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Gene Ontology: tool for the unification of biology

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web ( are being constructed: biological process, molecular function and cellular component.

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Figure 1: Examples of Gene Ontology.
Figure 2: Correspondence between hierarchical clustering of expression microarray experiments with GO terms.

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  1. Goffeau, A. et al. Life with 6000 genes. Science 274, 546 (1996).

    Article  CAS  Google Scholar 

  2. Worm Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium. Science 282, 2012–2018 (1998).

  3. Adams, M.D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000).

    Article  Google Scholar 

  4. Meinke, D.W. et al. Arabidopsis thaliana: a model plant for genome analysis. Science 282, 662–682 (1998).

    Article  CAS  Google Scholar 

  5. Chervitz, S.A. et al. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 27, 74–78 (1999).

    Article  CAS  Google Scholar 

  6. Rubin, G.M. et al. Comparative genomics of the eukaryotes. Science 287, 2204–2215 (2000).

    Article  CAS  Google Scholar 

  7. Tang, Z., Kuo, T., Shen, J. & Lin, R.J. Biochemical and genetic conservation of fission yeast Dsk1 and human SR protein-specific kinase 1. Mol. Cell. Biol. 20, 816–824 (2000).

    Article  CAS  Google Scholar 

  8. Vajo, Z. et al. Conservation of the Caenorhabditis elegans timing gene clk-1 from yeast to human: a gene required for ubiquinone biosynthesis with potential implications for aging. Mamm. Genome 10, 1000–1004 (1999).

    Article  CAS  Google Scholar 

  9. Ohi, R. et al. Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes. Mol. Cell. Biol. 18, 4097–4108 (1998).

    Article  CAS  Google Scholar 

  10. Bassett, D.E. Jr et al. Genome cross-referencing and XREFdb: implications for the identification and analysis of genes mutated in human disease. Nature Genet. 15, 339–344 (1997).

    Article  CAS  Google Scholar 

  11. Kataoka T. et al. Functional homology of mammalian and yeast RAS genes. Cell 40,19–26 (1985).

    Article  CAS  Google Scholar 

  12. Botstein, D. & Fink, G.R. Yeast: an experimental organism for modern biology. Science 240, 1439–1443 (1988).

    Article  CAS  Google Scholar 

  13. Tatusov, R.L., Galperin, M.Y., Natale, D.A. & Koonin, E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).

    Article  CAS  Google Scholar 

  14. Andrade, M.A. et al. Automated genome sequence analysis and annotation. Bioinformatics 15, 391–412 (1999).

    Article  CAS  Google Scholar 

  15. Fleischmann, W., Moller, S., Gateau, A. & Apweiler, R. A novel method for automatic functional annotation of proteins. Bioinformatics 15, 228–233 (1999).

    Article  CAS  Google Scholar 

  16. The FlyBase Consortium. The FlyBase database of the Drosophila Genome Projects and community literature. Nucleic Acids Res. 27, 85–88 (1999).

  17. Blake, J.A. et al. The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. Nucleic Acids Res. 28, 108–111 (2000).

    Article  CAS  Google Scholar 

  18. Ringwald, M. et al. GXD: a gene expression database for the laboratory mouse—current status and recent enhancements. Nucleic Acids Res. 28, 115–119 (2000).

    Article  CAS  Google Scholar 

  19. Ball, C.A. et al. Integrating functional genomic information into the Saccharomyces Genome Database. Nucleic Acids Res. 28, 77–80 (2000).

    Article  CAS  Google Scholar 

  20. Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000).

    Article  CAS  Google Scholar 

  21. Benson, D.A. et al. GenBank. Nucleic Acids Res. 28, 15–18 (2000).

    Article  CAS  Google Scholar 

  22. Baker, W. et al. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 28, 19–23 (2000).

    Article  CAS  Google Scholar 

  23. Tateno, Y. et al. DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res. 28, 24–26 (2000).

    Article  CAS  Google Scholar 

  24. Barker, W.C. et al. The Protein Information Resource (PIR). Nucleic Acids Res. 28, 41–44 (2000).

    Article  CAS  Google Scholar 

  25. Mewes, H.W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 28, 37–40 (2000).

    Article  CAS  Google Scholar 

  26. Costanzo, M.C. et al. The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28, 73–76 (2000).

    Article  CAS  Google Scholar 

  27. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 28, 263–266 (2000).

    Article  CAS  Google Scholar 

  28. Lo Conte, L. et al. SCOP: a structural classification of proteins database. Nucleic Acids Res. 28, 257–259 (2000).

    Article  CAS  Google Scholar 

  29. Bairoch, A. The ENZYME database in 2000. Nucleic Acids Res. 28, 304–305 (2000).

    Article  CAS  Google Scholar 

  30. Enzyme Nomenclature. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enyzmes. NC-IUBMB. (Academic, New York, 1992).

  31. Tye, B.K. MCM proteins in DNA replication. Annu. Rev. Biochem. 68, 649–686 (1999).

    Article  CAS  Google Scholar 

  32. Eisen, M., 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  CAS  Google Scholar 

  33. 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 

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We thank K. Fasman and M. Rebhan for useful discussions, and Astra Zeneca for financial support. SGD is supported by a P41, National Resources, grant from National Human Genome Research Institute (NHGRI) grant HG01315; MGD by a P41 from NHGRI grant HG00330; GXD by National Institute of Child Health and Human Development grant HD33745; and FlyBase by a P41 from NHGRI grant HG00739 and the Medical Research Council, London.

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  1. FlyBase (

    • Berkeley Drosophila Genome Project (

      • Saccharomyces Genome Database (

        • Mouse Genome Database and Gene Expression Database (

          • *The Gene Ontology Consortium


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            Ashburner, M., Ball, C., Blake, J. et al. Gene Ontology: tool for the unification of biology. Nat Genet 25, 25–29 (2000).

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