Identifying protein complexes in high-throughput protein interaction screens using an infinite latent feature model

Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006

Volumn , Issue , 2006, Pages 231-242

  Chu, Wei ^a   Ghahramani, Zoubin ^a   Krause, Roland ^b   Wild, David L ^c  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c KECK GRADUATE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFFINITY PURIFICATION; BAYESIAN APPROACHES; DIFFUSION KERNEL; EXPERIMENTAL DATUM; FEATURE MODELS; GIBBS SAMPLING; HIGH-THROUGHPUT; INDIVIDUAL PROTEINS; PROTEIN COMPLEXES; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS; VALIDATION RESULTS;

BAYESIAN NETWORKS; PROTEINS; RNA;

COMPLEXATION;

DNA DIRECTED RNA POLYMERASE; MULTIPROTEIN COMPLEX; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; STATISTICAL MODEL;

ALGORITHMS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA-DIRECTED RNA POLYMERASES; LIKELIHOOD FUNCTIONS; MASS SPECTROMETRY; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 34547466115     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (21)

1. P. Uetz, L. Giot, G. Cagney, et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature, 403, 623-627, (2000).
2. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori and Y. Sakaki, A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proc Natl Acad Sci USA, 98(8), 4569-4574 (2001).
3. A. Kumar and M. Snyder, Protein complexes take the bait, Nature, 415, 123-124, (2002).
4. A.C. Gavin, M. Bosche, R. Krause, et al., Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, 415, 141-147, (2002).
5. Y. Ho, A. Gruhler, A. Heilbut, et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature, 415, 180-183, (2002).
6. N.J. Krogan, W.T. Peng, G. Cagney, et al., High-definition macromolecular composition of yeast RNA-processing complexes, Molecular Cell, 13, 225-239, (2004).
7. G. Butland, J. M. Peregrin-Alvarez, J. Li, et al., Interaction network containing conserved and essential protein complexes in Escherichia Coli, Nature, 433, 531-537, (2005).
8. G.D. Bader and C.W. Hogue, Analyzing yeast protein-protein interaction data obtained from different sources, Nat Biotechnol, 20(10), 991-997, (2002).
9. G.D. Bader and C.W. Hogue, An automated method for finding molecular complexes in large protein interaction networks, BMC Bioinformatics, 4(1), (2003).
10. V, Spirin and L.A. Mirny, Protein complexes and functional modules in molecular networks, Proc Natl Acad Sci USA, 100(21), 12123-12128, (2003).
11. J. Hollunder, A. Beyer and T. Wilhelm, Identification and characterization of protein subcomplexes in yeast, Proteomics, 5(8), 2082-9, (2005), .
12. Z. Dezso, Z. Oltvai and A.L. Barabasi, Bioinformatics analysis of experimentally determined protein complexes in the Yeast Saccharomyces cerevisiae, Genome Res, 13, 2450-2454, (2003).
13. R. Krause, C. von Mering and P. Bork, A comprehensive set of protein complexes in yeast: Mining large scale protein-protein interaction screens, Bioinformatics, 19(15), 1901-1908, (2003).
14. D. Scholtens and R. Gentleman, Making Sense of High-throughput Proteinprotein Interaction Data, Statistical Applications in Genetics and Molecular Biology 3, Article 39, (2004).
15. R. Kondor and J. Lafferty, Diffusion kernels on graphs and other discrete structures, ICML, 315-322, (2002).
16. J. Shawe-Taylor and N. Cristianini, Kernel Methods for Pattern Analysis, (2004).
17. A. Ben-Hur and W.S. Noble, Kernel methods for predicting protein-protein interactions, Bioinformatics, 21, Suppl. 1, i38-i46, (2005).
18. K. Tsuda and W.S. Noble, Learning kernels from biological networks by maximizing entropy, Bioinformatics, 20, Suppl. 1, i326-i333, (2004).
19. T. L. Griffiths and Z. Ghahramani, Infinite latent feature models and the Indian buffet process Technical Report, GCNU TR 2005-001, University College London, (2005).
20. P. Cramer, D.A. Bushnell, J. Fu, et al., Architecture of RNA polymerase II and implications for the transcription mechnism, Science, 288, 640-649, (2000).
21. H.W. Mewes, D. Frishman, U. Guldener, et al., MIPS: a database for genomes and protein sequences, Nucleic Acids Res, 30, 31-34, (2002).