Proteomics and phosphoproteomics for the mapping of cellular signalling networks

Proteomics

Volumn 8, Issue 21, 2008, Pages 4402-4415

  Preisinger, Christian ^a,b   Von Kriegsheim, Alex ^a   Matallanas, David ^a   Kolch, Walter ^a,b  

^a BEATSON INSTITUTE FOR CANCER RESEARCH   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Phosphorylation; Signal transduction networks

Indexed keywords

PHOSPHATASE; PHOSPHOTRANSFERASE;

CYTOLOGY; GENETICS; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TWO DIMENSIONAL GEL ELECTROPHORESIS; TWO HYBRID SYSTEM;

ANIMALS; CELL PHYSIOLOGICAL PHENOMENA; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION PROFILING; HUMANS; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEIN INTERACTION MAPPING; PROTEOMICS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 55849150923     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800136     Document Type: Review

References (116)

1. Kolch, W., Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions. Biochem. J. 2000, 351 Pt 2, 289-305.
2. Hahn, W. C., Weinberg, R. A., Rules for making human tumor cells. N. Engl. J. Med. 2002, 347, 1593-1603.
3. Zhu, H., Snyder, M., "Omic" approaches for unraveling signaling networks. Curr. Opin. Cell. Biol. 2002, 14, 173-179.
4. Zhu, H., Bilgin, M., Snyder, M., Proteomics. Annu. Rev. Biochem. 2003, 72, 783-812.
5. Fields, S., Song, O., A novel genetic system to detect protein-protein interactions. Nature 1989, 340, 245-246.
6. Luban, J., Goff, S. P., The yeast two-hybrid system for studying protein-protein interactions. Curr. Opin. Biotechnol. 1995, 6, 59-64.
7. Aronheim, A., Protein recruitment systems for the analysis of protein-protein interactions. Biochem. Pharmacol. 2000, 60, 1009-1013.
8. Guo, D., Hazbun, T. R., Xu, X. J., Ng, S. L. et al., A tethered catalysis, two-hybrid system to identify protein-protein interactions requiring post-translational modifications. Nat. Biotechnol. 2004, 22, 888-892.
9. Michnick, S. W., Ear, P. H., Manderson, E. N., Remy, I., Stefan, E., Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nat. Rev. Drug Discov. 2007, 6, 569-582.
10. Ozawa, T., Designing split reporter proteins for analytical tools. Anal. Chim. Acta. 2006, 556, 58-68.
11. Michnick, S. W., MacDonald, M. L., Westwick, J. K., Chemical genetic strategies to delineate MAP kinase signaling pathways using protein-fragment complementation assays (PCA). Methods 2006, 40, 287-293.
12. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A. et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403, 623-627.
13. Ito, T., Chiba, T., Ozawa, R., Yoshida, M. et al., A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 2001, 98, 4569-4574.
14. Boulton, S. J., Gartner, A., Reboul, J., Vaglio, P. et al., Combined functional genomic maps of the C. elegans DNA damage response. Science 2002, 295, 127-131.
15. Li, S., Armstrong, C. M., Bertin, N., Ge, H. et al., A map of the interactome network of the metazoan C. elegans. Science 2004, 303, 540-543.
16. Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T. et al., Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437, 1173-1178.
17. Bauch, A., Superti-Furga, G., Charting protein complexes, signaling pathways, and networks in the immune system. Immunol. Rev. 2006, 210, 187-207.
18. Kocher, T., Superti-Furga, G., Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 2007, 4, 807-815.
19. Yan, G. R., He, Q. Y., Functional proteomics to identify critical proteins in signal transduction pathways. Amino Acids 2008, 35, 267-274.
20. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M. et al., A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 1999, 17, 1030-1032.
21. Gavin, A. C., Bosche, M., Krause, R., Grandi, P. et al., Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415, 141-147.
