메뉴 건너뛰기




Volumn 9, Issue 23, 2009, Pages 5233-5242

Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks

Author keywords

Bioinformatics; Databases; Protein phosphorylation; Protein protein interaction; Proteome analysis; Systems biology

Indexed keywords

PHOSPHOTRANSFERASE;

EID: 73249115991     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200900266     Document Type: Review
Times cited : (20)

References (93)
  • 1
    • 44249108848 scopus 로고    scopus 로고
    • Directional and quantitative phosphorylation networks
    • Jorgensen, C., Linding, R., Directional and quantitative phosphorylation networks. Brief Funct. Genomic Proteomic 2008, 7, 17-26.
    • (2008) Brief Funct. Genomic Proteomic , vol.7 , pp. 17-26
    • Jorgensen, C.1    Linding, R.2
  • 2
    • 34547623194 scopus 로고    scopus 로고
    • Common effector processing mediates cell-specific responses to stimuli
    • Miller-Jensen, K., Janes, K. A., Brugge, J. S., Lauffenburger, D. A., Common effector processing mediates cell-specific responses to stimuli. Nature 2007, 448, 604-608.
    • (2007) Nature , vol.448 , pp. 604-608
    • Miller-Jensen, K.1    Janes, K.A.2    Brugge, J.S.3    Lauffenburger, D.A.4
  • 3
    • 28844441230 scopus 로고    scopus 로고
    • A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis
    • Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K. et al., A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 2005, 310, 1646-1653.
    • (2005) Science , vol.310 , pp. 1646-1653
    • Janes, K.A.1    Albeck, J.G.2    Gaudet, S.3    Sorger, P.K.4
  • 4
    • 0034797512 scopus 로고    scopus 로고
    • The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture
    • Cohen, P., The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur. J. Biochem. 2001, 268, 5001-5010.
    • (2001) Eur. J. Biochem , vol.268 , pp. 5001-5010
    • Cohen, P.1
  • 6
    • 34249885757 scopus 로고    scopus 로고
    • Engineering synthetic signaling proteins with ultrasensitive input/output control
    • Dueber, J. E., Mirsky, E. A., Lim, W. A., Engineering synthetic signaling proteins with ultrasensitive input/output control. Nat. Biotechnol. 2007, 25, 660-662.
    • (2007) Nat. Biotechnol , vol.25 , pp. 660-662
    • Dueber, J.E.1    Mirsky, E.A.2    Lim, W.A.3
  • 7
    • 58649110598 scopus 로고    scopus 로고
    • Oncogenic B-RAF negatively regulates the tumor suppressor LKB1 to promote melanoma cell proliferation
    • Zheng, B., Jeong, J. H., Asara, J. M., Yuan, Y. Y. et al., Oncogenic B-RAF negatively regulates the tumor suppressor LKB1 to promote melanoma cell proliferation. Mol. Cell 2009, 33, 237-247.
    • (2009) Mol. Cell , vol.33 , pp. 237-247
    • Zheng, B.1    Jeong, J.H.2    Asara, J.M.3    Yuan, Y.Y.4
  • 8
    • 41149167511 scopus 로고    scopus 로고
    • Network medicine
    • Pawson, T., Linding, R., Network medicine. FEBS Lett. 2008, 582, 1266-1270.
    • (2008) FEBS Lett , vol.582 , pp. 1266-1270
    • Pawson, T.1    Linding, R.2
  • 9
    • 0027990255 scopus 로고
    • A cyclin-dependent kinase inhibitor, butyrolactone I, inhibits phosphorylation of RB protein and cell cycle progression
    • Kitagawa, M., Higashi, H., Takahashi, I. S., Okabe, T. et al., A cyclin-dependent kinase inhibitor, butyrolactone I, inhibits phosphorylation of RB protein and cell cycle progression. Oncogene 1994, 9, 2549-2557.
    • (1994) Oncogene , vol.9 , pp. 2549-2557
    • Kitagawa, M.1    Higashi, H.2    Takahashi, I.S.3    Okabe, T.4
  • 10
    • 3242715058 scopus 로고    scopus 로고
    • Hyperphosphorylation of pRb: A mechanism for RB tumour suppressor pathway inactivation in bladder cancer
    • Chatterjee, S. J., George, B., Goebell, P. J., Alavi-Tafreshi, M. et al., Hyperphosphorylation of pRb: a mechanism for RB tumour suppressor pathway inactivation in bladder cancer. J. Pathol. 2004, 203, 762-770.
