2012
Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae
Hodgins-Davis A, Adomas AB, Warringer J, Townsend JP. Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae. Genome Biology And Evolution 2012, 4: 1061-1079. PMID: 23019066, PMCID: PMC3514956, DOI: 10.1093/gbe/evs084.Peer-Reviewed Original ResearchMeSH KeywordsCluster AnalysisCopperDNA-Binding ProteinsDose-Response Relationship, DrugGene Expression ProfilingGene Expression Regulation, FungalGene-Environment InteractionGenes, FungalGenetic VariationMetabolic Networks and PathwaysMicroarray AnalysisNuclear ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsTranscriptomeConceptsPopulation variationReaction normsGene expression reaction normsGene expressionNovel ecological contextsGenome-wide mRNA levelsGenetic backgroundRelevant copper concentrationsAbundance of variationMitotic fitnessSulfur homeostasisPlastic phenotypesDownstream metabolic consequencesPlastic variationMost genesCopper stressPhenotypic variationGene networksAbundant genesGenetic variationCopper gradientExpression variationEcological contextDifferential expressionGenes
2011
SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae
Guo Z, Adomas AB, Jackson ED, Qin H, Townsend JP. SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae. FEMS Yeast Research 2011, 11: 345-355. PMID: 21306556, DOI: 10.1111/j.1567-1364.2011.00723.x.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell ProliferationGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalHSP30 Heat-Shock ProteinsHydrogen PeroxideMicrobial ViabilityMitochondrial Membrane Transport ProteinsMitochondrial Precursor Protein Import Complex ProteinsOligonucleotide Array Sequence AnalysisPhenotypePolymerase Chain ReactionSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSilent Information Regulator Proteins, Saccharomyces cerevisiaeSirtuin 2Up-RegulationConceptsReplicative agingWhole genome gene expressionNatural S. cerevisiaeExpression levelsLife span variationDifferential expression levelsDifferent expression levelsEffects of genesNatural populationsYeast SaccharomycesOrganelle organizationS. cerevisiaeGene expressionNatural variationCell cycleStress responseSir2Mitochondrial functionGenesSaccharomycesAllelic associationSpan variationProgenyMetabolic responseTim17
2008
Sleuthing the difference a nucleotide can make
Townsend JP. Sleuthing the difference a nucleotide can make. Molecular Ecology 2008, 17: 2793-2795. PMID: 18565029, DOI: 10.1111/j.1365-294x.2008.03824.x.Peer-Reviewed Original ResearchMeSH KeywordsFrameshift MutationGene Expression Regulation, FungalIntracellular Signaling Peptides and ProteinsMembrane ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription, GeneticConceptsGene expression polymorphismsExpression polymorphismsGenetic variationGene expressionGenome-wide gene expressionPotential evolutionary impactCis-regulatory regionsAmino acid sensorsDifferential gene expressionSingle nucleotide insertionEcological genomicsEvolutionary impactNatural populationsDifferential fitnessYeast SaccharomycesTranscription factorsGenetic basisNatural isolatesHomonucleotide repeatsNatural variationNucleotide insertionEnvironment interactionPolymorphismAcid sensorsSSY1
2002
Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
Townsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 2002, 3: research0071.1. PMID: 12537560, PMCID: PMC151173, DOI: 10.1186/gb-2002-3-12-research0071.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremDNA-Binding ProteinsEthanolGene DeletionGene Expression ProfilingGene Expression Regulation, FungalGenotypeModels, GeneticNuclear ProteinsOligonucleotide Array Sequence AnalysisRNA, FungalRNA, MessengerSaccharomyces cerevisiae ProteinsSpecies SpecificityTranscription FactorsZincConceptsGene of interestExpression levelsGene expression levelsTwofold thresholdGene basisTranscriptional responseMicroarray comparisonsMinimal mediumExpression differencesBiological insightsMicroarray analysisEthanol shockMicroarray dataRelative mRNA levelsGenesMRNA levelsMultiple strainsBayesian analysisDevelopmental state