Ontologies for proteomics: Towards a systematic definition of structure and function that scales to the genome level

Current Opinion in Chemical Biology

Volumn 7, Issue 1, 2003, Pages 44-54

  Lan, Ning ^a   Montelione, Gaetano T ^c   Gerstein, Mark ^a,b  

^a YALE UNIVERSITY   (United States)

^b Yale University   (United States)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

DATA BASE; GENOME; GENOMICS; MOLECULAR INTERACTION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; STANDARDIZATION;

EID: 0037305947     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(02)00020-0     Document Type: Review

References (71)

1. Thornton J.M. From genome to function. Science. 292:2001;2095-2097.
2. Genesereth M, Nilsson N: Logical Foundations of Artificial Intelligence. Los Altos, CA: Morgan Kaufmann; 1987.
3. Gruber T.R. A translation approach to portable ontologies. Knowledge Acquisition. 5:1993;199-220.
4. Zarembinski T.I., Hung L.W., Mueller-Dieckmann H.J., Kim K.K., Yokota H., Kim R., Kim S.H. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc. Natl. Acad. Sci. USA. 95:1998;15189-15193.
5. Cort J.R., Koonin E.V., Bash P.A., Kennedy M.A. A phylogenetic approach to target selection for structural genomics: solution structure of YciH. Nucleic Acids Res. 27:1999;4018-4027.
6. Montelione G.T., Anderson S. Structural genomics: keystone for a Human Proteome Project. Nat. Struct. Biol. 6:1999;11-12.
7. Burley S.K., Almo S.C., Bonanno J.B., Capel M., Chance M.R., Gaasterland T., Lin D., Sali A., Studier F.W., Swaminathan S. Structural genomics: beyond the human genome project. Nat. Genet. 23:1999;151-157.
8. Montelione G.T. Structural genomics: an approach to the protein folding problem. Proc. Natl. Acad. Sci. USA. 98:2001;13488-13489 The author reviews recent progress of genomic-scale 3D protein structure determination and its role in elucidating the protein folding problem.
9. Vitkup D., Melamud E., Moult J., Sander C. Completeness in structural genomics. Nat. Struct. Biol. 8:2001;559-566.
10. Holm L., Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 1:1996;206-209.
11. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., Thornton J.M. CATH-a hierarchic classification of protein domain structures. Structure. 5:1997;1093-1108.
12. Hubbard T.J., Ailey B., Brenner S.E., Murzin A.G., Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res. 27:1999;254-256.
13. Hadley C., Jones D.T. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure Fold Des. 7:1999;1099-1112.
14. Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA: From structure to function: approaches and limitations. Nat Struct Biol 2000, (Suppl):991-994.
15. Teichmann S.A., Murzin A.G., Chothia C. Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Struct. Biol. 11:2001;354-363 The authors review recent efforts on the determination of the function and evolutionary relationships of proteins by experimental structural genomics and the discovery of protein-protein interactions by computational structural genomics.
16. Brenner S.E., Levitt M. Expectations from structural genomics. Protein Sci. 9:2000;197-200.
17. Stevens R.C., Yokoyama S., Wilson I.A. Global efforts in structural genomics. Science. 294:2001;89-92 The authors describe the worldwide initiative in structural genomics and highlight the Second International Structural Genomics Meeting of 2001.
18. Heinemann U: Structural genomics in Europe: slow start, strong finish? Nat Struct Biol 2000, (Suppl):940-942.
19. Terwilliger TC: Structural genomics in North America. Nat Struct Biol 2000, (Suppl):935-939.
20. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S: Structural genomics projects in Japan. Nat Struct Biol 2000, (Suppl):943-945.
21. Burley F.C., Bonanno J.B. Structuring the universe of proteins. Annu. Rev. Genomics. Hum. Genet. 3:2002;243-262.
22. On World Wide Web URL: http://www.nesg.org.
23. Bertone P., Kluger Y., Lan N., Zheng D., Christendat D., Yee A., Edwards A.M., Arrowsmith C.H., Montelione G.T., Gerstein M. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res. 29:2001;2884-2898 The authors describe a structural genomics project tracking database specifically designed to enable distributed scientific collaboration via the Internet as well as an active vehicle to standardize proteomics data in a form that would enable systematic data mining.