    • (2004) J. Pathol , vol.203 , pp. 762-770
    • Chatterjee, S.J.1    George, B.2    Goebell, P.J.3    Alavi-Tafreshi, M.4
  • 12
    • 0034001611 scopus 로고    scopus 로고
    • Expression and phosphorylation status of retinoblastoma protein in adult T-cell leukemia/lymphoma
    • Nakayama, K., Yamada, Y., Koji, T., Hayashi, T. et al., Expression and phosphorylation status of retinoblastoma protein in adult T-cell leukemia/lymphoma. Leuk. Res. 2000, 24, 299-305.
    • (2000) Leuk. Res , vol.24 , pp. 299-305
    • Nakayama, K.1    Yamada, Y.2    Koji, T.3    Hayashi, T.4
  • 13
    • 20444383859 scopus 로고    scopus 로고
    • Protein phosphorylation in signaling - 50 years and counting
    • Pawson, T., Scott, J. D., Protein phosphorylation in signaling - 50 years and counting. Trends Biochem. Sci. 2005, 30, 286-290.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 286-290
    • Pawson, T.1    Scott, J.D.2
  • 14
    • 0001010573 scopus 로고
    • The enzymatic phosphorylation of proteins
    • Burnett, G., Kennedy, E. P., The enzymatic phosphorylation of proteins. J. Biol. Chem. 1954, 211, 969-980.
    • (1954) J. Biol. Chem , vol.211 , pp. 969-980
    • Burnett, G.1    Kennedy, E.P.2
  • 15
    • 0019413616 scopus 로고
    • Epidermal growth factor induces rapid tyrosine phosphorylation of proteins in A431 human tumor cells
    • Hunter, T., Cooper, J. A., Epidermal growth factor induces rapid tyrosine phosphorylation of proteins in A431 human tumor cells. Cell 1981, 24, 741-752.
    • (1981) Cell , vol.24 , pp. 741-752
    • Hunter, T.1    Cooper, J.A.2
  • 16
    • 34547881522 scopus 로고    scopus 로고
    • Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
    • Huang, P. H., Mukasa, A., Bonavia, R., Flynn, R. A. et al., Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc. Natl. Acad. Sci. USA 2007, 104, 12867-12872.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 12867-12872
    • Huang, P.H.1    Mukasa, A.2    Bonavia, R.3    Flynn, R.A.4
  • 17
    • 0033565503 scopus 로고    scopus 로고
    • Immobilized gallium(III) affinity chromatography of phosphopeptides
    • Posewitz, M. C., Tempst, P., Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal. Chem. 1999, 71, 2883-2892.
    • (1999) Anal. Chem , vol.71 , pp. 2883-2892
    • Posewitz, M.C.1    Tempst, P.2
  • 18
    • 0036198435 scopus 로고    scopus 로고
    • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
    • 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.
    • (2002) Nat. Biotechnol , vol.20 , pp. 301-305
    • Ficarro, S.B.1    McCleland, M.L.2    Stukenberg, P.T.3    Burke, D.J.4
  • 20
    • 3242688830 scopus 로고    scopus 로고
    • Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESIMS/ MS and titanium oxide precolumns
    • Pinkse, M. W., Uitto, P. M., Hilhorst, M.J., Ooms, B., Heck, A. J., Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESIMS/ MS and titanium oxide precolumns. Anal. Chem. 2004, 76, 3935-3943.
    • (2004) Anal. Chem , vol.76 , pp. 3935-3943
    • Pinkse, M.W.1    Uitto, P.M.2    Hilhorst, M.J.3    Ooms, B.4    Heck, A.J.5
  • 21
    • 24944519450 scopus 로고    scopus 로고
    • Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns
    • 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. Mol. Cell Proteomics 2005, 4, 873-886.
    • (2005) Mol. Cell Proteomics , vol.4 , pp. 873-886
    • Larsen, M.R.1    Thingholm, T.E.2    Jensen, O.N.3    Roepstorff, P.4    Jorgensen, T.J.5
  • 22
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • 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.
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4
  • 23
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3, 1154-1169.
