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PHOENIX, a web interface for (re)analysis of microarray data

  • Research Article
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Central European Journal of Biology

Abstract

Microarrays are tools to study the expression profile of an entire genome. Technology, statistical tools and biological knowledge in general have evolved over the past ten years and it is now possible to improve analysis of previous datasets. We have developed a web interface called PHOENIX that automates the analysis of microarray data from preprocessing to the evaluation of significance through manual or automated parameterization. At each analytical step, several methods are possible for (re)analysis of data. PHOENIX evaluates a consensus score from several methods and thus determines the performance level of the best methods (even if the best performing method is not known). With an estimate of the true gene list, PHOENIX can evaluate the performance of methods or compare the results with other experiments. Each method used for differential expression analysis and performance evaluation has been implemented in the PEGASE back-end package, along with additional tools to further improve PHOENIX. Future developments will involve the addition of steps (CDF selection, geneset analysis, meta-analysis), methods (PLIER, ANOVA, Limma), benchmarks (spike-in and simulated datasets), and illustration of the results (automatically generated report).

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Authors and Affiliations

  1. Unit of Research in Molecular Biology (URBM), University of Namur (F.U.N.D.P.), B-5000, Namur, Belgium

    Fabrice Berger, Benoît De Hertogh, Michaël Pierre, Eric Bareke, Anthoula Gaigneaux & Eric Depiereux

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  1. Fabrice Berger
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  2. Benoît De Hertogh
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  3. Michaël Pierre
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  4. Eric Bareke
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  5. Anthoula Gaigneaux
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  6. Eric Depiereux
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Corresponding author

Correspondence to Eric Depiereux.

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These authors contributed equally to this work

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Berger, F., De Hertogh, B., Pierre, M. et al. PHOENIX, a web interface for (re)analysis of microarray data. cent.eur.j.biol. 4, 603–618 (2009). https://doi.org/10.2478/s11535-009-0055-8

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  • DOI: https://doi.org/10.2478/s11535-009-0055-8

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