24. Adams P.D., Grosse-Kunstleve R.W., Hung L.W., Ioerger T.R., McCoy A.J., Moriarty N.W., Read R.J., Sacchettini J.C., Sauter N.K., Terwilliger T.C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D. 58:2002;1948-1954.
25. Seavey B.R., Farr E.A., Westler W.M., Markley J.L. A relational database for sequence-specific protein NMR data. J. Biomol. NMR. 1:1991;217-236.
26. Fogh R. The CCPN project: an interim report on a data model for the NMR community. Nat. Struct. Biol. 9:2002;416-418.
27. Baran M., Moseley H.N.B., Sahota G., Montelione G.T. SPINS: A data dictionary and object-oriented relational database for archiving protein NMR spectra. J. Biomol. NMR. 24:2002;113-121 The authors describe SPINS, an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and automatic submission of results to the public domain.
28. On World Wide Web URL: http://www.bmrb.wisc.edu.
29. On World Wide Web URL: http://www.bio.cam.ac.uk/nmr/ccp.
30. Berman H.M., Battistuz T., Bhat T.N., Bluhm W.F., Bourne P.E., Burkhardt K., Feng Z., Gilliland G.L., Iype L., Jain S.et al. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242 The authors describe the short-term and long-term goals of the PDB, the data deposition systems, and how to obtain further information.
31. On World Wide Web URL: http://www.targetdb.rutgers.edu/index.html.
32. Brenner S.E., Barken D., Levitt M. The PRESAGE database for structural genomics. Nucleic Acids Res. 27:1999;251-253.
33. Westbrook J., Feng Z., Jain S., Bhat T.N., Thanki N., Ravichandran V., Gilliland G.L., Bluhm W., Weissig H., Greer D.S.et al. The Protein Data Bank: unifying the archive. Nucleic Acids Res. 30:2002;245-248 The authors describe a validation process of all data in the PDB archive and the release of a uniform archive for the structural genomics community.
34. Newkirk K., Feng W., Jiang W., Tejero R., Emerson S.D., Inouye M., Montelione G.T. Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: Identification of a binding epitope for DNA. Proc. Natl. Acad. Sci. USA. 91:1994;5114-5118.
35. Feng W., Tejero R., Zimmerman D.E., Inouye M., Montelione G.T. Solution NMR structure and backbone dynamics of the major cold shock protein (CspA) from Escherichia coli: Evidence for conformational dynamics in the proposed ssRNA-binding site. Biochemistry. 37:1998;10881-10896.
36. Cort J.R., Chiang Y., Zheng D., Montelione G.T., Kennedy M.A. NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold. Prot. Struct. Funct. Genet. 48:2002;733-736.
37. Yang H., Jeffrey P.D., Miller J., Kinnucan E., Sun Y., Thoma N.H., Zheng N., Chen P.L., Lee W.H., Pavletich N.P. BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science. 297:2002;1837-1848.
38. Ross-Macdonald P. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 402:1999;413-418.
39. Ni L., Snyder M. A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol. Biol. Cell. 12:2001;2147-2170.
40. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H.et al. Functional characterization of the Saccharomyces cerevisiae genome by comprehensive and precise gene deletion and massively parallel analysis. Science. 285:1999;901-906.
41. Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., Yamamoto K., Kuhara S., Sakaki Y.et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA. 97:2000;1143-1147.
42. Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18:2000;1257-1261.
43. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P.et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
44. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA. 98:2001;4569-4574.
45. MacBeath G., Schreiber S.L. Printing proteins as microarrays for high throughput function determination. Science. 289:2000;1760-1762.
46. Zhu H., Klemic J.F., Chang S., Bertone P., Casamayor A., Klemic K.G., Smith D., Gerstein M., Reed M.A., Snyder M. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26:2000;283-289.
47. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S.et al. Global analysis of protein activities using proteome chips. Science. 293:2001;2101-2105.
48. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M.et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147.
49. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K.et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:2002;180-183.
50. Bork P., Koonin E.V. Protein sequence motifs. Curr. Opin. Struct. Biol. 6:1996;366-376.
51. Zhang Z., Schaffer A.A., Miller W., Madden T.L., Lipman D.J., Koonin E.V., Altschul S.F.et al. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. 26:1998;3986-3990.
52. Attwood T.K., Flower D.R., Lewis A.P., Mabey J.E., Morgan S.R., Scordis P., Selley J.N., Wright W.et al. PRINTS prepares for the new millennium. Nucleic Acids Res. 27:1999;220-225.
53. Hegyi H., Gerstein M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 11:2001;1632-1640.
54. Wilson C.A., Kreychman J., Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297:2000;233-249.
55. Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143 The authors explore the functional variation of homologous enzyme superfamilies containing two or more enzymes and find that almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling.
56. Vacek M: A gene by any other name. American Scientist 2001, 89: on World Wide Web URL http://www.sigmaxi.org/amsci/Issues/Sciobs01/sciobs0111gene.html.
57. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T.et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25:2000;25-29 The authors describe GO, a structured and precisely defined controlled vocabulary for describing gene function across several organisms. GO consists of three DAGs: biological process, molecular function and cellular component, which define gene function at various levels, including its biochemical activities, biological roles as well as cellular structure.
58. Mewes H.W., Frishman D., Guldener U., Mannhaupt G., Mayer K., Mokrejs M., Morgenstern B., Munsterkotter M., Rudd S., Weil B. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30:2000;31-34.
59. Webb EC: Enzyme Nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. New York: Academic Press; 1992.
60. On World Wide Web URL: http://www.geneontology.org/doc/gobo.html.
61. Karp P.D. An ontology for biological function based on molecular interactions. Bioinformatics. 16:2000;269-285 The author describes the functional ontology developed for the EcoCyc database, which encodes a diverse array of biochemical processes. The ontology is validated through its use to support complex functional queries for the EcoCyc DB.
62. Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;751-753.
63. Jansen R., Greenbaum D., Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res. 12:2002;37-46 The authors investigate the relationship of protein-protein interactions with mRNA expression levels, by integrating a variety of data sources for yeast and find that subunits of the same protein complex show significant coexpression, both in terms of similarities of absolute mRNA levels and expression profiles.
64. Lan N, Jansen R, Gerstein M: Towards a systematic definition of protein function that scales to the genome level: defining function in terms of interactions. Proc IEEE, in press.
65. Fromont-Racine M., Mayes A.E., Brunet-Simon A., Rain J.C., Colley A., Dix I., Decourty L., Joly N., Ricard F., Beggs J.D., Legrain P. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast. 17:2000;95-110.
66. Matthews L.R., Vaglio P., Reboul J., Ge H., Davis B.P., Garrels J., Vincent S., Vidal M. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or interologs. Genome Res. 11:2001;2120-2126.
67. Antonini E, Brunoni M: Hemoglobin and Myoglobin in their Reactions with Ligands. Amsterdam, Holland: Borth-Holland; 1971.
68. Hegyi H., Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288:1999;147-164.
69. Kumar A., Agarwal S., Heyman J.A., Matson S., Heidtman M., Piccirillo S., Umansky L., Drawid A., Jansen R., Liu Y.et al. Subcellular localization of the yeast proteome. Genes Dev. 16:2002;707-719.
70. Cho R., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J., Davis R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2:1998;65-73.
71. Hughes T., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D.et al. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126.