Integrating a functional proteomic approach into the target discovery process

Biochimie

Volumn 86, Issue 9-10, 2004, Pages 625-632

  Colland, Frédéric ^a   Daviet, Laurent ^a  

^a Hybrigenics SA   (France)

Author keywords

Functional proteomics; Protein interaction map; Signaling pathway; Target validation; Yeast two hybrid

Indexed keywords

ARTICLE; ASSAY; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; HUMAN; NONHUMAN; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; TWO HYBRID SYSTEM; VALIDATION PROCESS; YEAST;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; PROTEIN BINDING; PROTEOME; PROTEOMICS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 8844280078     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biochi.2004.09.014     Document Type: Article

References (29)

1. M. Vidal, and P. Legrain Yeast forward and reverse 'n'-hybrid systems Nucleic Acids Res. 27 1999 919 929
2. P.L. Bartel, J.A. Roecklein, D. SenGupta, and S. Fields A protein linkage map of Escherichia coli bacteriophage T7 Nat. Genet. 12 1996 72 77
3. M. Flajolet, G. Rotondo, L. Daviet, F. Bergametti, G. Inchauspe, P. Tiollais, C. Transy, and P. Legrain A genomic approach of the hepatitis C virus generates a protein interaction map Gene 242 2000 369 379
4. S. McCraith, T. Holtzman, B. Moss, and S. Fields Genome-wide analysis of vaccinia virus protein-protein interactions Proc. Natl. Acad. Sci. USA 97 2000 4879 4884
5. J.C. Rain, L. Selig, H. De Reuse, V. Battaglia, C. Reverdy, S. Simon, G. Lenzen, F. Petel, J. Wojcik, and V. Schachter The protein-protein interaction map of Helicobacter pylori Nature 409 2001 211 215
6. 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 2001 4569 4574
7. P. Uetz, L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, and P. Pochart A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 2000 623 627
8. S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, J.D. Han, A. Chesneau, and T. Hao A map of the interactome network of the metazoan C. elegans Science 303 2004 540 543
9. L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, C.E. Ooi, B. Godwin, and E. Vitols A protein interaction map of Drosophila melanogaster Science 302 2003 1727 1736
10. A.J. Walhout, R. Sordella, X. Lu, J.L. Hartley, G.F. Temple, M.A. Brasch, N. Thierry-Mieg, and M. Vidal Protein interaction mapping in C. elegans using proteins involved in vulval development Science 287 2000 116 122
11. S.J. Boulton, A. Gartner, J. Reboul, P. Vaglio, N. Dyson, D.E. Hill, and M. Vidal Combined functional genomic maps of the C. elegans DNA damage response Science 295 2002 127 131
12. P. Legrain, J. Wojcik, and J.M. Gauthier Protein-protein interaction maps: a lead towards cellular functions Trends Genet. 17 2001 346 352
13. P.J. Adam, R. Boyd, K.L. Tyson, G.C. Fletcher, A. Stamps, L. Hudson, H.R. Poyser, N. Redpath, M. Griffiths, and G. Steers Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer J. Biol. Chem. 278 2003 6482 6489
14. F. Colland, X. Jacq, V. Trouplin, C. Mougin, C. Groizeleau, and A. Hamburger Functional proteomic mapping of a human signaling pathway Genome Res. 14 2004 1324 1332
15. A.D. Strosberg, L. Daviet, and C. Borg-Capra Functional proteomics applied to obesity research G. Medeiros-Neto A. Halpern C. Bouchard Progress in Obesity Research, John Libbey Eurotext Ltd 2003 229 233
16. E. Formstecher, S. Aresta, V. Collura, A. Hamburger, A. Meil, A. Trehin, C. Reverdy, V. Betin, S. Maire, C. Brun, et al., High fidelity protein interaction mapping: a Drosophila case study, (submitted for publication).
17. B. Boeda, A. El-Amraoui, A. Bahloul, R. Goodyear, L. Daviet, S. Blanchard, I. Perfettini, K.R. Fath, S. Shorte, and J. Reiners Myosin VIIa, harmonin and cadherin 23, three Usher I gene products that cooperate to shape the sensory hair cell bundle EMBO J. 21 2002 6689 6699
18. M. Fromont-Racine, J.C. Rain, and P. Legrain Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens Nat. Genet. 16 1997 277 282
19. J. Wojcik, I.G. Boneca, and P. Legrain Prediction, assessment and validation of protein interaction maps in bacteria J. Mol. Biol. 323 2002 763 770
20. H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, and C. Von Mering The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data Nat. Biotechnol. 22 2004 177 183
21. H. Ge, Z. Liu, G.M. Church, and M. Vidal Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae Nat. Genet. 29 2001 482 486
22. P. Durand, C. Medigue, A. Morgat, Y. Vandenbrouck, A. Viari, and F. Rechenmann Integration of data and methods for genome analysis Curr. Opin. Drug Discov. Dev. 6 2003 346 352
23. M. Tewari, P.J. Hu, J.S. Ahn, N. Ayivi-Guedehoussou, P.O. Vidalain, S. Li, S. Milstein, C.M. Armstrong, M. Boxem, and M.D. Butler Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network Mol. Cell 13 2004 469 482
24. T. Bouwmeester, A. Bauch, H. Ruffner, P.O. Angrand, G. Bergamini, K. Croughton, C. Cruciat, D. Eberhard, J. Gagneur, and S. Ghidelli A physical and functional map of the human TNF-alpha/NF-kappaB signal transduction pathway Nat. Cell. Biol. 6 2004 97 105
25. J. Massague TGF-beta signal transduction Annu. Rev. Biochem. 67 1998 753 791
26. D. Bennett, and L. Alphey PP1 binds Sara and negatively regulates Dpp signaling in Drosophila melanogaster Nat. Genet. 31 2002 419 423
27. G.P. Raju, N. Dimova, P.S. Klein, and H.C. Huang SANE, a novel LEM domain protein, regulates bone morphogenetic protein signaling through interaction with Smad1 J. Biol. Chem. 278 2003 428 437
28. V. Subramaniam, H. Li, M. Wong, R. Kitching, L. Attisano, J. Wrana, J. Zubovits, A.M. Burger, and A. Seth The RING-H2 protein RNF11 is overexpressed in breast cancer and is a target of Smurf2 E3 ligase Br. J. Cancer 89 2003 1538 1544
29. K. Jiao, Y. Zhou, and B.L. Hogan Identification of mZnf8, a Mouse Kruppel-like transcriptional repressor, as a novel nuclear interaction partner of Smad1 Mol. Cell. Biol. 22 2002 7633 7644