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Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome

The genome of budding yeast (Saccharomyces cerevisiae) contains approximately 5800 protein-encoding genes, the majority of which are associated with some known biological function. Yet the extent of amino acid sequence conservation of these genes over all phyla has only been partially examined. Here...

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Autores principales: Gibney, Patrick A., Hickman, Mark J., Bradley, Patrick H., Matese, John C., Botstein, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737173/
https://www.ncbi.nlm.nih.gov/pubmed/23749449
http://dx.doi.org/10.1534/g3.113.006585
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author Gibney, Patrick A.
Hickman, Mark J.
Bradley, Patrick H.
Matese, John C.
Botstein, David
author_facet Gibney, Patrick A.
Hickman, Mark J.
Bradley, Patrick H.
Matese, John C.
Botstein, David
author_sort Gibney, Patrick A.
collection PubMed
description The genome of budding yeast (Saccharomyces cerevisiae) contains approximately 5800 protein-encoding genes, the majority of which are associated with some known biological function. Yet the extent of amino acid sequence conservation of these genes over all phyla has only been partially examined. Here we provide a more comprehensive overview and visualization of the conservation of yeast genes and a means for browsing and exploring the data in detail, down to the individual yeast gene, at http://yeast-phylogroups.princeton.edu. We used data from the OrthoMCL database, which has defined orthologs from approximately 150 completely sequenced genomes, including diverse representatives of the archeal, bacterial, and eukaryotic domains. By clustering genes based on similar patterns of conservation, we organized and visualized all the protein-encoding genes in yeast as a single heat map. Most genes fall into one of eight major clusters, called “phylogroups.” Gene ontology analysis of the phylogroups revealed that they were associated with specific, distinct trends in gene function, generalizations likely to be of interest to a wide range of biologists.
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spelling pubmed-37371732013-08-08 Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome Gibney, Patrick A. Hickman, Mark J. Bradley, Patrick H. Matese, John C. Botstein, David G3 (Bethesda) Investigations The genome of budding yeast (Saccharomyces cerevisiae) contains approximately 5800 protein-encoding genes, the majority of which are associated with some known biological function. Yet the extent of amino acid sequence conservation of these genes over all phyla has only been partially examined. Here we provide a more comprehensive overview and visualization of the conservation of yeast genes and a means for browsing and exploring the data in detail, down to the individual yeast gene, at http://yeast-phylogroups.princeton.edu. We used data from the OrthoMCL database, which has defined orthologs from approximately 150 completely sequenced genomes, including diverse representatives of the archeal, bacterial, and eukaryotic domains. By clustering genes based on similar patterns of conservation, we organized and visualized all the protein-encoding genes in yeast as a single heat map. Most genes fall into one of eight major clusters, called “phylogroups.” Gene ontology analysis of the phylogroups revealed that they were associated with specific, distinct trends in gene function, generalizations likely to be of interest to a wide range of biologists. Genetics Society of America 2013-08-01 /pmc/articles/PMC3737173/ /pubmed/23749449 http://dx.doi.org/10.1534/g3.113.006585 Text en Copyright © 2013 Gibney et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Gibney, Patrick A.
Hickman, Mark J.
Bradley, Patrick H.
Matese, John C.
Botstein, David
Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome
title Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome
title_full Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome
title_fullStr Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome
title_full_unstemmed Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome
title_short Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome
title_sort phylogenetic portrait of the saccharomyces cerevisiae functional genome
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737173/
https://www.ncbi.nlm.nih.gov/pubmed/23749449
http://dx.doi.org/10.1534/g3.113.006585
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