    • (2004) Mol. Cell Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3    Williamson, B.4
  • 24
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotopecoded affinity tags
    • Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotopecoded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
    • (1999) Nat. Biotechnol , vol.17 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4
  • 25
    • 55849109221 scopus 로고    scopus 로고
    • Quantitative assessment of the structural bias in protein-protein interaction assays
    • Bjö rklund, A. K., Light, S., Hedin, L., Elofsson, A., Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics 2008, 8, 4657-4667.
    • (2008) Proteomics , vol.8 , pp. 4657-4667
    • Bjö rklund, A.K.1    Light, S.2    Hedin, L.3    Elofsson, A.4
  • 26
    • 53349156368 scopus 로고    scopus 로고
    • Biochemistry. Not comparable, but complementary
    • Jensen, L. J., Bork, P., Biochemistry. Not comparable, but complementary. Science 2008, 322, 56-57.
    • (2008) Science , vol.322 , pp. 56-57
    • Jensen, L.J.1    Bork, P.2
  • 27
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • 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.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4
  • 28
    • 0037337310 scopus 로고    scopus 로고
    • A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
    • 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.
    • (2003) Nat. Biotechnol , vol.21 , pp. 315-318
    • Blagoev, B.1    Kratchmarova, I.2    Ong, S.E.3    Nielsen, M.4
  • 29
    • 26844576371 scopus 로고    scopus 로고
    • Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules
    • 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.
    • (2005) Mol. Cell Proteomics , vol.4 , pp. 1240-1250
    • Zhang, Y.1    Wolf-Yadlin, A.2    Ross, P.L.3    Pappin, D.J.4
  • 30
    • 33750696663 scopus 로고    scopus 로고
    • Effects of HER2 overexpression on cell signaling networks governing proliferation and migration
    • Wolf-Yadlin, A., Kumar, N., Zhang, Y., Hautaniemi, S. et al., Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol. Syst. Biol. 2006, 2, 54.
    • (2006) Mol. Syst. Biol , vol.2 , pp. 54
    • Wolf-Yadlin, A.1    Kumar, N.2    Zhang, Y.3    Hautaniemi, S.4
  • 31
    • 33846554088 scopus 로고    scopus 로고
    • Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data
    • Kumar, N., Wolf-Yadlin, A., White, F. M., Lauffenburger, D. A., Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput. Biol. 2007, 3, e4.
    • (2007) PLoS Comput. Biol , vol.3
    • Kumar, N.1    Wolf-Yadlin, A.2    White, F.M.3    Lauffenburger, D.A.4
  • 32
    • 58549118075 scopus 로고    scopus 로고
    • Linear combinations of docking affinities explain quantitative differences in RTK signaling
    • Gordus, A., Krall, J. A., Beyer, E. M., Kaushansky, A. et al., Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol. Syst. Biol. 2009, 5, 235.
    • (2009) Mol. Syst. Biol , vol.5 , pp. 235
    • Gordus, A.1    Krall, J.A.2    Beyer, E.M.3    Kaushansky, A.4
  • 33
    • 57449103754 scopus 로고    scopus 로고
    • An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells
    • Joughin, B. A., Naegle, K. M., Huang, P. H., Yaffe, M. B. et al., An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol. Biosyst. 2009, 5, 59-67.
    • (2009) Mol. Biosyst , vol.5 , pp. 59-67
    • Joughin, B.A.1    Naegle, K.M.2    Huang, P.H.3    Yaffe, M.B.4
  • 34
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S. et al., Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262, 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4
  • 35
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T. L., Elkan, C., Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994, 2, 28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 36
    • 0030670589 scopus 로고    scopus 로고
    • Efficient discovery of conserved patterns using a pattern graph
    • Jonassen, I., Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci. 1997, 13, 509-522.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 509-522
    • Jonassen, I.1
  • 37
    • 0031684427 scopus 로고    scopus 로고
    • Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
    • Rigoutsos, I., Floratos, A., Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 1998, 14, 55-67.
    • (1998) Bioinformatics , vol.14 , pp. 55-67
    • Rigoutsos, I.1    Floratos, A.2
  • 38
    • 33845276720 scopus 로고    scopus 로고
    • A correlated motif approach for finding short linear motifs from protein interaction networks
    • Tan, S. H., Hugo, W., Sung, W. K., Ng, S. K., A correlated motif approach for finding short linear motifs from protein interaction networks. BMC Bioinformatics 2006, 7, 502.