22. Brajenovic, M., Joberty, G., Kuster, B., Bouwmeester, T., Drewes, G., Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network. J. Biol. Chem. 2004, 279, 12804-12811.
23. Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P. O. et al., A physical and functional map of the human TNF-alpha/NFkappa B signal transduction pathway. Nat. Cell Biol. 2004, 6, 97-105.
24. Angrand, P. O., Segura, I., Volkel, P., Ghidelli, S. et al., Transgenic mouse proteomics identifies new 14-3-3-associated proteins involved in cytoskeletal rearrangements and cell signaling. Mol. Cell. Proteomics 2006, 5, 2211-2227.
25. Burckstummer, T., Bennett, K. L., Preradovic, A., Schutze, G. et al., An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat. Methods 2006, 3, 1013-1019.
26. Gloeckner, C. J., Boldt, K., Schumacher, A., Roepman, R., Ueffing, M., A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes. Proteomics 2007, 7, 4228-4234.
27. Short, B., Preisinger, C., Schaletzky, J., Kopajtich, R., Barr, F. A., The Rab6 GTPase regulates recruitment of the dynactin complex to Golgi membranes. Curr. Biol. 2002, 12, 1792-1795.
28. Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P. et al., Proteomic characterization of the human centrosome by protein correlation profiling. Nature 2003, 426, 570-574.
29. Kabuyama, Y., Resing, K. A., Ahn, N. G., Applying proteomics to signaling networks. Curr. Opin. Genet. Dev. 2004, 14, 492-498.
30. Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E. et al., Nucleolar proteome dynamics. Nature 2005, 433, 77-83.
31. Sauer, G., Korner, R., Hanisch, A., Ries, A. et al., Proteome analysis of the human mitotic spindle. Mol. Cell. Proteomics 2005, 4, 35-43.
32. Wu, C. C., Yates, J. R., 3rd, Neville, M. C., Howell, K. E., Proteomic analysis of two functional states of the Golgi complex in mammary epithelial cells. Traffic 2000, 1, 769-782.
33. Wu, C. C., MacCoss, M. J., Mardones, G., Finnigan, C. et al., Organellar proteomics reveals Golgi arginine dimethylation. Mol. Biol. Cell 2004, 15, 2907-2919.
34. Trinkle-Mulcahy, L., Andersen, J., Lam, Y. W., Moorhead, G. et al., Repo-Man recruits PP1 gamma to chromatin and is essential for cell viability. J. Cell. Biol. 2006, 172, 679-692.
35. Tu, X., Huang, A., Bae, D., Slaughter, N. et al., Proteome analysis of lipid rafts in Jurkat cells characterizes a raft subset that is involved in NF-kappaB activation. J. Proteome Res. 2004, 3, 445-454.
36. Kratchmarova, I., Blagoev, B., Haack-Sorensen, M., Kassem, M., Mann, M., Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 2005, 308, 1472-1477.
37. Matallanas, D., Romano, D., Yee, K., Meissl, K. et al., RASSF1A elicits apoptosis through an MST2 pathway directing proapoptotic transcription by the p73 tumor suppressor protein. Mol. Cell 2007, 27, 962-975.
38. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
39. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
40. Gygi, S. P., Rist, B., Griffin, T. J., Eng, J., Aebersold, R., Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res. 2002, 1, 47-54.
41. Ong, S. E., Foster, L. J., Mann, M., Mass spectrometric-based approaches in quantitative proteomics. Methods 2003, 29, 124-130.
42. Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
43. Ivakhno, S., Kornelyuk, A., Quantitative proteomics and its applications for systems biology. Biochemistry (Mosc) 2006, 71, 1060-1072.
44. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
45. Smith, P. D., Crocker, S. J., Jackson-Lewis, V., Jordan-Sciutto, K. L. et al., Cyclin-dependent kinase 5 is a mediator of dopaminergic neuron loss in a mouse model of Parkinson's disease. Proc. Natl. Acad. Sci. USA 2003, 100, 13650-13655.
46. Lochhead, P. A., Sibbet, G., Morrice, N., Cleghon, V., Activation-loop autophosphorylation is mediated by a novel transitional intermediate form of DYRKs. Cell 2005, 121, 925-936.
