Exploiting microarrays to reveal differential gene expression in the nervous system - PubMed (original) (raw)

Exploiting microarrays to reveal differential gene expression in the nervous system

Robert S Griffin et al. Genome Biol. 2003.

Abstract

Microarrays have been used in a wide variety of experimental systems, but realizing their full potential is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differential gene expression and regulation in the nervous system.

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Figures

Figure 1

Figure 1

Filtering array data. It is essential to remove as many false positives as possible at the earliest stages of analysis. Random errors occurring in oligonucleotide array data were assessed by comparing three biologically independent control arrays to three other biologically independent control arrays. Genes with a t test p < 0.05 in this comparison are plotted (a). Comparison of these results with the frequency of genes differing at p < 0.05 between control and experimental triplicate arrays (b) were used to define a set of criteria based on present/absent, fold change, t test p value, and a signal threshold that minimized the estimated random error [31].

Figure 2

Figure 2

Candidate gene identification. Schematic of a protocol that may be used to select a few genes that obey a defined set of criteria. See text for further details.

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