Not only diseases, evolution too!

In its latest issue, Nature is writing about how the one million gene expression data sets currently publicly available can help researchers understand diseases (Monya Baker, Gene data to hit milestone (2012) Nature 487: pp. 282-283). However, that’s not all of it. This wealth of data can also help scientists study evolution. How has the expression of your favorite gene evolved in different species? The answer is only one of the pieces of information hiding among these one million data sets, waiting to be recovered.

And that’s why the database Bgee is integrating public gene expression data from different animal species and mapping these data to anatomy and development. Our purpose is to bring resources to the community to compare gene expression between species and help answer evolutionary questions. To this aim Bgee also provides homology relationships between organs of different species.

Here are some examples of uses of Bgee:

  • How has the expression of your favorite gene evolved in different species? Philip et al. used Bgee to answer this very question for the Retinoid X receptors of vertebrates. During embryonic development and for various homologous anatomical structures, they compared the expression of the zebrafish paralogs between each other and versus the mouse ortholog singleton.
  • Analyses don’t need to be restricted to a single gene. The expression of scores of genes can be surveyed at the same time to assay its evolution after gene duplication as in Huerta-Cepas et al. or its conservation between homologous organs of different species as in Piasecka et al.
  • Data and studies aren’t solely limited to protein-coding genes either. Roux et al. retrieved miRNA expression data from Bgee and used it to study how it differed between miRNA of different ages and between human and mouse tissues.

Philip et al. Adaptive evolution of the Retinoid X receptor in vertebrates (2012) Genomics 99(2): pp. 81-89

Huerta-Cepas et al. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication (2011) Briefings in bioinformatics 12(5): pp. 442-448

Piasecka et al. Comparative modular analysis of gene expression in vertebrate organs (2012) BMC Genomics 13:124 doi:10.1186/1471-2164-13-124

Roux et al. Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs (2012) Nucleic Acids Research doi: 10.1093/nar/gks279

About bgeedb

This is the blog of the database of gene expression evolution Bgee, at University of Lausanne and Swiss Institute of Bioinformatics.
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