47. Hunter, T., The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol. Cell 2007, 28, 730-738.
48. Pawson, T., SH2 and SH3 domains in signal transduction. Adv. Cancer Res. 1994, 64, 87-110.
49. Seet, B. T., Dikic, I., Zhou,M.M., Pawson, T., Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 2006, 7, 473-483.
50. Koretzky, G. A., Abtahian, F., Silverman, M. A., SLP76 and SLP65: complex regulation of signalling in lymphocytes and beyond. Nat. Rev. Immunol. 2006, 6, 67-78.
51. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R. et al., Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl. Acad. Sci. USA 2000, 97, 179-184.
52. Elia, A. E., Cantley, L. C., Yaffe,M. B., Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science 2003, 299, 1228-1231.
53. Elia, A. E., Rellos, P., Haire, L. F., Chao, J. W. et al., The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain. Cell 2003, 115, 83-95.
54. Barr, F. A., Sillje, H. H., Nigg, E. A., Polo-like kinases and the orchestration of cell division. Nat. Rev. Mol. Cell Biol. 2004, 5, 429-440.
55. Baumann, C., Korner, R., Hofmann, K., Nigg, E. A., PICH, a centromere-associated SNF2 family ATPase, is regulated by Plk1 and required for the spindle checkpoint. Cell 2007, 128, 101-114.
56. Neef, R., Preisinger, C., Sutcliffe, J., Kopajtich, R. et al., Phosphorylation ofmitotic kinesin-like protein 2 by polo-like kinase 1 is required for cytokinesis. J. Cell Biol. 2003, 162, 863-875.
57. Preisinger, C., Korner, R., Wind, M., Lehmann, W. D. et al., Plk1 docking to GRASP65 phosphorylated by Cdk1 suggests a mechanism for Golgi checkpoint signalling. EMBO J. 2005, 24, 753-765.
58. Jin, J., Smith, F. D., Stark, C., Wells, C. D. et al., Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization. Curr. Biol. 2004, 14, 1436-1450.
59. Pozuelo Rubio, M., Geraghty, K. M., Wong, B. H., Wood, N. T. et al., 14-3-3-affinity purification of over 200 human phosphoproteins reveals new links to regulation of cellular metabolism, proliferation and trafficking. Biochem. J. 2004, 379, 395-408.
60. Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M. et al., A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 2003, 21, 315-318.
61. Manning, B. D., Cantley, L. C., Hitting the target: emerging technologies in the search for kinase substrates. Sci. STKE 2002, 2002, PE49.
62. Schutkowski, M., Reineke, U., Reimer, U., Peptide arrays for kinase profiling. Chembiochem. 2005, 6, 513-521.
63. Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A. et al., Systematic discovery of in vivo phosphorylation networks. Cell 2007, 129, 1415-1426.
64. Dammeier, S., Lovric, J., Eulitz, M., Kolch, W. et al., Identification of the smooth muscle-specific protein, sm22, as a novel protein kinase C substrate using two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis 2000, 21, 2443-2453.
65. Knebel, A., Morrice, N., Cohen, P., A novel method to identify protein kinase substrates: eEF2 kinase is phosphorylated and inhibited by SAPK4/p38delta. EMBO J. 2001, 20, 4360-4369.
66. Preisinger, C., Short, B., De Corte, V., Bruyneel, E. et al., YSK1 is activated by the Golgi matrix protein GM130 and plays a role in cell migration through its substrate 14-3-3zeta. J. Cell Biol. 2004, 164, 1009-1020.
67. Shah, K., Liu, Y., Deirmengian, C., Shokat, K. M., Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc. Natl. Acad. Sci. USA 1997, 94, 3565-3570.
68. Eblen, S. T., Kumar, N. V., Shah, K., Henderson, M. J. et al., Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs. J. Biol. Chem. 2003, 278, 14926-14935.
69. Habelhah, H., Shah, K., Huang, L., Burlingame, A. L. et al., Identification of new JNK substrate using ATP pocket mutant JNK and a corresponding ATP analogue. J. Biol. Chem. 2001, 276, 18090-18095.
