A combined algorithm for genome-wide prediction of protein function (original) (raw)

References

  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).
    Article ADS CAS Google Scholar
  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).
    Article ADS CAS Google Scholar
  3. Marcotte,E. M. et al. Detecting protein function and protein–protein interactions from genome sequences. Science 285, 751– 753 (1999).
    Article CAS Google Scholar
  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).
    Article Google Scholar
  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).
    Article CAS Google Scholar
  6. The yeast genome directory. Nature 387 (suppl), 1–105 (1997 ).
  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).
    Article CAS Google Scholar
  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).
    Article CAS Google Scholar
  9. Wickner,R. B. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science 264, 566– 569 (1994).
    Article ADS CAS Google Scholar
  10. Miyaki,M. et al. Germline mutation of MSH6 as the cause of hereditary nonpolyposis colorectal cancer. Nature Struct. Biol. 17, 271–272 (1997).
    CAS Google Scholar
  11. Fishel,R. et al. The human mutator gene homologue MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75, 1027–1038 (1993).
    Article CAS Google Scholar
  12. Kushirov,V. V. et al. Nucleotide sequence of the Sup2(Sup35) gene of Saccharomyces cerevisiae. Gene 66, 45– 54 (1988).
    Article Google Scholar
  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).
    Article CAS Google Scholar
  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).
    Article ADS CAS Google Scholar
  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).
    Article CAS Google Scholar
  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).
    Article ADS CAS Google Scholar
  17. Papadopolous,N. et al. Mutations of a MutL homolog in hereditary colon cancer. Science 263, 1625–1629 ( 1994).
    Article ADS Google Scholar
  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).
    Article CAS Google Scholar
  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).
    Article CAS Google Scholar
  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).
    Article ADS CAS Google Scholar
  21. Altschul,S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
    Article CAS Google Scholar
  22. 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).
    Article CAS Google Scholar
  23. 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).
    Article ADS Google Scholar
  24. Chu,S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699–705 ( 1998).
    Article ADS CAS Google Scholar
  25. 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).
    Article ADS CAS Google Scholar
  26. 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).
    CAS Google Scholar

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