    • (2006) BMC Bioinformatics , vol.7 , pp. 502
    • Tan, S.H.1    Hugo, W.2    Sung, W.K.3    Ng, S.K.4
  • 39
    • 29144455315 scopus 로고    scopus 로고
    • Systematic discovery of new recognition peptides mediating protein interaction networks
    • Neduva, V., Linding, R., Su-Angrand, I., Stark, A. et al., Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol. 2005, 3, e405.
    • (2005) PLoS Biol , vol.3
    • Neduva, V.1    Linding, R.2    Su-Angrand, I.3    Stark, A.4
  • 40
    • 28444460297 scopus 로고    scopus 로고
    • Global analysis of protein phosphorylation in yeast
    • Ptacek, J., Devgan, G., Michaud, G., Zhu, H. et al., Global analysis of protein phosphorylation in yeast. Nature 2005, 438, 679-684.
    • (2005) Nature , vol.438 , pp. 679-684
    • Ptacek, J.1    Devgan, G.2    Michaud, G.3    Zhu, H.4
  • 41
    • 27944499451 scopus 로고    scopus 로고
    • An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets
    • Schwartz, D., Gygi, S. P., An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat. Biotechnol. 2005, 23, 1391-1398.
    • (2005) Nat. Biotechnol , vol.23 , pp. 1391-1398
    • Schwartz, D.1    Gygi, S.P.2
  • 42
    • 34548158041 scopus 로고    scopus 로고
    • A differential phosphoproteomic analysis of retinoic acid-treated P19 cells
    • Smith, J. C., Duchesne, M. A., Tozzi, P., Ethier, M., Figeys, D., A differential phosphoproteomic analysis of retinoic acid-treated P19 cells. J. Proteome Res. 2007, 6, 3174-3186.
    • (2007) J. Proteome Res , vol.6 , pp. 3174-3186
    • Smith, J.C.1    Duchesne, M.A.2    Tozzi, P.3    Ethier, M.4    Figeys, D.5
  • 43
    • 55849147636 scopus 로고    scopus 로고
    • Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors
    • Pan, C., Gnad, F., Olsen, J. V., Mann, M., Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors. Proteomics 2008, 8, 4534-4546.
    • (2008) Proteomics , vol.8 , pp. 4534-4546
    • Pan, C.1    Gnad, F.2    Olsen, J.V.3    Mann, M.4
  • 44
    • 38649139336 scopus 로고    scopus 로고
    • Largescale identification and evolution indexing of tyrosine phosphorylation sites from murine brain
    • Ballif, B. A., Carey, G. R., Sunyaev, S. R., Gygi, S. P., Largescale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J. Proteome Res. 2008, 7, 311-318.
    • (2008) J. Proteome Res , vol.7 , pp. 311-318
    • Ballif, B.A.1    Carey, G.R.2    Sunyaev, S.R.3    Gygi, S.P.4
  • 45
    • 43249124511 scopus 로고    scopus 로고
    • Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis
    • Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A. et al., Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol. Syst. Biol. 2008, 4, 193.
    • (2008) Mol. Syst. Biol , vol.4 , pp. 193
    • Sugiyama, N.1    Nakagami, H.2    Mochida, K.3    Daudi, A.4
  • 46
    • 2442637820 scopus 로고    scopus 로고
    • Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity
    • Argetsinger, L. S., Kouadio, J. L., Steen, H., Stensballe, A. et al., Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity. Mol. Cell Biol. 2004, 24, 4955-4967.
    • (2004) Mol. Cell Biol , vol.24 , pp. 4955-4967
    • Argetsinger, L.S.1    Kouadio, J.L.2    Steen, H.3    Stensballe, A.4
  • 47
    • 58049204428 scopus 로고    scopus 로고
    • Discovery of phosphorylation motif mixtures in phosphoproteomics data
    • Ritz, A., Shakhnarovich, G., Salomon, A. R., Raphael, B. J., Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics 2009, 25, 14-21.
    • (2009) Bioinformatics , vol.25 , pp. 14-21
    • Ritz, A.1    Shakhnarovich, G.2    Salomon, A.R.3    Raphael, B.J.4
  • 48
    • 39049154319 scopus 로고    scopus 로고
    • Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
    • Miller, M. L., Hanke, S., Hinsby, A. M., Friis, C. et al., Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2. Mol. Cell Proteomics 2008, 7, 181-192.
