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Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data

Available DNA microarray time series that record gene expression along the developmental stages of multicellular eukaryotes, or in unicellular organisms subject to external perturbations such as stress and diauxie, are analyzed. By pairwise comparison of the gene expression profiles on the basis of...

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Detalles Bibliográficos
Autores principales: Rooman, Marianne, Albert, Jaroslav, Dehouck, Yves, Haye, Alexandre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240625/
https://www.ncbi.nlm.nih.gov/pubmed/22194799
http://dx.doi.org/10.1371/journal.pone.0027948
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author Rooman, Marianne
Albert, Jaroslav
Dehouck, Yves
Haye, Alexandre
author_facet Rooman, Marianne
Albert, Jaroslav
Dehouck, Yves
Haye, Alexandre
author_sort Rooman, Marianne
collection PubMed
description Available DNA microarray time series that record gene expression along the developmental stages of multicellular eukaryotes, or in unicellular organisms subject to external perturbations such as stress and diauxie, are analyzed. By pairwise comparison of the gene expression profiles on the basis of a translation-invariant and scale-invariant distance measure corresponding to least-rectangle regression, it is shown that peaks in the average distance values are noticeable and are localized around specific time points. These points systematically coincide with the transition points between developmental phases or just follow the external perturbations. This approach can thus be used to identify automatically, from microarray time series alone, the presence of external perturbations or the succession of developmental stages in arbitrary cell systems. Moreover, our results show that there is a striking similarity between the gene expression responses to these a priori very different phenomena. In contrast, the cell cycle does not involve a perturbation-like phase, but rather continuous gene expression remodeling. Similar analyses were conducted using three other standard distance measures, showing that the one we introduced was superior. Based on these findings, we set up an adapted clustering method that uses this distance measure and classifies the genes on the basis of their expression profiles within each developmental stage or between perturbation phases.
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spelling pubmed-32406252011-12-22 Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data Rooman, Marianne Albert, Jaroslav Dehouck, Yves Haye, Alexandre PLoS One Research Article Available DNA microarray time series that record gene expression along the developmental stages of multicellular eukaryotes, or in unicellular organisms subject to external perturbations such as stress and diauxie, are analyzed. By pairwise comparison of the gene expression profiles on the basis of a translation-invariant and scale-invariant distance measure corresponding to least-rectangle regression, it is shown that peaks in the average distance values are noticeable and are localized around specific time points. These points systematically coincide with the transition points between developmental phases or just follow the external perturbations. This approach can thus be used to identify automatically, from microarray time series alone, the presence of external perturbations or the succession of developmental stages in arbitrary cell systems. Moreover, our results show that there is a striking similarity between the gene expression responses to these a priori very different phenomena. In contrast, the cell cycle does not involve a perturbation-like phase, but rather continuous gene expression remodeling. Similar analyses were conducted using three other standard distance measures, showing that the one we introduced was superior. Based on these findings, we set up an adapted clustering method that uses this distance measure and classifies the genes on the basis of their expression profiles within each developmental stage or between perturbation phases. Public Library of Science 2011-12-15 /pmc/articles/PMC3240625/ /pubmed/22194799 http://dx.doi.org/10.1371/journal.pone.0027948 Text en Rooman et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Rooman, Marianne
Albert, Jaroslav
Dehouck, Yves
Haye, Alexandre
Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data
title Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data
title_full Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data
title_fullStr Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data
title_full_unstemmed Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data
title_short Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data
title_sort detection of perturbation phases and developmental stages in organisms from dna microarray time series data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240625/
https://www.ncbi.nlm.nih.gov/pubmed/22194799
http://dx.doi.org/10.1371/journal.pone.0027948
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