Registro:

Referencias:

• Cohen, P., Protein kinases-the major drug targets of the twenty-first century? (2002) Nat. Rev. Drug Discov., 1, pp. 309-315
• Hunter, T., Signaling-2000 and beyond (2000) Cell, 100, pp. 113-127
• Irish, J.M., Hovland, R., Krutzik, P.O., Perez, O.D., Bruserud Ø, Gjertsen, B.T., Nolan, G.P., Single cell profiling of potentiated phospho-protein networks in cancer cells (2004) Cell, 118, pp. 217-228
• Pelkmans, L., Fava, E., Grabner, H., Hannus, M., Habermann, B., Krausz, E., Zerial, M., Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis (2005) Nature, 436, pp. 78-86
• Savage, D.G., Antman, K.H., Imatinib mesylate-A new oral targeted therapy (2002) N. Engl. J. Med., 346, pp. 683-693
• Ptacek, J., Devgan, G., Michaud, G., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Snyder, M., Global analysis of protein phosphorylation in yeast (2005) Nature, 438 (7068), pp. 679-684. , DOI 10.1038/nature04187
• Linding, R., Jensen, L.J., Ostheimer, G.J., Van Vugt, M.A., Jorgensen, C., Miron, I.M., Diella, F., Pawson, T., Systematic discovery of in vivo phosphorylation networks (2007) Cell, 129, pp. 1415-1426
• Fiedler, D., Braberg, H., Mehta, M., Chechik, G., Cagney, G., Mukherjee, P., Silva, A.C., Krogan, N.J., Functional organization of the S. cerevisiae phosphorylation network (2009) Cell, 136, pp. 952-963
• Rishton, G.M., Failure and success in modern drug discovery: Guiding principles in the establishment of high probability of success drug discovery organizations (2005) Med. Chem., 1, pp. 519-527
• Holt, L.J., Tuch, B.B., Villen, J., Johnson, A.D., Gygi, S.P., Morgan, D.O., Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution (2009) Science, 325, pp. 1682-1686
• Huber, A., Bodenmiller, B., Uotila, A., Stahl, M., Wanka, S., Gerrits, B., Aebersold, R., Loewith, R., Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis (2009) Genes Dev., 23, pp. 1929-1943
• Olsen, J.V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., Mann, M., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks (2006) Cell, 127, pp. 635-648
• Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Linton, L.M., International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome (2001) Nature, 409, pp. 860-921
• Manning, G., Whyte, D.B., Martinez, R., Hunter, T., Sudarsanam, S., The protein kinase complement of the human genome (2002) Science, 298, pp. 1912-1934
• Mager, W.H., Winderickx, J., Yeast as a model for medical and medicinal research (2005) Trends Pharmacol. Sci., 26, pp. 265-273
• Lindquist, S., Krobitsch, S., Li, L., Sondheimer, N., Investigating protein conformationbased inheritance and disease in yeast (2001) Philos. Trans. R. Soc. Lond. B Biol. Sci., 356, pp. 169-176
• Outeiro, T.F., Muchowski, P.J., Molecular genetics approaches in yeast to study amyloid diseases (2004) J. Mol. Neurosci., 23, pp. 49-60
• Hunter, T., Plowman, G.D., The protein kinases of budding yeast: Six score and more (1997) Trends Biochem. Sci., 22, pp. 18-22
• Widmann, C., Gibson, S., Jarpe, M.B., Johnson, G.L., Mitogen-activated protein kinase: Conservation of a three-kinase module from yeast to human (1999) Physiol. Rev., 79, pp. 143-180
• Simon, J.A., Bedalov, A., Yeast as a model system for anticancer drug discovery (2004) Nat. Rev. Cancer, 4, pp. 481-492
• Bishop, A.C., Ubersax, J.A., Petsch, D.T., Matheos, D.P., Gray, N.S., Blethrow, J., Shimizu, E., Shokat, K.M., A chemical switch for inhibitor-sensitive alleles of any protein kinase (2000) Nature, 407, pp. 395-401
• Bodenmiller, B., Mueller, L.N., Mueller, M., Domon, B., Aebersold, R., Reproducible isolation of distinct, overlapping segments of the phosphoproteome (2007) Nat. Methods, 4, pp. 231-237
• Larsen, M.R., Thingholm, T.E., Jensen, O.N., Roepstorff, P., Jorgensen, T.J., Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns (2005) Mol. Cell. Proteomics, 4, pp. 873-886
• Mueller, L.N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M.Y., Vitek, O., Muller, M., SuperHirn-A novel tool for high resolution LC-MS-based peptide/protein profiling (2007) Proteomics, 7, pp. 3470-3480
• Brusniak, M.Y., Bodenmiller, B., Campbell, D., Cooke, K., Eddes, J., Garbutt, A., Lau, H., Watts, J.D., Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics (2008) BMC Bioinformatics, 9, p. 542
• Keller, A., Nesvizhskii, A.I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search (2002) Anal. Chem., 74, pp. 5383-5392
• Elias, J.E., Gygi, S.P., Target-decoy search strategy for increased confidence in largescale protein identifications by mass spectrometry (2007) Nat. Methods, 4, pp. 207-214
• Smyth, G., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments (2004) Stat. Appl. Genet. Mol. Biol., 3. , Article 3
• Benjamini, Y., Hochberg, Y., Controlling the false discovery rate-A practical and powerful approach to multiple testing (1995) J. R. Statist. Soc. Series B Stat. Methodol., 57, pp. 289-300