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 181-192
    • Miller, M.L.1    Hanke, S.2    Hinsby, A.M.3    Friis, C.4
  • 49
    • 55749111058 scopus 로고    scopus 로고
    • Linear motif atlas for phosphorylation-dependent signaling
    • Miller, M. L., Jensen, L. J., Diella, F., Jorgensen, C. et al., Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal. 2008, 1, ra2.
    • (2008) Sci. Signal , vol.1
    • Miller, M.L.1    Jensen, L.J.2    Diella, F.3    Jorgensen, C.4
  • 50
    • 0034622925 scopus 로고    scopus 로고
    • Printing proteins as microarrays for high-throughput function determination
    • MacBeath, G., Schreiber, S. L., Printing proteins as microarrays for high-throughput function determination. Science 2000, 289, 1760-1763.
    • (2000) Science , vol.289 , pp. 1760-1763
    • MacBeath, G.1    Schreiber, S.L.2
  • 51
    • 0033768106 scopus 로고    scopus 로고
    • Analysis of yeast protein kinases using protein chips
    • Zhu, H., Klemic, J. F., Chang, S., Bertone, P. et al., Analysis of yeast protein kinases using protein chips. Nat. Genet. 2000, 26, 283-289.
    • (2000) Nat. Genet , vol.26 , pp. 283-289
    • Zhu, H.1    Klemic, J.F.2    Chang, S.3    Bertone, P.4
  • 52
    • 0035860499 scopus 로고    scopus 로고
    • Global analysis of protein activities using proteome chips
    • Zhu, H., Bilgin, M., Bangham, R., Hall, D. et al., Global analysis of protein activities using proteome chips. Science 2001, 293, 2101-2105.
    • (2001) Science , vol.293 , pp. 2101-2105
    • Zhu, H.1    Bilgin, M.2    Bangham, R.3    Hall, D.4
  • 53
    • 0025336478 scopus 로고
    • Autoradiography using storage phosphor technology
    • Johnston, R. F., Pickett, S. C., Barker, D. L., Autoradiography using storage phosphor technology. Electrophoresis 1990, 11, 355-360.
    • (1990) Electrophoresis , vol.11 , pp. 355-360
    • Johnston, R.F.1    Pickett, S.C.2    Barker, D.L.3
  • 54
    • 33847284434 scopus 로고    scopus 로고
    • A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsal-wave formation
    • Boyle, S. N., Michaud, G. A., Schweitzer, B., Predki, P. F., Koleske, A. J., A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsal-wave formation. Curr. Biol. 2007, 17, 445-451.
    • (2007) Curr. Biol , vol.17 , pp. 445-451
    • Boyle, S.N.1    Michaud, G.A.2    Schweitzer, B.3    Predki, P.F.4    Koleske, A.J.5
  • 55
    • 0742272146 scopus 로고    scopus 로고
    • Target specificity analysis of the Abl kinase using peptide microarray data
    • Rychlewski, L., Kschischo, M., Dong, L., Schutkowski, M., Reimer, U., Target specificity analysis of the Abl kinase using peptide microarray data. J. Mol. Biol. 2004, 336, 307-311.
    • (2004) J. Mol. Biol , vol.336 , pp. 307-311
    • Rychlewski, L.1    Kschischo, M.2    Dong, L.3    Schutkowski, M.4    Reimer, U.5
  • 56
    • 0028540405 scopus 로고
    • Use of an oriented peptide library to determine the optimal substrates of protein kinases
    • Songyang, Z., Blechner, S., Hoagland, N., Hoekstra, M. F. et al., Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr. Biol. 1994, 4, 973-982.
    • (1994) Curr. Biol , vol.4 , pp. 973-982
    • Songyang, Z.1    Blechner, S.2    Hoagland, N.3    Hoekstra, M.F.4
  • 57
    • 38349031676 scopus 로고    scopus 로고
    • Protein-tyrosine kinase activity profiling in knock down zebrafish embryos
    • Lemeer, S., Jopling, C., Naji, F., Ruijtenbeek, R. et al., Protein-tyrosine kinase activity profiling in knock down zebrafish embryos. PLoS ONE 2007, 2, e581.
