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From genomics to proteomics

Abstract

Proteomics is the study of the function of all expressed proteins. Tremendous progress has been made in the past few years in generating large-scale data sets for protein–protein interactions, organelle composition, protein activity patterns and protein profiles in cancer patients. But further technological improvements, organization of international proteomics projects and open access to results are needed for proteomics to fulfil its potential.

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Figure 1: Platforms for proteomics and functional genomics.
Figure 2: Visualization of combined, large-scale interaction data sets in yeast.

References

  1. Wilkins, M. R. et al. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14, 61–65 (1996).

    ADS  CAS  PubMed  Google Scholar 

  2. Shoemaker, D. D. & Linsley, P. S. Recent developments in DNA microarrays. Curr. Opin. Microbiol. 5, 334–337 (2002).

    CAS  Article  Google Scholar 

  3. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).

    ADS  CAS  Article  Google Scholar 

  4. Gerlai, R. Phenomics: fiction or the future? Trends Neurosci. 25, 506–509 (2002).

    Article  Google Scholar 

  5. Tong, A. H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364–2368 (2001).

    ADS  CAS  Article  Google Scholar 

  6. Hannon, G. J. RNA interference. Nature 418, 244–251 (2002).

    ADS  CAS  Article  Google Scholar 

  7. Kuruvilla, F. G., Shamji, A. F., Sternson, S. M., Hergenrother, P. J. & Schreiber, S. L. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653–657 (2002).

    ADS  CAS  Article  Google Scholar 

  8. Csete, M. E. & Doyle, J. C. Reverse engineering of biological complexity. Science 295, 1664–1669 (2002).

    ADS  CAS  Article  Google Scholar 

  9. Ficarro, S. B. et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nature Biotechnol. 20, 301–305 (2002).

    CAS  Article  Google Scholar 

  10. Liu, H., Lin, D. & Yates, J. R. III Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques 32, 898–911 (2002).

    CAS  Article  Google Scholar 

  11. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929–934 (2001).

    ADS  CAS  Article  Google Scholar 

  12. Fields, S. & Song, O. A novel genetic system to detect protein–protein interactions. Nature 340, 245–246 (1989).

    ADS  CAS  Article  Google Scholar 

  13. MacBeath, G. Protein microarrays and proteomics. Nature Genet. 32 (Suppl.), 526–532 (2002).

    CAS  Article  Google Scholar 

  14. Wright, P. E. & Dyson, H. J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293, 321–331 (1999).

    CAS  Article  Google Scholar 

  15. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25–29 (2000).

    CAS  Article  Google Scholar 

  16. Bader, G. D. & Hogue, W. V. C. in Genomics and Bioinformatics (ed. Sensen, C. W.) 399–413 (Wiley-VCH, Weinheim, 2001).

    Google Scholar 

  17. Kitano, H. Systems biology: a brief overview. Science 295, 1662–1664 (2002).

    ADS  CAS  Article  Google Scholar 

  18. Petricoin, E. F., Zoon, K. C., Kohn, E. C., Barrett, J. C. & Liotta, L. A. Clinical proteomics: translating benchside promise into bedside reality. Nature Rev. Drug Discov. 1, 683–695 (2002).

    CAS  Article  Google Scholar 

  19. Andersen, J. S. et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1–11 (2002).

    Article  Google Scholar 

  20. Jorgensen, P., Nishikawa, J. L., Breitkreutz, B. J. & Tyers, M. Systematic identification of pathways that couple cell growth and division in yeast. Science 297, 395–400 (2002).

    ADS  CAS  Article  Google Scholar 

  21. Walhout, A. J. et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12, 1952–1958 (2002).

    CAS  Article  Google Scholar 

  22. Manning, B. D., Tee, A. R., Logsdon, M. N., Blenis, J. & Cantley, L. C. Identification of the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the phosphoinositide 3-kinase/akt pathway. Mol. Cell 10, 151–162 (2002).

    CAS  Article  Google Scholar 

  23. Yoon, H. J. et al. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Curr. Biol. 12, 2048–2054 (2002).

    MathSciNet  CAS  Article  Google Scholar 

  24. Mann, M. & Jensen, O. N. Proteomic analysis of post-translational modifications. Nature Biotechnol. (in the press).

  25. Huang, S. & Ingber, D. E. Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp. Cell Res. 261, 91–103 (2000).

    CAS  Article  Google Scholar 

  26. Ball, P. Data visualization: picture this. Nature 418, 11–13 (2002).

    ADS  CAS  Article  Google Scholar 

  27. Aebersold, R. & Watts, J. D. The need for national centers for proteomics. Nature Biotechnol. 20, 651 (2002).

    CAS  Article  Google Scholar 

  28. Marshall, E. Bermuda rules: community spirit, with teeth. Science 291, 1192 (2001).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank B.-J. Breitkreutz for preparing Fig. 2, D. Figeys and members of the Center for Experimental BioInformatics (CEBI) for critical reading of the manuscript. CEBI is supported by a grant from the Danish Natural Research Foundation.

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Tyers, M., Mann, M. From genomics to proteomics. Nature 422, 193–197 (2003). https://doi.org/10.1038/nature01510

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