Genes Confer Similar Robustness to Environmental, Stochastic, and Genetic Perturbations in Yeast
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{"title"=>"Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast", "type"=>"journal", "authors"=>[{"first_name"=>"Ben", "last_name"=>"Lehner", "scopus_author_id"=>"16402234200"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-77949386270", "doi"=>"10.1371/journal.pone.0009035", "sgr"=>"77949386270", "isbn"=>"1932-6203", "pmid"=>"20140261", "issn"=>"19326203", "pui"=>"358448411"}, "id"=>"2e97d064-8996-375d-bfdc-6b289e590b25", "abstract"=>"<p>Gene inactivation often has little or no apparent consequence for the phenotype of an organism. This property—enetic (or mutational) robustness—is pervasive, and has important implications for disease and evolution, but is not well understood. Dating back to at least Waddington, it has been suggested that mutational robustness may be related to the requirement to withstand environmental or stochastic perturbations. Here I show that global quantitative data from yeast are largely consistent with this idea. Considering the effects of mutations in all nonessential genes shows that genes that confer robustness to environmental or stochastic change also buffer the effects of genetic change, and with similar efficacy. This means that selection during evolution for environmental or stochastic robustness (also referred to as canalization) may frequently have the side effect of increasing genetic robustness. A dynamic environment may therefore promote the evolution of phenotypic complexity. It also means that “hub†genes in genetic interaction (synthetic lethal) networks are generally genes that confer environmental resilience and phenotypic stability.</p>", "link"=>"http://www.mendeley.com/research/genes-confer-similar-robustness-environmental-stochastic-genetic-perturbations-yeast", "reader_count"=>122, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Librarian"=>1, "Researcher"=>36, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>43, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>5, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Librarian"=>1, "Researcher"=>36, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>43, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>5, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>11, "Mathematics"=>1, "Agricultural and Biological Sciences"=>94, "Medicine and Dentistry"=>4, "Physics and Astronomy"=>2, "Psychology"=>1, "Social Sciences"=>1, "Computer Science"=>5, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>94}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Saudi Arabia"=>1, "Canada"=>1, "Austria"=>1, "United States"=>10, "United Kingdom"=>4, "Italy"=>1, "Mexico"=>2, "Portugal"=>1, "Switzerland"=>1, "Germany"=>1, "Spain"=>3}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/864847"], "description"=>"<p>The effects of deletions in nearly all non-essential genes on environmental, mutational and stochastic robustness can be estimated using global experiments performed with the haploid gene deletion collection (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#s4\" target=\"_blank\">materials and methods</a>). This allows one to ask whether gene deletions tend to have similar (i.e. correlated) consequences for the three measures of robustness, or whether they tend to affect genetic, environmental or stochastic robustness independently.</p>", "links"=>[], "tags"=>["quantitative", "datasets", "yeast", "relationships", "stochastic"], "article_id"=>535307, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Ben Lehner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009035.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Using_global_quantitative_genetic_datasets_in_yeast_to_examine_the_relationships_among_genetic_environmental_and_stochastic_robustness_/535307", "title"=>"Using global quantitative genetic datasets in yeast to examine the relationships among genetic, environmental and stochastic robustness.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:49:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/864891"], "description"=>"<p>The effects of mutations on environmental robustness (the number of different environmental conditions in which a gene is required for growth <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Hillenmeyer1\" target=\"_blank\">[31]</a>) and mutational robustness (the number of synthetic lethal interactions made by a mutation <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Pan1\" target=\"_blank\">[9]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Tong1\" target=\"_blank\">[11]</a>) are compared across 4656 gene deletions in yeast. Data are plotted for ten equally sized bins of genes. Error bars are +/− one standard error. Spearman rank correlation coefficient (ρ) = 0.39, p<2.2×10<sup>−16</sup>.</p>", "links"=>[], "tags"=>["correlated", "affects", "deletions", "robustness"], "article_id"=>535351, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Ben Lehner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009035.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_correlated_affects_of_gene_deletions_on_genetic_and_environmental_robustness_in_yeast_/535351", "title"=>"The correlated affects of gene deletions on genetic and environmental robustness in yeast.