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Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level

BACKGROUND: Genome projects have provided a vast amount of sequence information. Sequence comparison between species helps to establish functional catalogues within organisms and to study how they are maintained and modified across phylogenetic groups during evolution. Microarray studies allow us to...

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Autores principales: Jiménez, Jose L, Mitchell, Michael P, Sgouros, John G
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2003
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151285/
https://www.ncbi.nlm.nih.gov/pubmed/12537549
http://dx.doi.org/10.1186/gb-2002-4-1-r4
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author Jiménez, Jose L
Mitchell, Michael P
Sgouros, John G
author_facet Jiménez, Jose L
Mitchell, Michael P
Sgouros, John G
author_sort Jiménez, Jose L
collection PubMed
description BACKGROUND: Genome projects have provided a vast amount of sequence information. Sequence comparison between species helps to establish functional catalogues within organisms and to study how they are maintained and modified across phylogenetic groups during evolution. Microarray studies allow us to determine groups of genes with similar temporal regulation and perhaps also common regulatory upstream regions for binding of transcription factors. The integration of sequence and expression data is expected to refine our current annotations and provide some insight into the evolution of gene regulation across organisms. RESULTS: We have investigated how well the protein subcellular localization and functional categories established from clustering of orthologous genes agree with gene-expression data in Saccharomyces cerevisiae. An increase in the resolution of biologically meaningful classes is observed upon the combination of experiments under different conditions. The functional categories deduced by sequence comparison approaches are, in general, preserved at the level of expression and can sometimes interact into larger co-regulated networks, such as the protein translation process. Differences and similarities in the expression between cytoplasmic-mitochondrial and interspecies translation machineries complement evolutionary information from sequence similarity. CONCLUSIONS: Combination of several microarray experiments is a powerful tool for the identification of upstream regulatory motifs of yeast genes involved in protein synthesis. Comparison of these yeast co-regulated genes against the archaeal and bacterial operons indicates that the components of the protein translation process are conserved across organisms at the expression level with minor specific adaptations.
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spelling pubmed-1512852003-03-13 Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level Jiménez, Jose L Mitchell, Michael P Sgouros, John G Genome Biol Research BACKGROUND: Genome projects have provided a vast amount of sequence information. Sequence comparison between species helps to establish functional catalogues within organisms and to study how they are maintained and modified across phylogenetic groups during evolution. Microarray studies allow us to determine groups of genes with similar temporal regulation and perhaps also common regulatory upstream regions for binding of transcription factors. The integration of sequence and expression data is expected to refine our current annotations and provide some insight into the evolution of gene regulation across organisms. RESULTS: We have investigated how well the protein subcellular localization and functional categories established from clustering of orthologous genes agree with gene-expression data in Saccharomyces cerevisiae. An increase in the resolution of biologically meaningful classes is observed upon the combination of experiments under different conditions. The functional categories deduced by sequence comparison approaches are, in general, preserved at the level of expression and can sometimes interact into larger co-regulated networks, such as the protein translation process. Differences and similarities in the expression between cytoplasmic-mitochondrial and interspecies translation machineries complement evolutionary information from sequence similarity. CONCLUSIONS: Combination of several microarray experiments is a powerful tool for the identification of upstream regulatory motifs of yeast genes involved in protein synthesis. Comparison of these yeast co-regulated genes against the archaeal and bacterial operons indicates that the components of the protein translation process are conserved across organisms at the expression level with minor specific adaptations. BioMed Central 2003 2002-12-31 /pmc/articles/PMC151285/ /pubmed/12537549 http://dx.doi.org/10.1186/gb-2002-4-1-r4 Text en Copyright © 2002 Jiménez et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research
Jiménez, Jose L
Mitchell, Michael P
Sgouros, John G
Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
title Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
title_full Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
title_fullStr Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
title_full_unstemmed Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
title_short Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
title_sort microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151285/
https://www.ncbi.nlm.nih.gov/pubmed/12537549
http://dx.doi.org/10.1186/gb-2002-4-1-r4
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