Uncovering the rules for protein-protein interactions from yeast genomic data

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 10, 2009, Pages 3752-3757

  Wang, Jin ^a,b   Lia, Chunhe ^a,c   Wang, Erkang ^a   Wang, Xidi ^d  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

^b STONY BROOK UNIVERSITY   (United States)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d Citibank   (Brazil)

Author keywords

FPT; Frequent pattern tree search; Indentifications of protein functions; Predictions of protein protein interactions

Indexed keywords

MESSENGER RNA;

ARTICLE; BAYES THEOREM; CELL FUNCTION; COMPLEX FORMATION; COMPUTER PREDICTION; DIAGNOSTIC ACCURACY; DIAGNOSTIC VALUE; FREQUENT PATTERN TREE APPROACH; GENOMICS; LOGISTIC REGRESSION ANALYSIS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; STRUCTURE ACTIVITY RELATION;

GENOME, FUNGAL; MITOCHONDRIA; PROTEIN INTERACTION MAPPING; RIBOSOMES; ROC CURVE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 62649162748     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0806427106     Document Type: Article

References (35)

1. Jansen R, et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-453.
2. Lin N, Wu BL, Jansen R, Gerstein M, Zhao HY (2004) Information assessment on predicting protein-protein interactions. BMC Bioinformatics 5:154.
3. Cao JP, MA YC, Li YX, Shi TL (2005) The application of the computational methods in protein-protein interaction study. Chinese Bulletin of Life Sci 17:82-87.
4. Uetz P, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
5. Ito T, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574.
6. Rigaut G, et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol, 17:1030-1032.
7. Pellegrini M, Marcotte EM, Yeates TO (1999) Detecting protein function and protein-protein interactions. Proteins 35:440-446.
8. Sprinzak E, Sattath S, Margalit H (2003) Howreliable are experimental protein-protein interaction data? J Mol Biol 327:919-923.
9. Jaimovich A, Elidan G, and Margalit H (2004) Towards an Integrated Protein-Protein Interaction Map. MS Dissertation (Heberw University, Jerusalem).
10. Zhang LV, Wong SL, King OD, Roth FP (2004) Predicting cocomplexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5:38.
11. Friedman N (2004) Inferring cellular networks using probabilistic graphical models. Science 303:799-805.
12. Brown MP, et al. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 97:262-267.
13. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M (2005) Assessing the limits of genomic data integration for predicting protein networks. Genome Res 15:945-953.
14. Han J, Pei J, Yin Y, Mao R (2004) Mining frequent patterns without candidate generation: A frequent-pattern tree approach. Data Mining Knowledge Discovery 8:53-87.
15. Han J, Pei J (2000) Mining frequent patterns by pattern-growth: Methodology and implications. ACM SIGKDD Explorations Newslett 2:14-20.
16. Han JW, Kamber M (2006) In Data Mining Concepts and Techniques, eds Stephan A (Morgan Kaufmann, San Francisco), pp 1-40.
17. Mewes HW, et al. (2002) MIPS: A database for genomes and protein sequences. Nucleic Acids Res 30:31-34.
18. Friedman N, Koller D (2003) Being Bayesian about network structure: A Bayesian approach to structure discovery in Bayesian networks. Machine Learn 50:95-126.
19. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian network to analyze expression data. Comput Biol 7:601-620.
20. Batagelj V, Mrvar A (1998) Pajek - Program for large network analysis. Connections 21:47-57.
21. Gan X, et al. (2002) Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components. Eur J Biochem 269:5203-5214.
22. Graack HR, Wittmann-Liebold B (1998) Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J 329:433-448.
23. Myers1987 Myers AM, Crivellone MD, Tzagoloff A (1987) Characterization of the yeast HEM2 gene and transcriptional regulation of COX5 and COR1 by heme. J Biol Chem 262:3388-3397.
24. Pel1994 Pel HJ, Grivell LA (1994) Protein synthesis in mitochondria. Mol Biol Rep 19:183-194.
25. Lode A, et al. (2002) Molecular characterization of Saccharomyces cerevisiae Sco2p reveals high degree of redundancy with Sco1p. Yeast 19:909-922.
26. Coux O, Tanaka K, Goldberg AL (1996) Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem 65:801-847.
27. Venema J, Tollervey D (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311.
28. Vershoor A, et al. (1998) Three-dimensional structure of the yeast ribosome. Nucleic Acids Res 26:655-661.
29. Salgado-Garrido J, Bragado-Nilsson E, Kandels-Lewis S, Seraphin B (1999) Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. The EMBO J 18:3451-3462.
30. Vijayraghavan U, Company M, Abelson J (1989) Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes and Dev 3:1206-1216.
31. Neubauer G, et al. (1997) Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci USA 94:385-390.
32. James SA, et al. (2002) How Slu7 and Prp18 cooperate in the second step of yeast pre-mRNA splicing. RNA 8:1068-1077.
33. Agrawal R, Srikant R (1994) in Proceedings of the 20th VLDB Conference (Morgan Kaufmann, Santiago, Chile) pp 487-499.
34. Agarwal R, Aggarwal C, Prasad VVV (2001) A tree projection algorithm for generation of frequent item sets. J Parallel Distribut Comput 61:350-371.
35. Savasere A, Omiecinski E and Navathe S (1995) in Proceedings of the 21st VLDB Conference (Morgan Kaufmann, Zurich) pp 432-443.