Minimization of transcriptional temporal noise and scale invariance in the yeast genome
Autor(a) principal: | |
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Data de Publicação: | 2007 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNIFESP |
Texto Completo: | http://repositorio.unifesp.br/11600/43718 http://www.funpecrp.com.br/gmr/year2007/vol2-6/gmr0318_abstract.htm |
Resumo: | The analysis of transcriptional temporal noise could be an interesting means to study gene expression dynamics and stochasticity in eukaryotes. To study the statistical distributions of temporal noise in the eukaryotic model system Saccharomyces cerevisiae, we analyzed microarray data corresponding to one cell cycle for 6200 genes. We found that the temporal noise follows a lognormal distribution with scale invariance at the genome, chromosomal and sub-chromosomal levels. Correlation of temporal noise with the codon adaptation index suggests that at least 70% of all protein-coding genes are a noise minimization core of the genome. Accordingly, a mathematical model of individual gene expression dynamics was proposed, using an operator theoretical approach, which reveals strict conditions for noise variability and a possible global noise minimization/optimization strategy at the genome level. Our model and data show that minimal noise does not correspond to genes obeying a strictly deterministic dynamics. The natural strategy of minimization consists in equating the mean of the absolute value of the relative variation of the expression level (alpha) with noise (eta). We hypothesize that the temporal noise pattern is an emergent property of the genome and shows how the dynamics of gene expression could be related to chromosomal organization. |
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Ferreira, R. C. [UNIFESP]Bosco, Francisco [UNIFESP]Paiva, Paulo Bandiera [UNIFESP]Briones, Marcelo Ribeiro da Silva [UNIFESP]Universidade Federal de São Paulo (UNIFESP)2018-06-15T17:30:20Z2018-06-15T17:30:20Z2007-01-01Genetics And Molecular Research. Ribeirao Preto: Funpec-editora, v. 6, n. 2, p. 397-414, 2007.1676-5680http://repositorio.unifesp.br/11600/43718http://www.funpecrp.com.br/gmr/year2007/vol2-6/gmr0318_abstract.htmWOS000251696400018.pdfWOS:000251696400018The analysis of transcriptional temporal noise could be an interesting means to study gene expression dynamics and stochasticity in eukaryotes. To study the statistical distributions of temporal noise in the eukaryotic model system Saccharomyces cerevisiae, we analyzed microarray data corresponding to one cell cycle for 6200 genes. We found that the temporal noise follows a lognormal distribution with scale invariance at the genome, chromosomal and sub-chromosomal levels. Correlation of temporal noise with the codon adaptation index suggests that at least 70% of all protein-coding genes are a noise minimization core of the genome. Accordingly, a mathematical model of individual gene expression dynamics was proposed, using an operator theoretical approach, which reveals strict conditions for noise variability and a possible global noise minimization/optimization strategy at the genome level. Our model and data show that minimal noise does not correspond to genes obeying a strictly deterministic dynamics. The natural strategy of minimization consists in equating the mean of the absolute value of the relative variation of the expression level (alpha) with noise (eta). We hypothesize that the temporal noise pattern is an emergent property of the genome and shows how the dynamics of gene expression could be related to chromosomal organization.Univ Fed Sao Paulo, Dept Microbiol Immunol & Parasitol, Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Dept Informat Saude, Sao Paulo, BrazilUniv Fed Sao Paulo, Dept Microbiol Immunol & Parasitol, Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Dept Informat Saude, Sao Paulo, BrazilWeb of Science397-414engFunpec-editoraGenetics And Molecular Researchtranscriptionnoisescale invarianceyeast genomeMinimization of transcriptional temporal noise and scale invariance in the yeast genomeinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESPORIGINALWOS000251696400018.pdfapplication/pdf1097662${dspace.ui.url}/bitstream/11600/43718/1/WOS000251696400018.pdf115f9a948b7ce4e2d87936f4e948dac0MD51open access11600/437182021-10-05 16:10:01.055open accessoai:repositorio.unifesp.br:11600/43718Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestopendoar:34652023-05-25T12:09:51.448004Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false |
