BIOINFORMATICS APPLICATIONS NOTE
Vol. 18 no. 6 2002 Pages 888–889
Arrayplot for visualization and normalization of cDNA microarray data Philippe Marc ∗ and Claude Jacq ´ etique ´ ´ ´ Laboratoire de Gen Moleculaire (UMR CNRS 8541) Ecole Normale Superieure, 46 rue d’Ulm, 75005, Paris, France Received on November 24, 2001; revised on January 4, 2002; accepted on January 24, 2002
ABSTRACT Summary: Arrayplot is an application which allows filtering, visualization and normalization of raw cDNA microarray data. Availability: MS-Windows binaries are freely available for non-profit use at http://www.biologie.ens.fr/yeast-publi. html Contact:
[email protected] Supplementary information: Scripts for online creation of Arrayplot files are available at http://transcriptome.ens. fr/lgm bioinfo/
INTRODUCTION DNA microarrays are a very powerful tool for comparing gene expression of thousands of genes. This technology is becoming widely accessible, but the data analysis tools are rarely provided by microchip manufacturers. Arrayplot is a user-friendly tool which filters, normalizes and shows results from DNA microarray experiments. OVERVIEW The main purpose of Arrayplot is to show results from a cDNA microarray experiment as an interactive plot of fluorochrome intensities (Figure 1). This plot shows the ratio, but it also keeps the intensity data, thus allowing genes that show altered transcription profiles to be distinguished quickly by zooming on corresponding regions of the plot. All relevant available information can be displayed by clicking on a gene: ID, gene, ratio, normalized ratio (see below), and link to gene page from external databases. Some common cDNA microarray output file format (Genepix, Imagene, ScanAlyse, . . . ) can be converted to arrayplot files via an interface that can be used to choose foreground calculation mode and background correction, to filter data according to spot quality (flag status), to enter a normalization coefficient and to create links to external databases. ∗ To whom correspondence should be addressed.
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Fig. 1. Typical Arrayplot screen showing logarithmic representation of a yeast genome wide cDNA microarray experiment.
Arrayplot is also a convenient tool for handling the fluorochrome channels normalization step (Schena et al., 1995). The normalization coefficient can be obtained by manually adjusting the 1:1 ratio bar in the cloud. It can be adjusted in the median of points if one postulates that most gene expression is stable (Devaux et al., 2001), or it can be adjusted in invariant reference genes such as housekeeping genes, genomic DNA spots (DeRisi et al., 1997) or external references (Eickhoff et al., 1999). For this purpose, it is possible to highlight particular genes in the plot. A more detailed description of Arrayplot features and a tutorial can be found at our website (http://www.biologie. ens.fr/yeast-publi.html).
ACKNOWLEDGEMENTS Thanks to Bernard Martin, Frederic Devaux, Yann Denis and Marie Claude Potier for helpful discussion. This work was supported by the Association pour la Recherche contre le Cancer (ARC No. 5691) and by MENRT. c Oxford University Press 2002
Arrayplot and cDNA microarray data
REFERENCES DeRisi,J.L. et al. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680–686. Devaux,F. et al. (2001) An artificial transcription activator mimics the genome-wide properties of the yeast Pdr1 transcription factor. EMBO Rep., 2, 493–498.
Eickhoff,B. et al. (1999) Normalization of array hybridization experiments in differential gene expression analysis. Nucleic Acids Res., 27, e33. Schena,M.D. et al. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467–470.
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