    • (2007) PLoS ONE , vol.2
    • Lemeer, S.1    Jopling, C.2    Naji, F.3    Ruijtenbeek, R.4
  • 59
    • 0035072833 scopus 로고    scopus 로고
    • A motifbased profile scanning approach for genome-wide prediction of signaling pathways
    • Yaffe, M. B., Leparc, G. G., Lai, J., Obata, T. et al., A motifbased profile scanning approach for genome-wide prediction of signaling pathways. Nat. Biotechnol. 2001, 19, 348-353.
    • (2001) Nat. Biotechnol , vol.19 , pp. 348-353
    • Yaffe, M.B.1    Leparc, G.G.2    Lai, J.3    Obata, T.4
  • 60
    • 17644391197 scopus 로고    scopus 로고
    • A rapid method for determining protein kinase phosphorylation specificity
    • Hutti, J. E., Jarrell, E. T., Chang, J. D., Abbott, D. W. et al., A rapid method for determining protein kinase phosphorylation specificity. Nat. Methods 2004, 1, 27-29.
    • (2004) Nat. Methods , vol.1 , pp. 27-29
    • Hutti, J.E.1    Jarrell, E.T.2    Chang, J.D.3    Abbott, D.W.4
  • 61
    • 0036566003 scopus 로고    scopus 로고
    • Two novel phosphorylation sites on FKHR that are critical for its nuclear exclusion
    • Rena, G., Woods, Y. L., Prescott, A. R., Peggie, M. et al., Two novel phosphorylation sites on FKHR that are critical for its nuclear exclusion. EMBO J. 2002, 21, 2263-2271.
    • (2002) EMBO J , vol.21 , pp. 2263-2271
    • Rena, G.1    Woods, Y.L.2    Prescott, A.R.3    Peggie, M.4
  • 62
    • 34250743173 scopus 로고    scopus 로고
    • Systematic discovery of in vivo phosphorylation networks
    • 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.
    • (2007) Cell , vol.129 , pp. 1415-1426
    • Linding, R.1    Jensen, L.J.2    Ostheimer, G.J.3    van Vugt, M.A.4
  • 63
    • 34547499407 scopus 로고    scopus 로고
    • Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases
    • Smolka, M. B., Albuquerque, C. P., Chen, S. H., Zhou, H., Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc. Natl. Acad. Sci. USA 2007, 104, 10364-10369.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 10364-10369
    • Smolka, M.B.1    Albuquerque, C.P.2    Chen, S.H.3    Zhou, H.4
  • 64
    • 49949087278 scopus 로고    scopus 로고
    • Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos
    • Lemeer, S., Jopling, C., Gouw, J., Mohammed, S. et al., Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos. Mol. Cell Proteomics 2008, 7, 2176-2187.
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 2176-2187
    • Lemeer, S.1    Jopling, C.2    Gouw, J.3    Mohammed, S.4
  • 65
    • 54249117296 scopus 로고    scopus 로고
    • Phosphorylation networks regulating JNK activity in diverse genetic backgrounds
    • Bakal, C., Linding, R., Llense, F., Heffern, E. et al., Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science 2008, 322, 453-456.
    • (2008) Science , vol.322 , pp. 453-456
    • Bakal, C.1    Linding, R.2    Llense, F.3    Heffern, E.4
  • 66
    • 0030887842 scopus 로고    scopus 로고
    • Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates
    • 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.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 3565-3570
    • Shah, K.1    Liu, Y.2    Deirmengian, C.3    Shokat, K.M.4
  • 67
    • 0032008085 scopus 로고    scopus 로고
    • Engineering Src family protein kinases with unnatural nucleotide specificity
    • Liu, Y., Shah, K., Yang, F., Witucki, L., Shokat, K. M., Engineering Src family protein kinases with unnatural nucleotide specificity. Chem. Biol. 1998, 5, 91-101.
    • (1998) Chem. Biol , vol.5 , pp. 91-101
    • Liu, Y.1    Shah, K.2    Yang, F.3    Witucki, L.4    Shokat, K.M.5
  • 68
    • 0038351827 scopus 로고    scopus 로고
    • Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs
    • 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.
    • (2003) J. Biol. Chem , vol.278 , pp. 14926-14935
    • Eblen, S.T.1    Kumar, N.V.2    Shah, K.3    Henderson, M.J.4
  • 69
    • 0036008093 scopus 로고    scopus 로고
    • A chemical genetic screen for direct v-Src substrates reveals ordered assembly of a retrograde signaling pathway
    • Shah, K., Shokat, K. M., A chemical genetic screen for direct v-Src substrates reveals ordered assembly of a retrograde signaling pathway. Chem. Biol. 2002, 9, 35-47.
