메뉴 건너뛰기




Volumn 10, Issue 6, 2010, Pages 1297-1306

Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome

Author keywords

Bioinformatics; Evolution; Expression noise; Protein abundance; Shotgun proteomics; Spectral counting

Indexed keywords

PROTEOME;

EID: 77949686097     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200900414     Document Type: Article
Times cited : (61)

References (49)
  • 1
    • 33846978695 scopus 로고    scopus 로고
    • Relative impact of nucleotide and copy number variation on gene expression phenotypes
    • Stranger, B. E., Forrest, M. S., Dunning, M., Ingle, C. E. et al., Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315, 848-853.
    • (2007) Science , vol.315 , pp. 848-853
    • Stranger, B.E.1    Forrest, M.S.2    Dunning, M.3    Ingle, C.E.4
  • 3
    • 33745287724 scopus 로고    scopus 로고
    • Noise in protein expression scales with natural protein abundance
    • Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M. et al., Noise in protein expression scales with natural protein abundance. Nat. Genet. 2006, 38, 636-643.
    • (2006) Nat. Genet , vol.38 , pp. 636-643
    • Bar-Even, A.1    Paulsson, J.2    Maheshri, N.3    Carmi, M.4
  • 4
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    • Newman, J. R., Ghaemmaghami, S., Ihmels, J., Breslow, D. K. et al., Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441, 840-846.
    • (2006) Nature , vol.441 , pp. 840-846
    • Newman, J.R.1    Ghaemmaghami, S.2    Ihmels, J.3    Breslow, D.K.4
  • 5
    • 57349097152 scopus 로고    scopus 로고
    • Dynamic proteomics of individual cancer cells in response to a drug
    • Cohen, A. A., Geva-Zatorsky, N., Eden, E., Frenkel-Morgenstern, M. et al., Dynamic proteomics of individual cancer cells in response to a drug. Science 2008, 322, 1511-1516.
    • (2008) Science , vol.322 , pp. 1511-1516
    • Cohen, A.A.1    Geva-Zatorsky, N.2    Eden, E.3    Frenkel-Morgenstern, M.4
  • 7
    • 59049088893 scopus 로고    scopus 로고
    • Optimization of gene expression by natural selection
    • Bedford, T., Hartl, D. L., Optimization of gene expression by natural selection. Proc. Natl. Acad. Sci. USA 2009, 106, 1133-1138.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 1133-1138
    • Bedford, T.1    Hartl, D.L.2
  • 8
    • 1842631448 scopus 로고    scopus 로고
    • Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control
    • Yanai, I., Graur, D., Ophir, R., Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS 2004, 8, 15-24.
    • (2004) OMICS , vol.8 , pp. 15-24
    • Yanai, I.1    Graur, D.2    Ophir, R.3
  • 9
    • 38549084066 scopus 로고    scopus 로고
    • Evaluating the role of natural selection in the evolution of gene regulation
    • Fay, J. C., Wittkopp, P. J., Evaluating the role of natural selection in the evolution of gene regulation. Heredity 2008, 100, 191-199.
    • (2008) Heredity , vol.100 , pp. 191-199
    • Fay, J.C.1    Wittkopp, P.J.2
  • 10
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • Dekel, E., Alon, U., Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436, 588-592.
    • (2005) Nature , vol.436 , pp. 588-592
    • Dekel, E.1    Alon, U.2
  • 11
    • 0142215475 scopus 로고    scopus 로고
    • Global analysis of protein expression in yeast
    • Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W. et al., Global analysis of protein expression in yeast. Nature 2003, 425, 737-741.
    • (2003) Nature , vol.425 , pp. 737-741
    • Ghaemmaghami, S.1    Huh, W.K.2    Bower, K.3    Howson, R.W.4
  • 12
    • 33644524918 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics turns quantitative
    • Ong, S. E., Mann, M., Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1, 252-262.
    • (2005) Nat. Chem. Biol , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 13
    • 61849105469 scopus 로고    scopus 로고
    • Mass spectrometry based targeted protein quantification: Methods and applications
    • Pan, S., Aebersold, R., Chen, R., Rush, J. et al., Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 2009, 8, 787-797.
    • (2009) J. Proteome Res , vol.8 , pp. 787-797
    • Pan, S.1    Aebersold, R.2    Chen, R.3    Rush, J.4
  • 15
    • 68449102172 scopus 로고    scopus 로고
    • Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
    • Malmstrom, J., Beck, M., Schmidt, A., Lange, V. et al., Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 2009, 460, 762-765.
    • (2009) Nature , vol.460 , pp. 762-765
    • Malmstrom, J.1    Beck, M.2    Schmidt, A.3    Lange, V.4
  • 16
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
    • (2008) Nat. Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 17
    • 34249717879 scopus 로고    scopus 로고
    • A high-quality catalog of the Drosophila melanogaster proteome
    • Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H. et al., A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol. 2007, 25, 576-583.
