Abstract
BackgroundThe 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.ResultsAn Internet resource called ImmTree 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.ConclusionImmTree 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.
Highlights
The immune system, which is a complex machinery, is based on the highly coordinated expression of a wide array of genes and proteins
One can search for protein domains either by InterPro [19] id or name of the domain
ImmTree is a dedicated resource considering the special needs of researchers of evolution of the immune system
Summary
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. Numerous processes are necessary for mounting adaptive and innate immune responses to protect an individual from invading organisms and molecules. The different processes and pathways of the immune system have evolved gradually and become increasingly complex. More ancient innate or intrinsic immunity has been further complemented by adaptive processes, which provide a specific response when required. The evolution of certain immunological protein groups of the human immunome have already been studied. Five gene groups of the NF-κB signaling pathway in vertebrates and insects [1], or the evolution of the interleukin-1 protein family in vertebrates [2] are extensively studied. To explore the molecular evolution of the human immune system, a ref-
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