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Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae
A long-standing effort in biology is to precisely define and group phenotypes that characterize a biological process, and the genes that underpin them. In Saccharomyces cerevisiae and other organisms, functional screens have generated rich lists of phenotypes associated with individual genes. Howeve...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341148/ https://www.ncbi.nlm.nih.gov/pubmed/32376676 http://dx.doi.org/10.1534/g3.120.401350 |
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author | Bermudez, Rosa M. Wu, Peter I-Fan Callerame, Deanna Hammer, Staci Hu, James C. Polymenis, Michael |
author_facet | Bermudez, Rosa M. Wu, Peter I-Fan Callerame, Deanna Hammer, Staci Hu, James C. Polymenis, Michael |
author_sort | Bermudez, Rosa M. |
collection | PubMed |
description | A long-standing effort in biology is to precisely define and group phenotypes that characterize a biological process, and the genes that underpin them. In Saccharomyces cerevisiae and other organisms, functional screens have generated rich lists of phenotypes associated with individual genes. However, it is often challenging to identify sets of phenotypes and genes that are most closely associated with a given biological process. Here, we focused on the 166 phenotypes arising from loss-of-function and the 86 phenotypes from gain-of-function mutations in 571 genes currently assigned to cell cycle-related ontologies in S. cerevisiae. To reduce this complexity, we applied unbiased, computational approaches of correspondence analysis to identify a minimum set of phenotypic variables that accounts for as much of the variability in the data as possible. Loss-of-function phenotypes can be reduced to 20 dimensions, while gain-of-function ones to 14 dimensions. We also pinpoint the contributions of phenotypes and genes in each set. The approach we describe not only simplifies the categorization of phenotypes associated with cell cycle progression but might also potentially serve as a discovery tool for gene function. |
format | Online Article Text |
id | pubmed-7341148 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-73411482020-07-21 Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae Bermudez, Rosa M. Wu, Peter I-Fan Callerame, Deanna Hammer, Staci Hu, James C. Polymenis, Michael G3 (Bethesda) Investigations A long-standing effort in biology is to precisely define and group phenotypes that characterize a biological process, and the genes that underpin them. In Saccharomyces cerevisiae and other organisms, functional screens have generated rich lists of phenotypes associated with individual genes. However, it is often challenging to identify sets of phenotypes and genes that are most closely associated with a given biological process. Here, we focused on the 166 phenotypes arising from loss-of-function and the 86 phenotypes from gain-of-function mutations in 571 genes currently assigned to cell cycle-related ontologies in S. cerevisiae. To reduce this complexity, we applied unbiased, computational approaches of correspondence analysis to identify a minimum set of phenotypic variables that accounts for as much of the variability in the data as possible. Loss-of-function phenotypes can be reduced to 20 dimensions, while gain-of-function ones to 14 dimensions. We also pinpoint the contributions of phenotypes and genes in each set. The approach we describe not only simplifies the categorization of phenotypes associated with cell cycle progression but might also potentially serve as a discovery tool for gene function. Genetics Society of America 2020-05-06 /pmc/articles/PMC7341148/ /pubmed/32376676 http://dx.doi.org/10.1534/g3.120.401350 Text en Copyright © 2020 Bermudez et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Bermudez, Rosa M. Wu, Peter I-Fan Callerame, Deanna Hammer, Staci Hu, James C. Polymenis, Michael Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae |
title | Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae |
title_full | Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae |
title_fullStr | Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae |
title_full_unstemmed | Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae |
title_short | Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae |
title_sort | phenotypic associations among cell cycle genes in saccharomyces cerevisiae |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341148/ https://www.ncbi.nlm.nih.gov/pubmed/32376676 http://dx.doi.org/10.1534/g3.120.401350 |
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