    • (2002) Chem. Biol , vol.9 , pp. 35-47
    • Shah, K.1    Shokat, K.M.2
  • 71
    • 0242300176 scopus 로고    scopus 로고
    • Targets of the cyclin-dependent kinase Cdk1
    • Ubersax, J. A., Woodbury, E. L., Quang, P. N., Paraz, M. et al., Targets of the cyclin-dependent kinase Cdk1. Nature 2003, 425, 859-864.
    • (2003) Nature , vol.425 , pp. 859-864
    • Ubersax, J.A.1    Woodbury, E.L.2    Quang, P.N.3    Paraz, M.4
  • 72
    • 33644833555 scopus 로고    scopus 로고
    • Mapping normal and cancer cell signalling networks: Towards single-cell proteomics
    • Irish, J. M., Kotecha, N., Nolan, G. P., Mapping normal and cancer cell signalling networks: towards single-cell proteomics. Nat. Rev. Cancer 2006, 6, 146-155.
    • (2006) Nat. Rev. Cancer , vol.6 , pp. 146-155
    • Irish, J.M.1    Kotecha, N.2    Nolan, G.P.3
  • 73
    • 3242683662 scopus 로고    scopus 로고
    • Single cell profiling of potentiated phospho-protein networks in cancer cells
    • Irish, J. M., Hovland, R., Krutzik, P. O., Perez, O. D. et al., Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 2004, 118, 217-228.
    • (2004) Cell , vol.118 , pp. 217-228
    • Irish, J.M.1    Hovland, R.2    Krutzik, P.O.3    Perez, O.D.4
  • 74
    • 0034711405 scopus 로고    scopus 로고
    • Quantitative imaging of lateral ErbB1 receptor signal propagation in the plasma membrane
    • Verveer, P. J., Wouters, F. S., Reynolds, A. R., Bastiaens, P. I., Quantitative imaging of lateral ErbB1 receptor signal propagation in the plasma membrane. Science 2000, 290, 1567-1570.
    • (2000) Science , vol.290 , pp. 1567-1570
    • Verveer, P.J.1    Wouters, F.S.2    Reynolds, A.R.3    Bastiaens, P.I.4
  • 75
    • 33846678939 scopus 로고    scopus 로고
    • Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B
    • Yudushkin, I. A., Schleifenbaum, A., Kinkhabwala, A., Neel, B. G. et al., Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. Science 2007, 315, 115-119.
    • (2007) Science , vol.315 , pp. 115-119
    • Yudushkin, I.A.1    Schleifenbaum, A.2    Kinkhabwala, A.3    Neel, B.G.4
  • 76
    • 34250882643 scopus 로고    scopus 로고
    • Quantitative morphological signatures define local signaling networks regulating cell morphology
    • Bakal, C., Aach, J., Church, G., Perrimon, N., Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 2007, 316, 1753-1756.
    • (2007) Science , vol.316 , pp. 1753-1756
    • Bakal, C.1    Aach, J.2    Church, G.3    Perrimon, N.4
  • 77
    • 34249947699 scopus 로고    scopus 로고
    • ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    • 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.
    • (2007) Science , vol.316 , pp. 1160-1166
    • Matsuoka, S.1    Ballif, B.A.2    Smogorzewska, A.3    McDonald 3rd, E.R.4
  • 78
    • 34547555987 scopus 로고    scopus 로고
    • KinasePhos 2.0: A web server for identifying protein kinasespecific phosphorylation sites based on sequences and coupling patterns
    • Wong, Y. H., Lee, T.Y., Liang, H. K., Huang, C. M. et al., KinasePhos 2.0: a web server for identifying protein kinasespecific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 2007, 35, W588-594.
    • (2007) Nucleic Acids Res , vol.35
    • Wong, Y.H.1    Lee, T.Y.2    Liang, H.K.3    Huang, C.M.4
  • 79
    • 8844219516 scopus 로고    scopus 로고
    • Prediction of phosphorylation sites using SVMs
    • Kim, J. H., Lee, J., Oh, B., Kimm, K., Koh, I., Prediction of phosphorylation sites using SVMs. Bioinformatics 2004, 20, 3179-3184.
