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A combined algorithm for genome-wide prediction of protein function

Marcotte, Edward M., Pellegrini, Matteo, Thompson, Michael J., Yeates, Todd O., Eisenberg, David·1999·Nature
DOI 10.1038/47048
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Abstract

The availability of over 20 fully sequenced genomes has driven the development of new methods to find protein function and interactions. Here we group proteins by correlated evolution, correlated messenger RNA expression patterns and patterns of domain fusion to determine functional relationships among the 6,217 proteins of the yeast Saccharomyces cerevisiae. Using these methods, we discover over 93,000 pairwise links between functionally related yeast proteins. Links between characterized and uncharacterized proteins allow a general function to be assigned to more than half of the 2,557 previously uncharacterized yeast proteins. Examples of functional links are given for a protein family of previously unknown function, a protein whose human homologues are implicated in colon cancer and the yeast prion Sup35.

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Research works printed but not linked: 25

  1. Pellegrini,M., Marcotte,E. M., Thompson, M. J., Eisenberg,D. & Yeates,T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285–4288 (1999). · DOI
  2. Eisen,M. B., Spellman,P. T., Brown,P. O. & Botstein,D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863– 14868 (1998). · DOI · Paper page
  3. Marcotte,E. M. et al. Detecting protein function and protein–protein interactions from genome sequences. Science 285, 751– 753 (1999). · DOI · Paper page
  4. Mewes,H. W., Hani,J., Pfeiffer,F. & Frishman,D. MIPS: a database for protein sequences and complete genomes. Nucleic Acids Res. 26, 33–37 ( 1998). · DOI
  5. Karp,P., Riley,M., Paley,S. & Pellegrini-Toole,A. EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 26, 50–53 (1998). · DOI
  6. The yeast genome directory. Nature 387 (suppl), 1–105 (1997 ). · DOI
  7. Bairoch,A. & Apewiler,R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 27, 49–54 ( 1999). · DOI
  8. Bardosi,A., Eber,S. W., Hendrys,M. & Pekrun,A. Myopathy with altered mitochondria due to a triosephosphate isomerase (TPI) deficiency. Acta Neuropathol. (Berl.) 79, 387– 394 (1990). · DOI
  9. Wickner,R. B. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science 264, 566– 569 (1994). · DOI
  10. Miyaki,M. et al. Germline mutation of MSH6 as the cause of hereditary nonpolyposis colorectal cancer. Nature Struct. Biol. 17, 271–272 (1997).
  11. Fishel,R. et al. The human mutator gene homologue MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75, 1027–1038 (1993). · DOI
  12. Kushirov,V. V. et al. Nucleotide sequence of the Sup2(Sup35) gene of Saccharomyces cerevisiae. Gene 66, 45– 54 (1988). · DOI
  13. Stansfield,I. et al. The products of the SUP45 (eRF1) and SUP35 genes interact to mediate translation termination in Saccharomyces cerevisiae. EMBO J. 14, 4365–4373 ( 1995). · DOI
  14. Chen,X., Sullivan,D. S. & Huffaker, T. C. Two yeast genes with similarity to TCP-1 are required for microtubule and actin function in vivo. Proc. Natl Acad. Sci. USA 91, 9111–9115 ( 1994). · DOI
  15. Johnson,R. E., Kovvali,G. K., Prakash,L. & Prakash,S. Requirement of the yeast MSH3 and MSH6 genes for MSH2-dependent genomic stability. J. Biol. Chem. 271, 7285– 7288 (1996). · DOI
  16. Lynch,H. T., Fusaro,R. M. & Lynch, J. F. Cancer genetics in the new era of molecular biology. Ann. NY Acad. Sci. 833, 1– 28 (1997). · DOI
  17. Papadopolous,N. et al. Mutations of a MutL homolog in hereditary colon cancer. Science 263, 1625–1629 ( 1994). · DOI
  18. West,M. G., Horne,D. W. & Appling, D. R. Metabolic role of cytoplasmic isozymes of 5,10-methylenetetrahydrofolate dehydrogenase in Saccharomyces cerevisiae. Biochemistry 35, 3122–3132 ( 1996). · DOI
  19. Dandekar,T., Snel,B., Huynen,M. & Bork,P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324–328 (1998). · DOI
  20. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G. D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA 96, 2896– 2901 (1999). · DOI
  21. Spellman,P. T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273– 3297 (1998). · DOI
  22. DeRisi,J. L., Iyer,V. R. & Brown,P. O Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680– 686 (1998). · DOI
  23. Chu,S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699–705 ( 1998). · DOI
  24. Myers,L. C., Gustafsson,C. M., Hayashibara, K. C., Brown,P. O. & Kornberg,R. D. Mediator protein mutations that selectively abolish activated transcription. Proc. Natl Acad. Sci. USA 96, 67–72 ( 1999). · DOI · Paper page
  25. Horton,P. & Nakai,K. Better prediction of protein cellular localization sites with the k nearest neighbors classifier. Intell. Sys. Molec. Biol. 5, 147–152 (1997).

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Metadata

Authors
Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O., & Eisenberg, D.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
1999-11
Volume
402
Issue
6757
Pages
83-86
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/47048
Cited by
682
References
1
Language
en
Licence
www.springer.com/tdm (tdm)

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CoChat. (2026). Citation check: A combined algorithm for genome-wide prediction of protein function. https://app.cochat.ai/papers/10.1038/47048
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Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O., & Eisenberg, D. (1999). A combined algorithm for genome-wide prediction of protein function. Nature. https://doi.org/10.1038/47048