70. Hindley, A. D., Park, S., Wang, L., Shah, K. et al., Engineering the serine/threonine protein kinase Raf-1 to utilise an orthogonal analogue of ATP substituted at the N6 position. FEBS Lett. 2004, 556, 26-34.
71. Bishop, A. C., Ubersax, J. A., Petsch, D. T., Matheos, D. P. et al., A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 2000, 407, 395-401.
72. Allen, J. J., Li, M., Brinkworth, C. S., Paulson, J. L. et al., A semisynthetic epitope for kinase substrates. Nat. Methods 2007, 4, 511-516.
73. Ahn, N. G., Krebs, E. G., Evidence for an epidermal growth factor-stimulated protein kinase cascade in Swiss 3T3 cells. Activation of serine peptide kinase activity by myelin basic protein kinases in vitro. J. Biol. Chem. 1990, 265, 11495-11501.
74. Ahn, N. G., Seger, R., Bratlien, R. L., Diltz, C. D. et al., Multiple components in an epidermal growth factor-stimulated protein kinase cascade. In vitro activation of a myelin basic protein/microtubule- associated protein 2 kinase. J. Biol. Chem. 1991, 266, 4220-4227.
75. Ahn, N. G., Weiel, J. E., Chan, C. P., Krebs, E. G., Identification of multiple epidermal growth factor-stimulated protein serine/threonine kinases from Swiss 3T3 cells. J. Biol. Chem. 1990, 265, 11487-11494.
76. Schulze, W. X., Deng, L., Mann, M., Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol. Syst. Biol. 2005, 1, 2005 0008.
77. Lowery, D. M., Clauser, K. R., Hjerrild, M., Lim, D. et al., Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J. 2007, 26, 2262-2273.
78. Basu, S., Totty, N. F., Irwin, M. S., Sudol, M., Downward, J., Akt phosphorylates the Yes-associated protein, YAP, to induce interaction with 14-3-3 and attenuation of p73-mediated apoptosis. Mol. Cell 2003, 11, 11-23.
79. Cohen, P. T., Protein phosphatase 1-targeted in many directions. J. Cell Sci. 2002, 115, 241-256.
80. Liu, W., Silverstein, A. M., Shu, H., Martinez, B., Mumby, M. C., A functional genomics analysis of the B56 isoforms of Drosophila protein phosphatase 2A. Mol. Cell. Proteomics 2007, 6, 319-332.
81. von Kriegsheim, A., Pitt, A., Grindlay, G. J., Kolch, W., Dhillon, A. S., Regulation of the Raf-MEK-ERK pathway by protein phosphatase 5. Nat. Cell Biol. 2006, 8, 1011-1016.
82. Kane, S., Sano, H., Liu, S. C., Asara, J. M. et al., A method to identify serine kinase substrates. Akt phosphorylates a novel adipocyte protein with a Rab GTPase-activating protein (GAP) domain. J. Biol. Chem. 2002, 277, 22115-22118.
83. Matsuoka, S., Ballif, B. A., Smogorzewska, A., McDonald, E. R., 3rd et al., ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007, 316, 1160-1166.
84. Stokes, M. P., Rush, J., Macneill, J., Ren, J. M. et al., Profiling of UV-induced ATM/ATR signaling pathways. Proc. Natl. Acad. Sci. USA 2007, 104, 19855-19860.
85. Gronborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S. et al., A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol. Cell. Proteomics 2002, 1, 517-527.
86. Seger, R., Rodeck, U., Yarden, Y., Meeting Report: Receptor tyrosine kinases: the emerging tip of systems control. IET Syst. Biol. 2008, 2, 1.
87. Guo, A., Villen, J., Kornhauser, J., Lee, K. A. et al., Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. USA 2008, 105, 692-697.
88. Lovric, J., Dammeier, S., Kieser, A., Mischak, H., Kolch, W., Activated raf induces the hyperphosphorylation of stathmin and the reorganization of the microtubule network. J. Biol. Chem. 1998, 273, 22848-22855.
89. Lewis, T. S., Hunt, J. B., Aveline, L. D., Jonscher, K. R. et al., Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol. Cell 2000, 6, 1343-1354.
90. Steinberg, T. H., Agnew, B. J., Gee, K. R., Leung, W. Y. et al., Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology. Proteomics 2003, 3, 1128-1144.
