Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species

  • Frederic Bastian
  • Gilles Parmentier
  • Julien Roux
  • Sebastien Moretti
  • Vincent Laudet
  • Marc Robinson-Rechavi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5109)

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 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Carroll, S.: Endless Forms Most Beautiful: The New Science of Evo Devo and The Making of the Animal Kingdom. W. W. Norton & Company, New York (2005)Google Scholar
  2. 2.
    Yanai, I., Graur, D., et al.: Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. Omics 8, 15–24 (2004)CrossRefGoogle Scholar
  3. 3.
    Jordan, I.K., Marino-Ramirez, L., et al.: Evolutionary significance of gene expression divergence. Gene 345, 119–126 (2005)CrossRefGoogle Scholar
  4. 4.
    Schlicht, M., Matysiak, B., et al.: Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium. BMC Genomics 5, 58 (2004)CrossRefGoogle Scholar
  5. 5.
    Gu, Z., Nicolae, D., et al.: Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 18, 609–613 (2002)CrossRefGoogle Scholar
  6. 6.
    Gu, X., Zhang, Z., et al.: Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc. Natl. Acad. Sci. USA 102, 707–712 (2005)CrossRefGoogle Scholar
  7. 7.
    He, X., Zhang, J.: Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169, 1157–1164 (2005)CrossRefGoogle Scholar
  8. 8.
    Sprague, J., Clements, D., et al.: The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. 31, 241–243 (2003)CrossRefGoogle Scholar
  9. 9.
    Shvaiko, P., Euzenat, J.: Ontology Matching. Springer, Heidelberg (2007)MATHGoogle Scholar
  10. 10.
    Smith, B., Ashburner, M., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255 (2007)CrossRefGoogle Scholar
  11. 11.
    Jeffery, J.E., Bininda-Emonds, O.R., et al.: A new technique for identifying sequence heterochrony. Syst. Biol. 54, 230–240 (2005)CrossRefGoogle Scholar
  12. 12.
    Lee, C.K., Sunkin, S.M., et al.: Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data. Genome biology 9, R23 (2008)Google Scholar
  13. 13.
    Kuo, W.P., Liu, F., et al.: A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat. Biotechnol. 24, 832–840 (2006)CrossRefGoogle Scholar
  14. 14.
    Wheeler, D.L., Barrett, T., et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36, 13–21 (2008)Google Scholar
  15. 15.
    Parkinson, H., Kapushesky, M., et al.: ArrayExpress–a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35, 747–750 (2007)Google Scholar
  16. 16.
    Audic, S., Claverie, J.M.: The significance of digital gene expression profiles. Genome Res. 7, 986–995 (1997)Google Scholar
  17. 17.
    Liu, W.M., Mei, R., et al.: Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18, 1593–1599 (2002)CrossRefGoogle Scholar
  18. 18.
    Choe, S.E., Boutros, M., et al.: Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome biology 6, R16 (2005)Google Scholar
  19. 19.
    Schuster, E.F., Blanc, E., et al.: Correcting for sequence biases in present/absent calls. Genome biology 8, R125 (2007)Google Scholar
  20. 20.
    Wu, Z., Irizarry, R.A., et al.: A Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association 99, 909–917 (2004)MATHCrossRefMathSciNetGoogle Scholar
  21. 21.
    Kruger, A., Hofmann, O., et al.: Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome biology 8, R229 (2007)Google Scholar
  22. 22.
    Aitken, S.: Formalizing concepts of species, sex and developmental stage in anatomical ontologies. Bioinformatics 21, 2773–2779 (2005)CrossRefGoogle Scholar
  23. 23.
    Eppig, J.T., Blake, J.A., et al.: The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res. 35, 630–637 (2007)CrossRefGoogle Scholar
  24. 24.
    Bowes, J.B., Snyder, K.A., et al.: Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 36, 761–767 (2008)CrossRefGoogle Scholar
  25. 25.
    Magdaleno, S., Jensen, P., et al.: BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol. 4, e86 (2006)Google Scholar
  26. 26.
    Ashburner, M., Ball, C.A., et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25–29 (2000)CrossRefGoogle Scholar
  27. 27.
    Hubbard, T.J., Aken, B.L., et al.: Ensembl 2007. Nucleic Acids Res. 35, 610–617 (2007)CrossRefGoogle Scholar

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

Personalised recommendations