    • (2007) Nat. Biotechnol , vol.25 , pp. 576-583
    • Brunner, E.1    Ahrens, C.H.2    Mohanty, S.3    Baetschmann, H.4
  • 18
    • 44249091879 scopus 로고    scopus 로고
    • Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics
    • Baerenfaller, K., Grossmann, J., Grobei, M. A., Hull, R. et al., Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 2008, 320, 938-941.
    • (2008) Science , vol.320 , pp. 938-941
    • Baerenfaller, K.1    Grossmann, J.2    Grobei, M.A.3    Hull, R.4
  • 19
    • 65949096636 scopus 로고    scopus 로고
    • Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes
    • Schrimpf, S. P., Weiss, M., Reiter, L., Ahrens, C. H. et al., Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 2009, 7, e48.
    • (2009) PLoS Biol , vol.7
    • Schrimpf, S.P.1    Weiss, M.2    Reiter, L.3    Ahrens, C.H.4
  • 20
    • 0348142993 scopus 로고    scopus 로고
    • Changes in the protein expression of yeast as a function of carbon source
    • Gao, J., Opiteck, G. J., Friedrichs, M. S., Dongre, A. R., Hefta, S. A., Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2003, 2, 643-649.
    • (2003) J. Proteome Res , vol.2 , pp. 643-649
    • Gao, J.1    Opiteck, G.J.2    Friedrichs, M.S.3    Dongre, A.R.4    Hefta, S.A.5
  • 21
    • 3242731195 scopus 로고    scopus 로고
    • Liu, H., Sadygov, R. G., Yates,J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
    • Liu, H., Sadygov, R. G., Yates,J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
  • 22
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4
  • 23
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu, P., Vogel, C., Wang, R., Yao, X., Marcotte, E. M., Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25, 117-124.
    • (2007) Nat. Biotechnol , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 24
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick, P., Schirle, M., Chen, S. S., Flory, M. R. et al., Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25, 125-131.
    • (2007) Nat. Biotechnol , vol.25 , pp. 125-131
    • Mallick, P.1    Schirle, M.2    Chen, S.S.3    Flory, M.R.4
  • 25
    • 33748319353 scopus 로고    scopus 로고
    • Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
    • Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K. et al., Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 2006, 5, 2339-2347.
    • (2006) J. Proteome Res , vol.5 , pp. 2339-2347
    • Zybailov, B.1    Mosley, A.L.2    Sardiu, M.E.3    Coleman, M.K.4
  • 26
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
    • (2008) EMBO Rep , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 27
    • 58149193234 scopus 로고    scopus 로고
    • STRING 8 - a global view on proteins and their functional interactions in 630 organisms
    • Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S. et al., STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009, 37, D412-D416.
    • (2009) Nucleic Acids Res , vol.37
    • Jensen, L.J.1    Kuhn, M.2    Stark, M.3    Chaffron, S.4
  • 28
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov, R. L., Koonin, E. V., Lipman, D. J., A genomic perspective on protein families. Science 1997, 278, 631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 29
    • 38549177928 scopus 로고    scopus 로고
    • eggNOG: Automated construction and annotation of orthologous groups of genes
    • Jensen, L. J., Julien, P., Kuhn, M., von Mering, C. et al., eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 2008, 36, D250-D254.
    • (2008) Nucleic Acids Res , vol.36
    • Jensen, L.J.1    Julien, P.2    Kuhn, M.3    von Mering, C.4
  • 30
    • 38549123363 scopus 로고    scopus 로고
    • Gene Ontology annotations at SGD: New data sources and annotation methods
    • Hong, E. L., Balakrishnan, R., Dong, Q., Christie, K. R. et al., Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008, 36, D577-D581.
    • (2008) Nucleic Acids Res , vol.36
    • Hong, E.L.1    Balakrishnan, R.2    Dong, Q.3    Christie, K.R.4
  • 31
  • 32
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 1995, 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 33
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L. et al., Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1254.
    • (2008) Nature , vol.455 , pp. 1251-1254
    • de Godoy, L.M.1    Olsen, J.V.2    Cox, J.3    Nielsen, M.L.4
  • 34
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • Gygi, S. P., Rochon, Y., Franza, B. R., Aebersold, R., Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19, 1720-1730.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 35
    • 65649083411 scopus 로고    scopus 로고
    • Estimating accuracy of RNA-Seq and microarrays with proteomics
    • Fu, X., Fu, N., Guo, S., Yan, Z. et al., Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009, 10, 161.
    • (2009) BMC Genomics , vol.10 , pp. 161
    • Fu, X.1    Fu, N.2    Guo, S.3    Yan, Z.4
  • 36
    • 0346801873 scopus 로고    scopus 로고
