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ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system

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 immuno...

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Detalles Bibliográficos
Autores principales: Ortutay, Csaba, Siermala, Markku, Vihinen, Mauno
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1845140/
https://www.ncbi.nlm.nih.gov/pubmed/17376226
http://dx.doi.org/10.1186/1745-7580-3-4
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author Ortutay, Csaba
Siermala, Markku
Vihinen, Mauno
author_facet Ortutay, Csaba
Siermala, Markku
Vihinen, Mauno
author_sort Ortutay, Csaba
collection PubMed
description 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 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 K(a)/K(s )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.
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spelling pubmed-18451402007-04-01 ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system Ortutay, Csaba Siermala, Markku Vihinen, Mauno Immunome Res Database 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 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 K(a)/K(s )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. BioMed Central 2007-03-21 /pmc/articles/PMC1845140/ /pubmed/17376226 http://dx.doi.org/10.1186/1745-7580-3-4 Text en Copyright © 2007 Ortutay et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Ortutay, Csaba
Siermala, Markku
Vihinen, Mauno
ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
title ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
title_full ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
title_fullStr ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
title_full_unstemmed ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
title_short ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system
title_sort immtree: database of evolutionary relationships of genes and proteins in the human immune system
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1845140/
https://www.ncbi.nlm.nih.gov/pubmed/17376226
http://dx.doi.org/10.1186/1745-7580-3-4
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