A critical and integrated view of the yeast interactome

Comparative and Functional Genomics

Volumn 5, Issue 5, 2004, Pages 382-402

  Cornell, Michael ^a   Paton, Norman W ^a   Oliver, Stephen G ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Data integration; Protein interactions; Saccharomyces cerevisiae

Indexed keywords

FUNGAL PROTEIN;

ARTICLE; CELL FUNCTION; DATA ANALYSIS; DATA BASE; GENE FUNCTION; GENOME INFORMATION MANAGEMENT SYSTEM; HIGH THROUGHPUT SCREENING; INFORMATION SYSTEM; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RELIABILITY; SAMPLING; YEAST;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 4444366661     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.412     Document Type: Article

References (29)

1. Aloy P, Russell RB. 2002. The third dimension for protein interactions and complexes. Trends Biochem Sci 27: 633-638.
2. Ashburner M, Ball CA, Blake JA, et al. 2000. Gene ontology: tool for the unification of biology. Nature Genet 25: 25-29.
3. Bader GD, Hogue CW. 2002. Analyzing yeast protein-protein interaction data obtained from different sources. Nature Biotechnol 20: 991-997.
4. Bader JS, Chaudhuri A, Rothberg JM, Chant J. 2004. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnol 22: 78-85.
5. Blackstock W, Mann M. 2001. A boundless future for proteomics? Trends Biotechnol 19: S1-S2.
6. Cornell M, Paton NW, Hedeler C, et al. 2003. GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast 20: 1291-1306.
7. Deane CM, Salwinski L, Xenarios I, Eisenberg D. 2002. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 1: 349-356.
8. Deng M, Zhang K, Mehta S, Chen T, Sun F. 2003. Prediction of protein function using protein-protein interaction data. J Comput Biol 10: 947-960.
9. Gavin AC, Boesche M, Krause R, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-17.
10. Gu W, Malik S, Ito M, et al. 1999. A novel human srb/med-containing cofactor complex, smcc, involved in transcription regulation. Mol Cell 3: 97-108.
11. Goldberg DS, Roth FP. 2003. Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA 100: 4372-4376.
12. Grigoriev A. 2003. On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res 31: 4157-4161.
13. Hahn MW, Conant GC, Wagner A. 2004. Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol 58: 203-211.
14. Hazbun TR, Fields S. 2001. Networking proteins in yeast. Proc Natl Acad Sci USA 98: 4277-4278.
15. Ho Y, Gruhler A, Heilbut A, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
16. Hughes TR, Marton MJ, Jones AR, et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
17. Ito T, Chiba T, Ozawa R, et al. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98: 4569-4574.
18. Jansen R, Greenbaum D, Gerstein, M. 2002. Relating whole-genome expression data with protein-protein interactions. Genome Res 12: 37-46.
19. Jeong H, Mason SP, Barabasi A-L, Oltvai ZN. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
20. Kemmeren P. van Berkum NL, Vilo J, et al. 2002. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 9: 1133-1143.
21. Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F. 1997. MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res 25: 28-30.
22. Paton NW, Khan SA, Hayes A, et al. 2000. Conceptual modelling of genomic information. Bioinformatics 16: 548-557.
23. Pereira-Leal JB, Enright AJ, Ouzounis CA. 2004. Detection of functional modules from protein interaction networks. Proteins 54: 49-57.
24. Przulj N, Wigle DA, Jurisica I. 2004. Functional topology in a network of protein interactions. Bioinformatics 20: 340-348.
25. Rain JC, Selig L, De Reuse H, et al. 2000. The protein-protein interaction map of Helicobacter pylori. Nature 409: 211-215.
26. Saito R, Suzuki H, Hayashizaki Y. 2002. Interaction generality, a measurement to assess the reliability of a protein-protein interaction. Nucleic Acids Res 30: 1163-1168.
27. Samanta MP, Liang S. 2003. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci USA 100: 12579-12583.
28. Uetz P, Giot L, Cagney G, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
29. von Mering C, Krause R, Snel B, et al. 2002. Comparative assessment of large-scale datasets of protein-protein interactions. Nature 417: 399-403.