View Item 

Show simple item record

Positive selection for elevated gene expression noise in yeast

dc.contributor.authorZhang, Zhihuaen_US
dc.contributor.authorQian, Wenfengen_US
dc.contributor.authorZhang, Jianzhien_US
dc.date.accessioned2014-02-11T17:56:57Z
dc.date.available2014-02-11T17:56:57Z
dc.date.issued2009en_US
dc.identifier.citationZhang, Zhihua; Qian, Wenfeng; Zhang, Jianzhi (2009). "Positive selection for elevated gene expression noise in yeast." Molecular Systems Biology 5(1): n/a-n/a. <http://hdl.handle.net/2027.42/102642>en_US
dc.identifier.issn1744-4292en_US
dc.identifier.issn1744-4292en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/102642
dc.publisherJohn Wiley & Sons, Ltden_US
dc.subject.otherPositive Selectionen_US
dc.subject.otherYeasten_US
dc.subject.otherPlasma‐Membrane Transportersen_US
dc.subject.otherExpression Noiseen_US
dc.subject.otherAdaptive Evolutionen_US
dc.titlePositive selection for elevated gene expression noise in yeasten_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biologyen_US
dc.subject.hlbtoplevelHealth Sciencesen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102642/1/msb200958.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102642/2/msb200958-sup-0001.pdf
dc.identifier.doi10.1038/msb.2009.58en_US
dc.identifier.sourceMolecular Systems Biologyen_US
dc.identifier.citedreferenceRaser JM, O‧Shea EK ( 2005 ) Noise in gene expression: origins, consequences, and control. Science 309: 2010 – 2013en_US
dc.identifier.citedreferenceOzbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A ( 2002 ) Regulation of noise in the expression of a single gene. Nat Genet 31: 69 – 73en_US
dc.identifier.citedreferencePedraza JM, van Oudenaarden A ( 2005 ) Noise propagation in gene networks. Science 307: 1965 – 1969en_US
dc.identifier.citedreferencePerez‐Ortin JE, Alepuz PM, Moreno J ( 2007 ) Genomics and gene transcription kinetics in yeast. Trends Genet 23: 250 – 257en_US
dc.identifier.citedreferenceRaj A, van Oudenaarden A ( 2008 ) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216 – 226en_US
dc.identifier.citedreferenceRamsey S, Ozinsky A, Clark A, Smith KD, de Atauri P, Thorsson V, Orrell D, Bolouri H ( 2006 ) Transcriptional noise and cellular heterogeneity in mammalian macrophages. Philos Trans R Soc Lond B Biol Sci 361: 495 – 506en_US
dc.identifier.citedreferenceRao CV, Wolf DM, Arkin AP ( 2002 ) Control, exploitation and tolerance of intracellular noise. Nature 420: 231 – 237en_US
dc.identifier.citedreferenceRaser JM, O‧Shea EK ( 2004 ) Control of stochasticity in eukaryotic gene expression. Science 304: 1811 – 1814en_US
dc.identifier.citedreferenceRosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB ( 2005 ) Gene regulation at the single‐cell level. Science 307: 1962 – 1965en_US
dc.identifier.citedreferenceSchrodinger E ( 1944 ) What is Life? Cambridge, UK: Cambridge University Pressen_US
dc.identifier.citedreferenceSean D, Meltzer PS ( 2007 ) GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 23: 1846 – 1847en_US
dc.identifier.citedreferenceSopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, Andrews B ( 2006 ) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21: 319 – 330en_US
dc.identifier.citedreferenceSteinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW ( 2002 ) Systematic screen for human disease genes in yeast. Nat Genet 31: 400 – 404en_US
dc.identifier.citedreferenceStoebel DM, Dean AM, Dykhuizen DE ( 2008 ) The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 178: 1653 – 1660en_US
dc.identifier.citedreferenceStorey JD, Tibshirani R ( 2003 ) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440 – 9445en_US
dc.identifier.citedreferenceThattai M, van Oudenaarden A ( 2004 ) Stochastic gene expression in fluctuating environments. Genetics 167: 523 – 530en_US
dc.identifier.citedreferenceTirosh I, Weinberger A, Carmi M, Barkai N ( 2006 ) A genetic signature of interspecies variations in gene expression. Nat Genet 38: 830 – 834en_US
dc.identifier.citedreferenceTirosh I, Barkai N ( 2008 ) Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet 24: 109 – 113en_US
dc.identifier.citedreferenceVolfson D, Marciniak J, Blake WJ, Ostroff N, Tsimring LS, Hasty J ( 2006 ) Origins of extrinsic variability in eukaryotic gene expression. Nature 439: 861 – 864en_US
dc.identifier.citedreferenceWagner A ( 2005 ) Energy constraints on the evolution of gene expression. Mol Biol Evol 22: 1365 – 1374en_US
dc.identifier.citedreferenceZeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN ( 2003 ) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4: R28en_US
dc.identifier.citedreferenceAcar M, Mettetal JT, van Oudenaarden A ( 2008 ) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40: 471 – 475en_US
dc.identifier.citedreferenceAnsel J, Bottin H, Rodriguez‐Beltran C, Damon C, Nagarajan M, Fehrmann S, Francois J, Yvert G ( 2008 ) Cell‐to‐cell stochastic variation in gene expression is a complex genetic trait. PLoS Genet 4: e1000049en_US
dc.identifier.citedreferenceAshburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel‐Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G ( 2000 ) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25 – 29en_US
dc.identifier.citedreferenceBahar R, Hartmann CH, Rodriguez KA, Denny AD, Busuttil RA, Dolle ME, Calder RB, Chisholm GB, Pollock BH, Klein CA, Vijg J ( 2006 ) Increased cell‐to‐cell variation in gene expression in ageing mouse heart. Nature 441: 1011 – 1014en_US
