Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species

  • Frederic Bastian
  • Gilles Parmentier
  • Julien Roux
  • Sebastien Moretti
  • Vincent Laudet
  • Marc Robinson-Rechavi
Conference paper

DOI: 10.1007/978-3-540-69828-9_12

Volume 5109 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Bastian F., Parmentier G., Roux J., Moretti S., Laudet V., Robinson-Rechavi M. (2008) Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. In: Bairoch A., Cohen-Boulakia S., Froidevaux C. (eds) Data Integration in the Life Sciences. DILS 2008. Lecture Notes in Computer Science, vol 5109. Springer, Berlin, Heidelberg

Abstract

Gene expression patterns are a key feature in understanding gene function, notably in development. Comparing gene expression patterns between animals is a major step in the study of gene function as well as of animal evolution. It also provides a link between genes and phenotypes. Thus we have developed Bgee, a database designed to compare expression patterns between animals, by implementing ontologies describing anatomies and developmental stages of species, and then designing homology relationships between anatomies and comparison criteria between developmental stages. To define homology relationships between anatomical features we have developed the software Homolonto, which uses a modified ontology alignment approach to propose homology relationships between ontologies. Bgee then uses these aligned ontologies, onto which heterogeneous expression data types are mapped. These already include microarrays and ESTs. Bgee is available at http://bgee.unil.ch/

Keywords

gene expression pattern homology ontology data integration 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Frederic Bastian
    • 1
    • 2
  • Gilles Parmentier
    • 1
    • 2
  • Julien Roux
    • 1
    • 2
  • Sebastien Moretti
    • 1
    • 2
  • Vincent Laudet
    • 3
  • Marc Robinson-Rechavi
    • 1
    • 2
  1. 1.Department of Ecology and EvolutionUniversity of Lausanne, quartier UNIL-SorgeLausanneSwitzerland
  2. 2.Swiss institute of bioinformaticsLausanneSwitzerland
  3. 3.Institut FédératifUniversité de Lyon, Institut de Génomique Fonctionnelle de Lyon, ENS Lyon, Université Lyon 1, CNRS, INRAFrance