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Meta-Analysis and Gene Set Analysis of Archived Microarrays Suggest Implication of the Spliceosome in Metastatic and Hypoxic Phenotypes

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  • Bertrand De Meulder
  • Fabrice Berger
  • Eric Bareke
  • Sophie Depiereux
  • Carine Michiels
  • Eric Depiereux

Abstract

We propose to make use of the wealth of underused DNA chip data available in public repositories to study the molecular mechanisms behind the adaptation of cancer cells to hypoxic conditions leading to the metastatic phenotype. We have developed new bioinformatics tools and adapted others to identify with maximum sensitivity those genes which are expressed differentially across several experiments. The comparison of two analytical approaches, based on either Over Representation Analysis or Functional Class Scoring, by a meta-analysis-based approach, led to the retrieval of known information about the biological situation – thus validating the model – but also more importantly to the discovery of the previously unknown implication of the spliceosome, the cellular machinery responsible for mRNA splicing, in the development of metastasis.

Suggested Citation

  • Bertrand De Meulder & Fabrice Berger & Eric Bareke & Sophie Depiereux & Carine Michiels & Eric Depiereux, 2014. "Meta-Analysis and Gene Set Analysis of Archived Microarrays Suggest Implication of the Spliceosome in Metastatic and Hypoxic Phenotypes," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-13, January.
    • Handle: RePEc:plo:pone00:0086699
    DOI: 10.1371/journal.pone.0086699
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    Cited by:

    1. Sophie Depiereux & Florence Le Gac & Bertrand De Meulder & Michael Pierre & Raphaël Helaers & Yann Guiguen & Patrick Kestemont & Eric Depiereux, 2015. "Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol," PLOS ONE, Public Library of Science, vol. 10(9), pages 1-27, September.

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