dc.title.en.fl_str_mv |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
title |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
spellingShingle |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome Ferreira, R. C. [UNIFESP] transcription noise scale invariance yeast genome |
title_short |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
title_full |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
title_fullStr |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
title_full_unstemmed |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
title_sort |
Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
author |
Ferreira, R. C. [UNIFESP] |
author_facet |
Ferreira, R. C. [UNIFESP] Bosco, Francisco [UNIFESP] Paiva, Paulo Bandiera [UNIFESP] Briones, Marcelo Ribeiro da Silva [UNIFESP] |
author_role |
author |
author2 |
Bosco, Francisco [UNIFESP] Paiva, Paulo Bandiera [UNIFESP] Briones, Marcelo Ribeiro da Silva [UNIFESP] |
author2_role |
author author author |
dc.contributor.institution.none.fl_str_mv |
Universidade Federal de São Paulo (UNIFESP) |
dc.contributor.author.fl_str_mv |
Ferreira, R. C. [UNIFESP] Bosco, Francisco [UNIFESP] Paiva, Paulo Bandiera [UNIFESP] Briones, Marcelo Ribeiro da Silva [UNIFESP] |
dc.subject.eng.fl_str_mv |
transcription noise scale invariance yeast genome |
topic |
transcription noise scale invariance yeast genome |
description |
The analysis of transcriptional temporal noise could be an interesting means to study gene expression dynamics and stochasticity in eukaryotes. To study the statistical distributions of temporal noise in the eukaryotic model system Saccharomyces cerevisiae, we analyzed microarray data corresponding to one cell cycle for 6200 genes. We found that the temporal noise follows a lognormal distribution with scale invariance at the genome, chromosomal and sub-chromosomal levels. Correlation of temporal noise with the codon adaptation index suggests that at least 70% of all protein-coding genes are a noise minimization core of the genome. Accordingly, a mathematical model of individual gene expression dynamics was proposed, using an operator theoretical approach, which reveals strict conditions for noise variability and a possible global noise minimization/optimization strategy at the genome level. Our model and data show that minimal noise does not correspond to genes obeying a strictly deterministic dynamics. The natural strategy of minimization consists in equating the mean of the absolute value of the relative variation of the expression level (alpha) with noise (eta). We hypothesize that the temporal noise pattern is an emergent property of the genome and shows how the dynamics of gene expression could be related to chromosomal organization. |
publishDate |
2007 |
dc.date.issued.fl_str_mv |
2007-01-01 |
dc.date.accessioned.fl_str_mv |
2018-06-15T17:30:20Z |
dc.date.available.fl_str_mv |
2018-06-15T17:30:20Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
Genetics And Molecular Research. Ribeirao Preto: Funpec-editora, v. 6, n. 2, p. 397-414, 2007. |
dc.identifier.uri.fl_str_mv |
http://repositorio.unifesp.br/11600/43718 http://www.funpecrp.com.br/gmr/year2007/vol2-6/gmr0318_abstract.htm |
dc.identifier.issn.none.fl_str_mv |
1676-5680 |
dc.identifier.file.none.fl_str_mv |
WOS000251696400018.pdf |
dc.identifier.wos.none.fl_str_mv |
WOS:000251696400018 |
identifier_str_mv |
Genetics And Molecular Research. Ribeirao Preto: Funpec-editora, v. 6, n. 2, p. 397-414, 2007. 1676-5680 WOS000251696400018.pdf WOS:000251696400018 |
url |
http://repositorio.unifesp.br/11600/43718 http://www.funpecrp.com.br/gmr/year2007/vol2-6/gmr0318_abstract.htm |
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eng |
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eng |
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Genetics And Molecular Research |
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openAccess |
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397-414 |
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Funpec-editora |
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Universidade Federal de São Paulo (UNIFESP) |
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