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/
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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)
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)
Jordan, I.K., Marino-Ramirez, L., et al.: Evolutionary significance of gene expression divergence. Gene 345, 119–126 (2005)
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)
Gu, Z., Nicolae, D., et al.: Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 18, 609–613 (2002)
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)
He, X., Zhang, J.: Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169, 1157–1164 (2005)
Sprague, J., Clements, D., et al.: The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. 31, 241–243 (2003)
Shvaiko, P., Euzenat, J.: Ontology Matching. Springer, Heidelberg (2007)
Smith, B., Ashburner, M., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255 (2007)
Jeffery, J.E., Bininda-Emonds, O.R., et al.: A new technique for identifying sequence heterochrony. Syst. Biol. 54, 230–240 (2005)
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)
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)
Wheeler, D.L., Barrett, T., et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36, 13–21 (2008)
Parkinson, H., Kapushesky, M., et al.: ArrayExpress–a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35, 747–750 (2007)
Audic, S., Claverie, J.M.: The significance of digital gene expression profiles. Genome Res. 7, 986–995 (1997)
Liu, W.M., Mei, R., et al.: Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18, 1593–1599 (2002)
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)
Schuster, E.F., Blanc, E., et al.: Correcting for sequence biases in present/absent calls. Genome biology 8, R125 (2007)
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)
Kruger, A., Hofmann, O., et al.: Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome biology 8, R229 (2007)
Aitken, S.: Formalizing concepts of species, sex and developmental stage in anatomical ontologies. Bioinformatics 21, 2773–2779 (2005)
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)
Bowes, J.B., Snyder, K.A., et al.: Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 36, 761–767 (2008)
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)
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)
Hubbard, T.J., Aken, B.L., et al.: Ensembl 2007. Nucleic Acids Res. 35, 610–617 (2007)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
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. https://doi.org/10.1007/978-3-540-69828-9_12
Download citation
DOI: https://doi.org/10.1007/978-3-540-69828-9_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69827-2
Online ISBN: 978-3-540-69828-9
eBook Packages: Computer ScienceComputer Science (R0)