m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence

We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and...

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Detalles Bibliográficos
Autores principales: Reimand, Jüri, Aun, Anu, Vilo, Jaak, Vaquerizas, Juan M, Sedman, Juhan, Luscombe, Nicholas M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446321/
https://www.ncbi.nlm.nih.gov/pubmed/22720667
http://dx.doi.org/10.1186/gb-2012-13-6-r55
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author Reimand, Jüri
Aun, Anu
Vilo, Jaak
Vaquerizas, Juan M
Sedman, Juhan
Luscombe, Nicholas M
author_facet Reimand, Jüri
Aun, Anu
Vilo, Jaak
Vaquerizas, Juan M
Sedman, Juhan
Luscombe, Nicholas M
author_sort Reimand, Jüri
collection PubMed
description We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G(0)), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G(0 )TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G(0)-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data.
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spelling pubmed-34463212012-09-21 m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence Reimand, Jüri Aun, Anu Vilo, Jaak Vaquerizas, Juan M Sedman, Juhan Luscombe, Nicholas M Genome Biol Method We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G(0)), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G(0 )TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G(0)-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data. BioMed Central 2012 2012-06-21 /pmc/articles/PMC3446321/ /pubmed/22720667 http://dx.doi.org/10.1186/gb-2012-13-6-r55 Text en Copyright ©2012 Reimand 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 Method
Reimand, Jüri
Aun, Anu
Vilo, Jaak
Vaquerizas, Juan M
Sedman, Juhan
Luscombe, Nicholas M
m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
title m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
title_full m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
title_fullStr m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
title_full_unstemmed m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
title_short m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
title_sort m:explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446321/
https://www.ncbi.nlm.nih.gov/pubmed/22720667
http://dx.doi.org/10.1186/gb-2012-13-6-r55
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