• Bodenmiller, B., Malmstrom, J., Gerrits, B., Campbell, D., Lam, H., Schmidt, A., Rinner, O., Aebersold, R., PhosphoPep-A phosphoproteome resource for systems biology research in Drosophila Kc167 cells (2007) Mol. Syst. Biol., 3, p. 139
• Schwartz, D., Chou, M.F., Church, G.M., (2009) Predicting protein post-translational modifications using meta-Analysis of proteome scale data sets. Mol. Cell. Proteomics, 8, pp. 365-379
• Breitkreutz, B.J., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M., Oughtred, R., Tyers, M., The BioGRID Interaction Database: 2008 update (2008) Nucleic Acids Res., 36, pp. D637-D640
• Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Von Mering, C., STRING 8-A global view on proteins and their functional interactions in 630 organisms (2009) Nucleic Acids Res., 37, pp. D412-D416
• Mok, J., Kim, P.M., Lam, H.Y., Piccirillo, S., Zhou, X., Jeschke, G.R., Sheridan, D.L., Turk, B.E., (2010) Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci. Signal., 3. , ra12
• Stark, C., Su, T.C., Breitkreutz, A., Lourenco, P., Dahabieh, M., Breitkreutz, B.J., Tyers, M., Sadowski, I., PhosphoGRID: A database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae (2010) Database (Oxford ), p. 2010. , bap026
• Ubersax, J.A., Woodbury, E.L., Quang, P.N., Paraz, M., Blethrow, J.D., Shah, K., Shokat, K.M., Morgan, D.O., Targets of the cyclin-dependent kinase Cdk1 (2003) Nature, 425, pp. 859-864
• Hirata, Y., Andoh, T., Asahara, T., Kikuchi, A., Yeast glycogen synthase kinase-3 activates Msn2p-dependent transcription of stress responsive genes (2003) Mol. Biol. Cell, 14, pp. 302-312
• Hinnebusch, A.G., Natarajan, K., Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress (2002) Eukaryot. Cell, 1, pp. 22-32
• Sterner, D.E., Lee, J.M., Hardin, S.E., Greenleaf, A.L., The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex (1995) Mol. Cell. Biol, 15, pp. 5716-5724
• Grose, J.H., Smith, T.L., Sabic, H., Rutter, J., Yeast PAS kinase coordinates glucose partitioning in response to metabolic and cell integrity signaling (2007) EMBO J., 26, pp. 4824-4830
• Hillenmeyer, M.E., Fung, E., Wildenhain, J., Pierce, S.E., Hoon, S., Lee, W., Proctor, M., Giaever, G., The chemical genomic portrait of yeast: Uncovering a phenotype for all genes (2008) Science, 320, pp. 362-365
• Ohya, Y., Sese, J., Yukawa, M., Sano, F., Nakatani, Y., Saito, T.L., Saka, A., Morishita, S., High-dimensional and large-scale phenotyping of yeast mutants (2005) Proc. Natl. Acad. Sci. U.S.A., 102, pp. 19015-19020
• Blacketer, M.J., Koehler, C.M., Coats, S.G., Myers, A.M., Madaule, P., Regulation of dimorphism in Saccharomyces cerevisiae: Involvement of the novel protein kinase homolog Elm1p and protein phosphatase 2A (1993) Mol. Cell. Biol., 13, pp. 5567-5581
• Thomson, M., Gunawardena, J., Unlimited multistability in multisite phosphorylation systems (2009) Nature, 460, pp. 274-277
• Ashby, W.R., (1956) An Introduction to Cybernetics, , Chapman & Hall Ltd.,London
• Ashby, W.R., Requisite variety and its implications for the control of complex systems (1958) Cybernetica, 1, pp. 83-99
• Kimura, M., Evolutionary rate at the molecular level (1968) Nature, 217, pp. 624-626
• Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: A tutorial (2008) Mol. Syst. Biol., 4, p. 222
• Picotti, P., Aebersold, R., Domon, B., The implications of proteolytic background for shotgun proteomics (2007) Mol. Cell. Proteomics, 6, pp. 1589-1598
• Picotti, P., Lam, H., Campbell, D., Deutsch, E.W., Mirzaei, H., Ranish, J., Domon, B., Aebersold, R., A database of mass spectrometric assays for the yeast proteome (2008) Nat. Methods, 5, pp. 913-914
• Bodenmiller, B., Campbell, D., Gerrits, B., Lam, H., Jovanovic, M., Picotti, P., Schlapbach, R., Aebersold, R., PhosphoPep-A database of protein phosphorylation sites in model organisms (2008) Nat. Biotechnol., 26, pp. 1339-1340
• Acknowledgments: We thank the whole team of the Functional Genomics Center Zurich (FGCZ) for fruitful discussions. We thank C. Zheng, Department of Statistics, Purdue University, for help with use and interpretation of the Limma package. Funding: This project was funded in part by ETH Zurich; Federal funds from the National Heart, Lung, and Blood Institute, NIH, under contract no. N01-HV-28179; the PhosphoNetX project of SystemsX.ch, the Swiss initiative for systems biology; and the European Research Council (grant ERC-2008-AdG 233226) to R.A. Work at the FGCZ and at the von Mering laboratory has been supported by the University Research Priority Program Systems Biology and Functional Genomics of the University of Zurich. B.G. is supported by the Bonizzi-Theler Foundation. C.K. is supported by a Marie-Heim Vögtlin fellowship from the Swiss National Science Foundation (SNF)

Citas:

---------- APA ----------

---------- CHICAGO ----------

---------- MLA ----------

---------- VANCOUVER ----------