91. Stasyk, T., Morandell, S., Bakry, R., Feuerstein, I. et al., Quantitative detection of phosphoproteins by combination of two-dimensional difference gel electrophoresis and phosphospecific fluorescent staining. Electrophoresis 2005, 26, 2850-2854.
92. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J. et al., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20, 301-305.
93. Villen, J., Beausoleil, S. A., Gerber, S. A., Gygi, S. P., Largescale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. USA 2007, 104, 1488-1493.
94. Thingholm, T. E., Jorgensen, T. J., Jensen, O. N., Larsen, M. R., Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat. Protoc. 2006, 1, 1929-1935.
95. Wilson-Grady, J. T., Villen, J., Gygi, S. P., Phosphoproteome analysis of fission yeast. J. Proteome Res. 2008, 7, 1088-1097.
96. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E. et al., Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. USA 2004, 101, 12130-12135.
97. Zhang, Y., Wolf-Yadlin, A., Ross, P. L., Pappin, D. J. et al., Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics 2005, 4, 1240-1250.
98. Cao, L., Yu, K., Banh, C., Nguyen, V. et al., Quantitative time-resolved phosphoproteomic analysis of mast cell signaling. J. Immunol. 2007, 179, 5864-5876.
99. Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P. et al., Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 2005, 4, 310-327.
100. Kolch, W., Coordinating ERK/MAPK signalling through scaffolds and inhibitors. Nat. Rev. Mol. Cell Biol. 2005, 6, 827-837.
101. Yoon, S., Seger, R., The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions. Growth Factors 2006, 24, 21-44.
102. Mikula, M., Schreiber, M., Husak, Z., Kucerova, L. et al., Embryonic lethality and fetal liver apoptosis in mice lacking the c-raf-1 gene. EMBO J. 2001, 20, 1952-1962.
103. Huser, M., Luckett, J., Chiloeches, A., Mercer, K. et al., MEK kinase activity is not necessary for Raf-1 function. EMBO J. 2001, 20, 1940-1951.
104. O'Neill, E., Rushworth, L., Baccarini, M., Kolch, W., Role of the kinase MST2 in suppression of apoptosis by the protooncogene product Raf-1. Science 2004, 306, 2267-2270.
105. Agathanggelou, A., Cooper, W. N., Latif, F., Role of the Ras-association domain family 1 tumor suppressor gene in human cancers. Cancer Res. 2005, 65, 3497-3508.
106. Camargo, F. D., Gokhale, S., Johnnidis, J. B., Fu, D. et al., YAP1 increases organ size and expands undifferentiated progenitor cells. Curr. Biol. 2007, 17, 2054-2060.
107. Zhao, B., Wei, X., Li, W., Udan, R. S. et al., Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control. Genes Dev. 2007, 21, 2747-2761.
108. Dong, J., Feldmann, G., Huang, J., Wu, S. et al., Elucidation of a universal size-control mechanism in Drosophila and mammals. Cell 2007, 130, 1120-1133.
109. Hao, Y., Chun, A., Cheung, K., Rashidi, B., Yang, X., Tumor suppressor LATS1 is a negative regulator of oncogene YAP. J. Biol. Chem. 2008, 283, 5496-5509.
110. Overholtzer, M., Zhang, J., Smolen, G. A., Muir, B. et al., Transforming properties of YAP, a candidate oncogene on the chromosome 11q22 amplicon. Proc. Natl. Acad. Sci. USA 2006, 103, 12405-12410.
111. Zender, L., Spector, M. S., Xue, W., Flemming, P. et al., Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 2006, 125, 1253-1267.
112. Meyer, N., Kim, S. S., Penn, L. Z., The Oscar-worthy role of Myc in apoptosis. Semin. Cancer Biol. 2006, 16, 275-287.
113. Reinders, J., Sickmann, A., State-of-the-art in phosphoproteomics. Proteomics 2005, 5, 4052-4061.
114. Morandell, S., Stasyk, T., Grosstessner-Hain, K., Roitinger, E. et al., Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 2006, 6, 4047-4056.
115. Collins, M. O., Yu, L., Choudhary, J. S., Analysis of protein phosphorylation on a proteome-scale. Proteomics 2007, 7, 2751-2768.
116. Mumby, M., Brekken, D., Phosphoproteomics: new insights into cellular signaling. Genome Biol. 2005, 6, 230.