A pooling-deconvolution strategy for biological network elucidation (original) (raw)

• Phizicky, E., Bastiaens, P.I., Zhu, H., Snyder, M. & Fields, S. Protein analysis on a proteomic scale. Nature 422, 208–215 (2003).
  CAS PubMed Google Scholar
• Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000).
  CAS PubMed Google Scholar
• Ito, T. 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, 1143–1147 (2000).
  CAS PubMed PubMed Central Google Scholar
• Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736 (2003).
  CAS PubMed Google Scholar
• Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540–543 (2004).
  CAS PubMed PubMed Central Google Scholar
• Stelzl, U. et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968 (2005).
  CAS PubMed Google Scholar
• Rual, J.F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178 (2005).
  CAS PubMed Google Scholar
• Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).
  CAS PubMed Google Scholar
• Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002).
  CAS PubMed Google Scholar
• Butland, G. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537 (2005).
  CAS PubMed Google Scholar
• Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101–2105 (2001).
  CAS PubMed Google Scholar
• Michaud, G.A. et al. Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509–1512 (2003).
  CAS PubMed Google Scholar
• Zhong, J., Zhang, H., Stanyon, C.A., Tromp, G. & Finley, R.L., Jr. A strategy for constructing large protein interaction maps using the yeast two-hybrid system: regulated expression arrays and two-phase mating. Genome Res. 13, 2691–2699 (2003).
  CAS PubMed PubMed Central Google Scholar
• Hazbun, T.R. et al. Assigning function to yeast proteins by integration of technologies. Mol. Cell 12, 1353–1365 (2003).
  CAS PubMed Google Scholar
• Wu, X., Hart, H., Cheng, C., Roach, P.J. & Tatchell, K. Characterization of Gac1p, a regulatory subunit of protein phosphatase type I involved in glycogen accumulation in Saccharomyces cerevisiae. Mol. Genet. Genomics 265, 622–635 (2001).
  CAS PubMed Google Scholar
• Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).
  CAS PubMed Google Scholar
• Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).
  CAS PubMed Google Scholar
• Heitman, J., Movva, N.R. & Hall, M.N. Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253, 905–909 (1991).
  CAS PubMed Google Scholar
• Carpenter, C.L. & Cantley, L.C. Phosphoinositide kinases. Biochemistry 29, 11147–11156 (1990).
  CAS PubMed Google Scholar
• Salwinski, L. et al. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32 (Database issue), D449–D451 (2004).
  CAS PubMed PubMed Central Google Scholar
• Grigoriev, A. On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res. 31, 4157–4161 (2003).
  CAS PubMed PubMed Central Google Scholar
• Bork, P. et al. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14, 292–299 (2004).
  CAS PubMed Google Scholar
• Janda, K.D. Tagged versus untagged libraries: methods for the generation and screening of combinatorial chemical libraries. Proc. Natl. Acad. Sci. USA 91, 10779–10785 (1994).
  CAS PubMed PubMed Central Google Scholar
• Agyare, F.D. et al. Mapping expressed sequence tag sites on yeast artificial chromosome clones of Arabidopsis thaliana DNA. Genome Res. 7, 1–9 (1997).
  CAS PubMed Google Scholar
• Jeong, H., Mason, S.P., Barabasi, A.L. & Oltvai, Z.N. Lethality and centrality in protein networks. Nature 411, 41–42 (2001).
  CAS PubMed Google Scholar
• Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N. & Barabasi, A.L. The large-scale organization of metabolic networks. Nature 407, 651–654 (2000).
  CAS PubMed Google Scholar
• Massoud, T.F. & Gambhir, S.S. Molecular imaging in living subjects: seeing fundamental biological processes in a new light. Genes Dev. 17, 545–580 (2003).
  CAS PubMed Google Scholar
• Gray, P.A. et al. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306, 2255–2257 (2004).
  CAS PubMed Google Scholar
• Barry, J.R., Lee, E.A. & Messerschmitt, D.G. Digital communication 3rd edn. (Kluwer Academic Publishers, Boston, 2004).
  Google Scholar
• Khan, A.H., Ossadtchi, A., Leahy, R.M. & Smith, D.J. Error-correcting microarray design. Genomics 81, 157–165 (2003).
  CAS PubMed Google Scholar
• Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002).
  CAS PubMed Google Scholar
• Zewail, A. et al. Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc. Natl. Acad. Sci. USA 100, 3345–3350 (2003).
  CAS PubMed PubMed Central Google Scholar
• Xie, M.W. et al. Insights into TOR function and rapamycin response: Chemical genomic profiling by using a high-density cell array method. Proc. Natl. Acad. Sci. USA 102, 7215–7220 (2005).
  CAS PubMed PubMed Central Google Scholar