A simple analysis of gene expression and variability in gene arrays based on repeated observations.

B. D. Jovanovic, S. Huang, Y. Liu, K. N. Naguib, Raymond Bergan

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

BACKGROUND AND AIM: At the present time there is an explosion of research in the area of gene arrays, and their application for detection of genes related to disease as well as its therapeutic manipulation. However, as individual arrays are expensive, comparisons of gene expression are often not repeated. In the current study, gene array experiments were repeated multiple times in order to understand the variability associated with measurements of gene expression. By focusing upon the pharmacologically important target of prostate cancer cell detachment, the current study employed multiple repeats of gene array experiments. This was used as a model system to demonstrate the utility of the experimental approach and statistical methods used. METHODS: To identify genes involved in detachment of prostate cancer cells (a prerequisite for metastases), we analyzed gene expression changes in metastatic variant PC3-M cells undergoing spontaneous detachment in culture. The data were interpreted using an elementary statistical approach. The between-experiment and within-repeated-observations variability in expression of 3582 genes possibly related to prostate cancer was also evaluated. RESULTS: One important gene related to prostate cell detachment was identified, based on the magnitude of its change in expression, as measured by a ratio of the expression after cell detachment and expression before detachment. On average, the variation between experiments was greater by about 30 to 40% than the variation between repeated observations. CONCLUSION: These findings have implications relating to the use of gene arrays to detect variance of gene expression, and should be taken into consideration in the prospective design of array experiments.

Original languageEnglish (US)
Pages (from-to)145-152
Number of pages8
JournalAmerican journal of pharmacogenomics : genomics-related research in drug development and clinical practice
Volume1
Issue number2
StatePublished - 2001
Externally publishedYes

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Gene Expression
Genes
Prostatic Neoplasms
Explosions
Prostate
Neoplasm Metastasis
Research
Therapeutics

ASJC Scopus subject areas

  • Pharmacology
  • Molecular Medicine
  • Genetics

Cite this

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title = "A simple analysis of gene expression and variability in gene arrays based on repeated observations.",
abstract = "BACKGROUND AND AIM: At the present time there is an explosion of research in the area of gene arrays, and their application for detection of genes related to disease as well as its therapeutic manipulation. However, as individual arrays are expensive, comparisons of gene expression are often not repeated. In the current study, gene array experiments were repeated multiple times in order to understand the variability associated with measurements of gene expression. By focusing upon the pharmacologically important target of prostate cancer cell detachment, the current study employed multiple repeats of gene array experiments. This was used as a model system to demonstrate the utility of the experimental approach and statistical methods used. METHODS: To identify genes involved in detachment of prostate cancer cells (a prerequisite for metastases), we analyzed gene expression changes in metastatic variant PC3-M cells undergoing spontaneous detachment in culture. The data were interpreted using an elementary statistical approach. The between-experiment and within-repeated-observations variability in expression of 3582 genes possibly related to prostate cancer was also evaluated. RESULTS: One important gene related to prostate cell detachment was identified, based on the magnitude of its change in expression, as measured by a ratio of the expression after cell detachment and expression before detachment. On average, the variation between experiments was greater by about 30 to 40{\%} than the variation between repeated observations. CONCLUSION: These findings have implications relating to the use of gene arrays to detect variance of gene expression, and should be taken into consideration in the prospective design of array experiments.",
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AU - Huang, S.

AU - Liu, Y.

AU - Naguib, K. N.

AU - Bergan, Raymond

PY - 2001

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