    • The Gene Ontology (GO) database and informatics resource
    • Harris, M. A., Clark, J., Ireland, A., Lomax, J. et al., The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32, D258-D261.
    • (2004) Nucleic Acids Res , vol.32
    • Harris, M.A.1    Clark, J.2    Ireland, A.3    Lomax, J.4
  • 37
    • 0037173615 scopus 로고    scopus 로고
    • Functional profiling of the Saccharomyces cerevisiae genome
    • Giaever, G., Chu, A. M., Ni, L., Connelly, C. et al., Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418, 387-391.
    • (2002) Nature , vol.418 , pp. 387-391
    • Giaever, G.1    Chu, A.M.2    Ni, L.3    Connelly, C.4
  • 38
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: Origins, consequences, and control
    • Raser, J. M., O'Shea, E. K., Noise in gene expression: origins, consequences, and control. Science 2005, 309, 2010-2013.
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.M.1    O'Shea, E.K.2
  • 39
    • 25144450143 scopus 로고    scopus 로고
    • Contributions of low molecule number and chromosomal positioning to stochastic gene expression
    • Becskei, A., Kaufmann, B. B., van Oudenaarden, A., Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 2005, 37, 937-944.
    • (2005) Nat. Genet , vol.37 , pp. 937-944
    • Becskei, A.1    Kaufmann, B.B.2    van Oudenaarden, A.3
  • 40
    • 43349090699 scopus 로고    scopus 로고
    • Comparison of protein and mRNA expression evolution in humans and chimpanzees
    • Fu, N., Drinnenberg, I., Kelso, J., Wu, J. R. et al., Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS ONE 2007, 2, e216.
    • (2007) PLoS ONE , vol.2
    • Fu, N.1    Drinnenberg, I.2    Kelso, J.3    Wu, J.R.4
  • 41
    • 58149354386 scopus 로고    scopus 로고
    • Protein material costs: Single atoms can make an evolutionary difference
    • Bragg, J. G., Wagner, A., Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 2009, 25, 5-8.
    • (2009) Trends Genet , vol.25 , pp. 5-8
    • Bragg, J.G.1    Wagner, A.2
  • 42
    • 65349162170 scopus 로고    scopus 로고
    • Conservation of core gene expression in vertebrate tissues
    • Chan, E. T., Quon, G. T., Chua, G., Babak, T. et al., Conservation of core gene expression in vertebrate tissues. J. Biol. 2009, 8, 33.
    • (2009) J. Biol , vol.8 , pp. 33
    • Chan, E.T.1    Quon, G.T.2    Chua, G.3    Babak, T.4
  • 43
    • 73249116559 scopus 로고    scopus 로고
    • Comparison of diverse developmental transcriptomes reveals that co-expression of gene neighbors is not evolutionarily conserved
    • Yanai, I., Hunter, C. P., Comparison of diverse developmental transcriptomes reveals that co-expression of gene neighbors is not evolutionarily conserved. Genome Res. 2009, 12, 2214-2220.
    • (2009) Genome Res , vol.12 , pp. 2214-2220
    • Yanai, I.1    Hunter, C.P.2
  • 44
    • 34548076977 scopus 로고    scopus 로고
    • Assessing the conservation of mammalian gene expression using high-density exon arrays
    • Xing, Y., Ouyang, Z., Kapur, K., Scott, M. P., Wong, W. H., Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol. Biol. Evol. 2007, 24, 1283-1285.
    • (2007) Mol. Biol. Evol , vol.24 , pp. 1283-1285
    • Xing, Y.1    Ouyang, Z.2    Kapur, K.3    Scott, M.P.4    Wong, W.H.5
  • 45
    • 33746265259 scopus 로고    scopus 로고
    • Natural selection on gene expression
    • Gilad, Y., Oshlack, A., Rifkin, S. A., Natural selection on gene expression. Trends Genet. 2006, 22, 456-461.
    • (2006) Trends Genet , vol.22 , pp. 456-461
    • Gilad, Y.1    Oshlack, A.2    Rifkin, S.A.3
  • 46
    • 42049108914 scopus 로고    scopus 로고
    • Protein abundance profiling of the Escherichia coli cytosol
    • Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M. et al., Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 2008, 9, 102.
    • (2008) BMC Genomics , vol.9 , pp. 102
    • Ishihama, Y.1    Schmidt, T.2    Rappsilber, J.3    Mann, M.4
  • 47
    • 33847081243 scopus 로고    scopus 로고
    • Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
    • Schmidt, M. W., Houseman, A., Ivanov, A. R., Wolf, D. A., Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 2007, 3, 79.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 79
    • Schmidt, M.W.1    Houseman, A.2    Ivanov, A.R.3    Wolf, D.A.4
  • 48
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on codingsequence evolution
    • Drummond, D. A., Wilke, C. O., Mistranslation-induced protein misfolding as a dominant constraint on codingsequence evolution. Cell 2008, 134, 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 49
    • 47549108636 scopus 로고    scopus 로고
    • Costly mistakes: Translational infidelity and protein homeostasis
    • Powers, E. T., Balch, W. E., Costly mistakes: translational infidelity and protein homeostasis. Cell 2008, 134, 204-206.
    • (2008) Cell , vol.134 , pp. 204-206
    • Powers, E.T.1    Balch, W.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.