dc.identifier.citedreferenceBar‐Even A, Paulsson J, Maheshri N, Carmi M, O‧Shea E, Pilpel Y, Barkai N ( 2006 ) Noise in protein expression scales with natural protein abundance. Nat Genet 38: 636 – 643en_US
dc.identifier.citedreferenceBasehoar AD, Zanton SJ, Pugh BF ( 2004 ) Identification and distinct regulation of yeast TATA box‐containing genes. Cell 116: 699 – 709en_US
dc.identifier.citedreferenceBatada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hurst LD, Tyers M ( 2006 ) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol 4: e317en_US
dc.identifier.citedreferenceBatada NN, Hurst LD ( 2007 ) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39: 945 – 949en_US
dc.identifier.citedreferenceBecskei A, Serrano L ( 2000 ) Engineering stability in gene networks by autoregulation. Nature 405: 590 – 593en_US
dc.identifier.citedreferenceBedford T, Hartl DL ( 2009 ) Optimization of gene expression by natural selection. Proc Natl Acad Sci USA 106: 1133 – 1138en_US
dc.identifier.citedreferenceBlake WJ, Kærn M, Cantor CR, Collins JJ ( 2003 ) Noise in eukaryotic gene expression. Nature 422: 633 – 637en_US
dc.identifier.citedreferenceBlake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ ( 2006 ) Phenotypic consequences of promoter‐mediated transcriptional noise. Mol Cell 24: 853 – 865en_US
dc.identifier.citedreferenceBrem RB, Kruglyak L ( 2005 ) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci USA 102: 1572 – 1577en_US
dc.identifier.citedreferenceColman‐Lerner A, Gordon A, Serra E, Chin T, Resnekov O, Endy D, Pesce CG, Brent R ( 2005 ) Regulated cell‐to‐cell variation in a cell‐fate decision system. Nature 437: 699 – 706en_US
dc.identifier.citedreferenceCook DL, Gerber AN, Tapscott SJ ( 1998 ) Modeling stochastic gene expression: implications for haploinsufficiency. Proc Natl Acad Sci USA 95: 15641 – 15646en_US
dc.identifier.citedreferenceDekel E, Alon U ( 2005 ) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588 – 592en_US
dc.identifier.citedreferenceDeutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Nislow C, Giaever G ( 2005 ) Mechanisms of haploinsufficiency revealed by genome‐wide profiling in yeast. Genetics 169: 1915 – 1925en_US
dc.identifier.citedreferenceElowitz MB, Levine AJ, Siggia ED, Swain PS ( 2002 ) Stochastic gene expression in a single cell. Science 297: 1183 – 1186en_US
dc.identifier.citedreferenceFisher RA ( 1924 ) The distribution of the partial correlation coefficient. Metron 3: 329 – 332en_US
dc.identifier.citedreferenceFraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB ( 2004 ) Noise minimization in eukaryotic gene expression. PLoS Biol 2: e137en_US
dc.identifier.citedreferenceGentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G et al. ( 2004 ) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80en_US
dc.identifier.citedreferenceGiaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau‐Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El‐Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A et al. ( 2002 ) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387 – 391en_US
dc.identifier.citedreferenceHartl DL, Dykhuizen DE, Dean AM ( 1985 ) Limits of adaptation: the evolution of selective neutrality. Genetics 111: 655 – 674en_US
dc.identifier.citedreferenceKacser H, Burns JA ( 1981 ) The molecular basis of dominance. Genetics 97: 639 – 666en_US
dc.identifier.citedreferenceKaern M, Elston TC, Blake WJ, Collins JJ ( 2005 ) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451 – 464en_US
dc.identifier.citedreferenceKaneko K, Furusawa C ( 2008 ) Relevance of phenotypic noise to adaptation and evolution. IET Syst Biol 2: 234 – 246en_US
dc.identifier.citedreferenceKemkemer R, Schrank S, Vogel W, Gruler H, Kaufmann D ( 2002 ) Increased noise as an effect of haploinsufficiency of the tumor‐suppressor gene neurofibromatosis type 1 in vitro. Proc Natl Acad Sci USA 99: 13783 – 13788en_US
dc.identifier.citedreferenceKhaitovich P, Enard W, Lachmann M, Paabo S ( 2006 ) Evolution of primate gene expression. Nat Rev Genet 7: 693 – 702en_US
dc.identifier.citedreferenceLandry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL ( 2007 ) Genetic properties influencing the evolvability of gene expression. Science 317: 118 – 121en_US
dc.identifier.citedreferenceLehner B ( 2008 ) Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 4: 170en_US
dc.identifier.citedreferenceLopez‐Maury L, Marguerat S, Bahler J ( 2008 ) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet 9: 583 – 593en_US
dc.identifier.citedreferenceLosick R, Desplan C ( 2008 ) Stochasticity and cell fate. Science 320: 65 – 68en_US
dc.identifier.citedreferenceMaheshri N, O‧Shea EK ( 2007 ) Living with noisy genes: how cells function reliably with inherent variability in gene expression. Annu Rev Biophys Biomol Struct 36: 413 – 434en_US
dc.identifier.citedreferenceNewman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS ( 2006 ) Single‐cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840 – 846en_US
dc.identifier.citedreferenceOrphanides G, Reinberg D ( 2002 ) A unified theory of gene expression. Cell 108: 439 – 451en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
msb200958.pdf
Size:
360.3KB
Format:
PDF
View/Open
Name:
msb200958-sup-0001.pdf
Size:
472.4KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.