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Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs

BACKGROUND: Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correla...

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Detalles Bibliográficos
Autores principales: Chiba, Hirokazu, Yamashita, Riu, Kinoshita, Kengo, Nakai, Kenta
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335122/
https://www.ncbi.nlm.nih.gov/pubmed/18384671
http://dx.doi.org/10.1186/1471-2164-9-152
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author Chiba, Hirokazu
Yamashita, Riu
Kinoshita, Kengo
Nakai, Kenta
author_facet Chiba, Hirokazu
Yamashita, Riu
Kinoshita, Kengo
Nakai, Kenta
author_sort Chiba, Hirokazu
collection PubMed
description BACKGROUND: Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial. RESULTS: We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation. CONCLUSION: Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.
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spelling pubmed-23351222008-04-25 Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs Chiba, Hirokazu Yamashita, Riu Kinoshita, Kengo Nakai, Kenta BMC Genomics Research Article BACKGROUND: Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial. RESULTS: We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation. CONCLUSION: Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution. BioMed Central 2008-04-02 /pmc/articles/PMC2335122/ /pubmed/18384671 http://dx.doi.org/10.1186/1471-2164-9-152 Text en Copyright © 2008 Chiba 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 Research Article
Chiba, Hirokazu
Yamashita, Riu
Kinoshita, Kengo
Nakai, Kenta
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
title Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
title_full Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
title_fullStr Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
title_full_unstemmed Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
title_short Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
title_sort weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335122/
https://www.ncbi.nlm.nih.gov/pubmed/18384671
http://dx.doi.org/10.1186/1471-2164-9-152
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