The “street light syndrome”, or how protein taxonomy can bias experimental manipulations

Authors

  • Gabriel Markov,

    1. USM 501, Evolution des Régulations Endocriniennes. Muséum National d'Histoire Naturelle, Paris, France
    2. Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, Molecular Zoology team, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, INRA, Institut Fédératif 128 Biosciences Gerland Lyon Sud, France
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  • Guillaume Lecointre,

    1. UMR 7138 CNRS-UPMC-IRD-MNHN-ENS CP26 Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France
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  • Barbara Demeneix,

    1. USM 501, Evolution des Régulations Endocriniennes. Muséum National d'Histoire Naturelle, Paris, France
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  • Vincent Laudet

    Corresponding author
    1. Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, Molecular Zoology team, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, INRA, Institut Fédératif 128 Biosciences Gerland Lyon Sud, France
    • UMR 5242 du CNRS, Institut de Génomique Fonctionnelle de Lyon, Equipe de Zoologie Moléculaire. Université de Lyon, INRA IFR 128 BioSciences Lyon-Gerland, Ecole Normale Supérieure de Lyon 46, allée d'Italie 69364 Lyon Cedex 07, France.
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Abstract

In the genomics era, bioinformatic analysis, especially in non-model species, facilitates the identification and naming of numerous new proteins, the function of which is then inferred through homology searches. Here, we question certain aspects of these approaches. What are the criteria that permit such a determination? What are their limits? Naming is classifying. We review the different criteria that are used to name a protein and discuss their constraints. We observe that the name given to a protein often introduces a bias for further functional analyses, a bias that is not often taken into account when analysing results. Last but not least, the heterogeneity of criteria used for naming proteins leads to self-inconsistent or contradictory protein classification that is potentially misleading. Finally, we recommend a wider use of phylogenetic criteria in protein naming. BioEssays 30:349–357, 2008. © 2008 Wiley Periodicals, Inc.

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