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Combined analysis reveals a core set of cycling genes

BACKGROUND: Global transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species. More recently, a number of studies have concluded that a surprisingly small number of genes conserved in two...

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Autores principales: Lu, Yong, Mahony, Shaun, Benos, Panayiotis V, Rosenfeld, Roni, Simon, Itamar, Breeden, Linda L, Bar-Joseph, Ziv
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323241/
https://www.ncbi.nlm.nih.gov/pubmed/17650318
http://dx.doi.org/10.1186/gb-2007-8-7-r146
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author Lu, Yong
Mahony, Shaun
Benos, Panayiotis V
Rosenfeld, Roni
Simon, Itamar
Breeden, Linda L
Bar-Joseph, Ziv
author_facet Lu, Yong
Mahony, Shaun
Benos, Panayiotis V
Rosenfeld, Roni
Simon, Itamar
Breeden, Linda L
Bar-Joseph, Ziv
author_sort Lu, Yong
collection PubMed
description BACKGROUND: Global transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species. More recently, a number of studies have concluded that a surprisingly small number of genes conserved in two or more species are periodically transcribed in these species. Combining and comparing data from multiple species is challenging because of noise in expression data, the different synchronization and scoring methods used, and the need to determine an accurate set of homologs. RESULTS: To solve these problems, we developed and applied a new algorithm to analyze expression data from multiple species simultaneously. Unlike previous studies, we find that more than 20% of cycling genes in budding yeast have cycling homologs in fission yeast and 5% to 7% of cycling genes in each of four species have cycling homologs in all other species. These conserved cycling genes display much stronger cell cycle characteristics in several complementary high throughput datasets. Essentiality analysis for yeast and human genes confirms these findings. Motif analysis indicates conservation in the corresponding regulatory mechanisms. Gene Ontology analysis and analysis of the genes in the conserved sets sheds light on the evolution of specific subfunctions within the cell cycle. CONCLUSION: Our results indicate that the conservation in cyclic expression patterns is much greater than was previously thought. These genes are highly enriched for most cell cycle categories, and a large percentage of them are essential, supporting our claim that cross-species analysis can identify the core set of cycling genes.
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spelling pubmed-23232412008-04-19 Combined analysis reveals a core set of cycling genes Lu, Yong Mahony, Shaun Benos, Panayiotis V Rosenfeld, Roni Simon, Itamar Breeden, Linda L Bar-Joseph, Ziv Genome Biol Research BACKGROUND: Global transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species. More recently, a number of studies have concluded that a surprisingly small number of genes conserved in two or more species are periodically transcribed in these species. Combining and comparing data from multiple species is challenging because of noise in expression data, the different synchronization and scoring methods used, and the need to determine an accurate set of homologs. RESULTS: To solve these problems, we developed and applied a new algorithm to analyze expression data from multiple species simultaneously. Unlike previous studies, we find that more than 20% of cycling genes in budding yeast have cycling homologs in fission yeast and 5% to 7% of cycling genes in each of four species have cycling homologs in all other species. These conserved cycling genes display much stronger cell cycle characteristics in several complementary high throughput datasets. Essentiality analysis for yeast and human genes confirms these findings. Motif analysis indicates conservation in the corresponding regulatory mechanisms. Gene Ontology analysis and analysis of the genes in the conserved sets sheds light on the evolution of specific subfunctions within the cell cycle. CONCLUSION: Our results indicate that the conservation in cyclic expression patterns is much greater than was previously thought. These genes are highly enriched for most cell cycle categories, and a large percentage of them are essential, supporting our claim that cross-species analysis can identify the core set of cycling genes. BioMed Central 2007 2007-07-24 /pmc/articles/PMC2323241/ /pubmed/17650318 http://dx.doi.org/10.1186/gb-2007-8-7-r146 Text en Copyright © 2007 Lu 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
Lu, Yong
Mahony, Shaun
Benos, Panayiotis V
Rosenfeld, Roni
Simon, Itamar
Breeden, Linda L
Bar-Joseph, Ziv
Combined analysis reveals a core set of cycling genes
title Combined analysis reveals a core set of cycling genes
title_full Combined analysis reveals a core set of cycling genes
title_fullStr Combined analysis reveals a core set of cycling genes
title_full_unstemmed Combined analysis reveals a core set of cycling genes
title_short Combined analysis reveals a core set of cycling genes
title_sort combined analysis reveals a core set of cycling genes
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323241/
https://www.ncbi.nlm.nih.gov/pubmed/17650318
http://dx.doi.org/10.1186/gb-2007-8-7-r146
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