Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
10.1038/nature04785
Crossref journal-article
Springer Science and Business Media LLC
Nature (297)
Bibliography

Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441(7095), 840–846.

Authors 7
  1. John R. S. Newman (first)
  2. Sina Ghaemmaghami (additional)
  3. Jan Ihmels (additional)
  4. David K. Breslow (additional)
  5. Matthew Noble (additional)
  6. Joseph L. DeRisi (additional)
  7. Jonathan S. Weissman (additional)
References 45 Referenced 1,364
  1. Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002) (10.1038/nature01107) / Nature by L Florens (2002)
  2. Kumar, A. et al. Subcellular localization of the yeast proteome. Genes Dev. 16, 707–719 (2002) (10.1101/gad.970902) / Genes Dev. by A Kumar (2002)
  3. Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003) (10.1038/nature02026) / Nature by WK Huh (2003)
  4. Andersen, J. S. et al. Nucleolar proteome dynamics. Nature 433, 77–83 (2005) (10.1038/nature03207) / Nature by JS Andersen (2005)
  5. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003) (10.1038/nature01644) / Nature by M Kellis (2003)
  6. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003) (10.1038/nature02046) / Nature by S Ghaemmaghami (2003)
  7. Wei, J. et al. Global proteome discovery using an online three-dimensional LC–MS/MS. J. Proteome Res. 4, 801–808 (2005) (10.1021/pr0497632) / J. Proteome Res. by J Wei (2005)
  8. Futcher, B., Latter, G. I., Monardo, P., McLaughlin, C. S. & Garrels, J. I. A sampling of the yeast proteome. Mol. Cell. Biol. 19, 7357–7368 (1999) (10.1128/MCB.19.11.7357) / Mol. Cell. Biol. by B Futcher (1999)
  9. Gygi, S. P., Rochon, Y., Franza, B. R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720–1730 (1999) (10.1128/MCB.19.3.1720) / Mol. Cell. Biol. by SP Gygi (1999)
  10. Washburn, M. P. et al. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 100, 3107–3112 (2003) (10.1073/pnas.0634629100) / Proc. Natl Acad. Sci. USA by MP Washburn (2003)
  11. Schrödinger, E. What is Life? The Physical Aspect of the Living Cell (Cambridge Univ. Press, Cambridge, UK, 1944) / What is Life? The Physical Aspect of the Living Cell by E Schrödinger (1944)
  12. Barkai, N. & Leibler, S. Circadian clocks limited by noise. Nature 403, 267–268 (2000) (10.1038/35002258) / Nature by N Barkai (2000)
  13. Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004) (10.1126/science.1099390) / Science by NQ Balaban (2004)
  14. Samoilov, M., Plyasunov, S. & Arkin, A. P. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc. Natl Acad. Sci. USA 102, 2310–2315 (2005) (10.1073/pnas.0406841102) / Proc. Natl Acad. Sci. USA by M Samoilov (2005)
  15. Raser, J. M. & O'Shea, E. K. Noise in gene expression: origins, consequences, and control. Science 309, 2010–2013 (2005) (10.1126/science.1105891) / Science by JM Raser (2005)
  16. Novick, A. & Weiner, M. Enzyme induction as an all-or-none phenomenon. Proc. Natl Acad. Sci. USA 43, 553–566 (1957) (10.1073/pnas.43.7.553) / Proc. Natl Acad. Sci. USA by A Novick (1957)
  17. Ferrell, J. E. Jr & Machleder, E. M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280, 895–898 (1998) (10.1126/science.280.5365.895) / Science by JE Ferrell Jr (1998)
  18. Biggar, S. R. & Crabtree, G. R. Cell signaling can direct either binary or graded transcriptional responses. EMBO J. 20, 3167–3176 (2001) (10.1093/emboj/20.12.3167) / EMBO J. by SR Biggar (2001)
  19. Lahav, G. et al. Dynamics of the p53–Mdm2 feedback loop in individual cells. Nature Genet. 36, 147–150 (2004) (10.1038/ng1293) / Nature Genet. by G Lahav (2004)
  20. Eitzman, P. D., Hendrick, J. L. & Srienc, F. Quantitative immunofluorescence in single Saccharomyces cerevisiae cells. Cytometry 10, 475–483 (1989) (10.1002/cyto.990100417) / Cytometry by PD Eitzman (1989)
  21. Edwards, B. S., Kuckuck, F. & Sklar, L. A. Plug flow cytometry: an automated coupling device for rapid sequential flow cytometric sample analysis. Cytometry 37, 156–159 (1999) (10.1002/(SICI)1097-0320(19991001)37:2<156::AID-CYTO9>3.0.CO;2-T) / Cytometry by BS Edwards (1999)
  22. Becskei, A., Kaufmann, B. B. & van Oudenaarden, A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nature Genet. 37, 937–944 (2005) (10.1038/ng1616) / Nature Genet. by A Becskei (2005)
  23. Blake, W. J., Kaern, M., Cantor, C. R. & Collins, J. J. Noise in eukaryotic gene expression. Nature 422, 633–637 (2003) (10.1038/nature01546) / Nature by WJ Blake (2003)
  24. Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002) (10.1126/science.1070919) / Science by MB Elowitz (2002)