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/864962"], "description"=>"<p>Correlation coefficients between the effects of mutations on measures of robustness are represented as a heat-map. Datasets: genetic robustness–proportion of synthetic lethal interactions from Tong <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Tong1\" target=\"_blank\">[11]</a>, Pan <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Pan1\" target=\"_blank\">[9]</a>; environmental robustness–number of environmental conditions in which a strain is required for growth from Hillenmeyer <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Hillenmeyer1\" target=\"_blank\">[31]</a>, and Dudley <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Dudley1\" target=\"_blank\">[30]</a>. ‘1’–synthetic lethal degree for ‘target’ genes, ‘2’–synthetic lethal degree for ‘bait’ genes. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone-0009035-t001\" target=\"_blank\">Table 1</a> for P-values.</p>", "links"=>[], "tags"=>["genes", "mutational", "robustness", "confirmed"], "article_id"=>535427, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Ben Lehner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009035.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_correlation_between_the_requirement_of_genes_for_mutational_and_environmental_robustness_is_confirmed_using_multiple_different_datasets_/535427", "title"=>"The correlation between the requirement of genes for mutational and environmental robustness is confirmed using multiple different datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:50:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/865039"], "description"=>"<p>Stochastic robustness is quantified as the variability of cellular morphology among individuals, as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#s4\" target=\"_blank\">materials and methods </a><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Levy1\" target=\"_blank\">[29]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Ohya1\" target=\"_blank\">[32]</a>. The correlation of each measure of environmental or genetic robustness across mutant strains with morphological variability is shown. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone-0009035-t001\" target=\"_blank\">Table 1</a> for P-values. Datasets used are as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone-0009035-g003\" target=\"_blank\">Figure 3</a>.</p>", "links"=>[], "tags"=>["mutations", "mutational", "robustness", "correlated", "reductions", "stochastic"], "article_id"=>535500, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Ben Lehner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009035.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_effects_of_mutations_on_mutational_and_environmental_robustness_are_also_correlated_with_reductions_in_stochastic_robustness_/535500", "title"=>"The effects of mutations on mutational and environmental robustness are also correlated with reductions in stochastic robustness.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:50:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/865097"], "description"=>"<p>The coupling between the requirement of genes for genetic (‘G’) and environmental (‘E’) robustness means that during evolution, selection for adaptive increases in environmental resilience may often have the side-effect of increasing mutational robustness.</p>", "links"=>[], "tags"=>["mutational"], "article_id"=>535562, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Ben Lehner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009035.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_model_for_the_evolution_of_mutational_robustness_/535562", "title"=>"A model for the evolution of mutational robustness.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:51:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/865137"], "description"=>"<p>Spearman Rank Correlation coefficients (ρ), P-values (P) and number of genes considered (n) comparing different measures of genetic, environmental, and stochastic robustness for gene deletions in yeast. Datasets are referred to by first author–Tong <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Tong1\" target=\"_blank\">[11]</a>, Pan <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Pan1\" target=\"_blank\">[9]</a>, Hillenmeyer <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Hillenmeyer1\" target=\"_blank\">[31]</a>, Dudley <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Dudley1\" target=\"_blank\">[30]</a>, Levy/Ohya <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Levy1\" target=\"_blank\">[29]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009035#pone.0009035-Ohya1\" target=\"_blank\">[32]</a>.</p>", "links"=>[], "tags"=>["confer", "correlated", "robustness", "stochastic", "perturbations"], "article_id"=>535598, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["Ben Lehner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009035.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_confer_correlated_robustness_to_genetic_environmental_and_stochastic_perturbations_in_yeast_/535598", "title"=>"Genes confer correlated robustness to genetic, environmental and stochastic perturbations in yeast.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 02:51:24"}

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Relative Metric

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