Improved procedures to mine data obtained from spotted cDNA arrays

Andrei D. Iacobas, Marcia Urban, Aldo B. Massimi, David C. Spray

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

We studied six types of errors that affect the experimental results obtained with the spotted cDNA technology, proposing a new experimental strategy and a four-step algorithm to improve data accuracy. In an experiment analyzed with this method, mRNA extracted from neuroblastoma (N2A) cells and a clone transfected with the neuronal gap junction protein C × 36 were hybridized on 10 chips, each spotted with 2512 known mouse cDNAs.We found 53 upregulated and 23 downregulated genes with expression ratios exceeding 1.5-fold. By contrast, the newly introduced standard gene expression score, which considers the normal variability of gene expression in the reference cells, revealed that C × 36 transfection (p < 0.05) upregulated 161 genes and downregulated 61 genes.These results demonstrate the necessity to correct the raw data obtained from cDNA microarrays for systematic errors and indicate that use of the standard expression score significantly extends the identification of gene expression changes following experimental intervention.

Original languageEnglish (US)
Pages (from-to)5-19
Number of pages15
JournalJournal of Biomolecular Techniques
Volume13
Issue number1
StatePublished - Mar 2002

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Oligonucleotide Array Sequence Analysis
Gene Expression
Down-Regulation
Complementary DNA
Electrical Synapses
Connexins
Protein C
Neuroblastoma
Genes
Transfection
Clone Cells
Technology
Messenger RNA

Keywords

  • CDNA microarray
  • Connexin 36
  • Gap junction
  • Neuroblastoma
  • Standard score of gene expression

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Improved procedures to mine data obtained from spotted cDNA arrays. / Iacobas, Andrei D.; Urban, Marcia; Massimi, Aldo B.; Spray, David C.

In: Journal of Biomolecular Techniques, Vol. 13, No. 1, 03.2002, p. 5-19.

Research output: Contribution to journalArticle

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