Northern blotting. The PC3 to PC3-M ratio of gene expression was determined for each of 24 different genes evaluated, by each of the three methods. Comparison of gene expression ratios between Northern and microarray, Northern and qRT/PCR, and microarray and qRT/PCR, gave correlation coefficients (r) of 0.72, 0.39, and 0.63, respectively. In each instance, one to two outlier genes were apparent. Their exclusion from analysis gave r values of 0.79, 0.72, and 0.83, respectively. These findings demonstrate that the assessment of differential gene expression is dependent upon the methodology used. In each situation where outcome between different methodologies was compared, the presence of a relatively limited number of outlier genes precludes high overall correlation between the methods. Validation of gene expression by different methods should be performed whenever possible.

Original languageEnglish (US)
Pages (from-to)321-330
Number of pages10
JournalJournal of Biomolecular Techniques
Volume18
Issue number5
StatePublished - Dec 1 2007

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Gene Expression
Polymerase Chain Reaction
Genes
Northern Blotting
Prostatic Neoplasms
Cell Line

Keywords

  • Gene expression
  • Microarray
  • Northern blot
  • Quantitative PCR

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Ding, Y., Xu, L., Jovanovic, B. D., Helenowski, I. B., Kelly, D. L., Catalona, W. J., ... Bergan, R. C. (2007). The methodology used to measure differential gene expression affects the outcome. Journal of Biomolecular Techniques, 18(5), 321-330.

The methodology used to measure differential gene expression affects the outcome. / Ding, Yongzeng; Xu, Li; Jovanovic, Borko D.; Helenowski, Irene B.; Kelly, David Lee; Catalona, William J.; Yang, Ximing J.; Pins, Michael; Bergan, Raymond C.

In: Journal of Biomolecular Techniques, Vol. 18, No. 5, 01.12.2007, p. 321-330.

Research output: Contribution to journalArticle

Ding, Y, Xu, L, Jovanovic, BD, Helenowski, IB, Kelly, DL, Catalona, WJ, Yang, XJ, Pins, M & Bergan, RC 2007, 'The methodology used to measure differential gene expression affects the outcome', Journal of Biomolecular Techniques, vol. 18, no. 5, pp. 321-330.
Ding Y, Xu L, Jovanovic BD, Helenowski IB, Kelly DL, Catalona WJ et al. The methodology used to measure differential gene expression affects the outcome. Journal of Biomolecular Techniques. 2007 Dec 1;18(5):321-330.
Ding, Yongzeng ; Xu, Li ; Jovanovic, Borko D. ; Helenowski, Irene B. ; Kelly, David Lee ; Catalona, William J. ; Yang, Ximing J. ; Pins, Michael ; Bergan, Raymond C. / The methodology used to measure differential gene expression affects the outcome. In: Journal of Biomolecular Techniques. 2007 ; Vol. 18, No. 5. pp. 321-330.
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