  25. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden, A. Regulation of noise in the expression of a single gene. Nature Genet. 31, 69–73 (2002) (10.1038/ng869) / Nature Genet. by EM Ozbudak (2002)
  26. Paulsson, J. Prime movers of noisy gene expression. Nature Genet. 37, 925–926 (2005) (10.1038/ng0905-925) / Nature Genet. by J Paulsson (2005)
  27. Zaslaver, A. et al. Just-in-time transcription program in metabolic pathways. Nature Genet. 36, 486–491 (2004) (10.1038/ng1348) / Nature Genet. by A Zaslaver (2004)
  28. Cormack, B. P., Valdivia, R. H. & Falkow, S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173, 33–38 (1996) (10.1016/0378-1119(95)00685-0) / Gene by BP Cormack (1996)
  29. Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nature Biotechnol. 22, 1567–1572 (2004) (10.1038/nbt1037) / Nature Biotechnol. by NC Shaner (2004)
  30. Wu, J. Q. & Pollard, T. D. Counting cytokinesis proteins globally and locally in fission yeast. Science 310, 310–314 (2005) (10.1126/science.1113230) / Science by JQ Wu (2005)
  31. Hershko, A. & Ciechanover, A. The ubiquitin system. Annu. Rev. Biochem. 67, 425–479 (1998) (10.1146/annurev.biochem.67.1.425) / Annu. Rev. Biochem. by A Hershko (1998)
  32. Wodicka, L., Dong, H., Mittmann, M., Ho, M. H. & Lockhart, D. J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnol. 15, 1359–1367 (1997) (10.1038/nbt1297-1359) / Nature Biotechnol. by L Wodicka (1997)
  33. Felice, M. R. et al. Post-transcriptional regulation of the yeast high affinity iron transport system. J. Biol. Chem. 280, 22181–22190 (2005) (10.1074/jbc.M414663200) / J. Biol. Chem. by MR Felice (2005)
  34. Colman-Lerner, A. et al. Regulated cell-to-cell variation in a cell-fate decision system. Nature 437, 699–706 (2005) (10.1038/nature03998) / Nature by A Colman-Lerner (2005)
  35. Raser, J. M. & O'Shea, E. K. Control of stochasticity in eukaryotic gene expression. Science 304, 1811–1814 (2004) (10.1126/science.1098641) / Science by JM Raser (2004)
  36. Paulsson, J. Summing up the noise in gene networks. Nature 427, 415–418 (2004) (10.1038/nature02257) / Nature by J Paulsson (2004)
  37. Fraser, H. B., Hirsh, A. E., Giaever, G., Kumm, J. & Eisen, M. B. Noise minimization in eukaryotic gene expression. PLoS Biol. 2, e137 (2004) (10.1371/journal.pbio.0020137) / PLoS Biol. by HB Fraser (2004)
  38. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25–29 (2000) (10.1038/75556) / Nature Genet. by M Ashburner (2000)
  39. Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004) (10.1038/nature02800) / Nature by CT Harbison (2004)
  40. Yu, L. & Morse, R. H. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 5279–5288 (1999) (10.1128/MCB.19.8.5279) / Mol. Cell. Biol. by L Yu (1999)
  41. Huisinga, K. L. & Pugh, B. F. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573–585 (2004) (10.1016/S1097-2765(04)00087-5) / Mol. Cell by KL Huisinga (2004)
  42. Warner, J. R. Synthesis of ribosomes in Saccharomyces cerevisiae. Microbiol. Rev. 53, 256–271 (1989) (10.1128/MMBR.53.2.256-271.1989) / Microbiol. Rev. by JR Warner (1989)
  43. Fagarasanu, M., Fagarasanu, A., Tam, Y. Y., Aitchison, J. D. & Rachubinski, R. A. Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. J. Cell Biol. 169, 765–775 (2005) (10.1083/jcb.200503083) / J. Cell Biol. by M Fagarasanu (2005)
  44. Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998) (10.1016/S0092-8674(00)81641-4) / Cell by FC Holstege (1998)
  45. Wang, Y. et al. Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci. USA 99, 5860–5865 (2002) (10.1073/pnas.092538799) / Proc. Natl Acad. Sci. USA by Y Wang (2002)
Dates
Type When
Created 19 years, 3 months ago (May 14, 2006, 3:15 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 1:55 p.m.)
Indexed 2 weeks, 1 day ago (Aug. 19, 2025, 6:52 a.m.)
Issued 19 years, 3 months ago (May 14, 2006)
Published 19 years, 3 months ago (May 14, 2006)
Published Online 19 years, 3 months ago (May 14, 2006)
Published Print 19 years, 3 months ago (June 1, 2006)
Funders 0

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@article{Newman_2006, title={Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise}, volume={441}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature04785}, DOI={10.1038/nature04785}, number={7095}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Newman, John R. S. and Ghaemmaghami, Sina and Ihmels, Jan and Breslow, David K. and Noble, Matthew and DeRisi, Joseph L. and Weissman, Jonathan S.}, year={2006}, month=may, pages={840–846} }