Database
ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
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* Corresponding author: Mauno Vihinen mauno.vihinen@uta.fi
1 Institute of Medical Technology, FI-33014 University of Tampere, Finland
2 Research Unit, Tampere University Hospital, FI-33520 Tampere, Finland
Immunome Research 2007, 3:4 doi:10.1186/1745-7580-3-4
Published: 21 March 2007Abstract
Background
The immune system, which is a complex machinery, is based on the highly coordinated expression of a wide array of genes and proteins. The evolutionary history of the human immune system is not well characterised. Although several studies related to the development and evolution of immunological processes have been published, a full-scale genome-based analysis is still missing. A database focused on the evolutionary relationships of immune related genes would contribute to and facilitate research on immunology and evolutionary biology.
Results
An Internet resource called ImmTree http://bioinf.uta.fi/ImmTree webcite was constructed for studying the evolution and evolutionary trees of the human immune system. ImmTree contains information about orthologs in 80 species collected from the HomoloGene, OrthoMCL and EGO databases. In addition to phylogenetic trees, the service provides data for the comparison of human-mouse ortholog pairs, including synonymous and non-synonymous mutation rates, Z values, and Ka/Ks quotients. A versatile search engine allows complex queries from the database. Currently, data is available for 847 human immune system related genes and proteins.
Conclusion
ImmTree provides a unique data set of genes and proteins from the human immune system, their phylogenetics, and information for comparisons of human-mouse ortholog pairs, synonymous and non-synonymous mutation rates, as well as other statistical information.