    • (2004) Bioinformatics , vol.20 , pp. 3179-3184
    • Kim, J.H.1    Lee, J.2    Oh, B.3    Kimm, K.4    Koh, I.5
  • 80
    • 4444320150 scopus 로고    scopus 로고
    • Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry
    • Hjerrild, M., Stensballe, A., Rasmussen, T. E., Kofoed, C. B. et al., Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J. Proteome Res. 2004, 3, 426-433.
    • (2004) J. Proteome Res , vol.3 , pp. 426-433
    • Hjerrild, M.1    Stensballe, A.2    Rasmussen, T.E.3    Kofoed, C.B.4
  • 81
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • Blom, N., Sicheritz-Ponten, T., Gupta, R., Gammeltoft, S., Brunak, S., Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4, 1633-1649.
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Ponten, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 82
    • 34548770172 scopus 로고    scopus 로고
    • GANNPhos: A new phosphorylation site predictor based on a genetic algorithm integrated neural network
    • Tang, Y. R., Chen, Y. Z., Canchaya, C. A., Zhang, Z., GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network. Protein Eng. Des. Sel. 2007, 20, 405-412.
    • (2007) Protein Eng. Des. Sel , vol.20 , pp. 405-412
    • Tang, Y.R.1    Chen, Y.Z.2    Canchaya, C.A.3    Zhang, Z.4
  • 83
    • 33645758540 scopus 로고    scopus 로고
    • prediction of PK-specific phosphorylation site with Bayesian decision theory
    • PPSP
    • Xue, Y., Li, A., Wang, L., Feng, H., Yao, X., PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics 2006, 7, 163.
    • (2006) BMC Bioinformatics , vol.7 , pp. 163
    • Xue, Y.1    Li, A.2    Wang, L.3    Feng, H.4    Yao, X.5
  • 84
    • 40249113353 scopus 로고    scopus 로고
    • Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection
    • Wan, J., Kang, S., Tang, C., Yan, J. et al., Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection. Nucleic Acids Res. 2008, 36, e22.
    • (2008) Nucleic Acids Res , vol.36
    • Wan, J.1    Kang, S.2    Tang, C.3    Yan, J.4
  • 85
    • 52649145895 scopus 로고    scopus 로고
    • GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy
    • Xue, Y., Ren, J., Gao, X., Jin, C. et al., GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol. Cell Proteomics 2008, 7, 1598-1608.
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 1598-1608
    • Xue, Y.1    Ren, J.2    Gao, X.3    Jin, C.4
  • 86
    • 0037422596 scopus 로고    scopus 로고
    • Structural basis and prediction of substrate specificity in protein serine/threonine kinases
    • Brinkworth, R. I., Breinl, R. A., Kobe, B., Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc. Natl. Acad. Sci. USA 2003, 100, 74-79.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 74-79
    • Brinkworth, R.I.1    Breinl, R.A.2    Kobe, B.3
  • 87
    • 34248213042 scopus 로고    scopus 로고
    • pkaPS: Prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model
    • Neuberger, G., Schneider, G., Eisenhaber, F., pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol. Direct. 2007, 2, 1.
    • (2007) Biol. Direct , vol.2 , pp. 1
    • Neuberger, G.1    Schneider, G.2    Eisenhaber, F.3
  • 89
    • 38549109487 scopus 로고    scopus 로고
    • a resource for exploring cellular phosphorylation networks
    • NetworKIN
    • Linding, R., Jensen, L. J., Pasculescu, A., Olhovsky, M. et al., NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 2008, 36, D695-699.
    • (2008) Nucleic Acids Res , vol.36
    • Linding, R.1    Jensen, L.J.2    Pasculescu, A.3    Olhovsky, M.4
  • 91
    • 44149105911 scopus 로고    scopus 로고
    • management, structural and evolutionary investigation, and prediction of phosphosites
    • PHOSIDA phosphorylation site database
    • Gnad, F., Ren, S., Cox, J., Olsen, J. V. et al., PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol. 2007, 8, R250.
    • (2007) Genome Biol , vol.8
    • Gnad, F.1    Ren, S.2    Cox, J.3    Olsen, J.V.4
  • 93
    • 57449105428 scopus 로고    scopus 로고
    • PhosphoPep - a database of protein phosphorylation sites in model organisms
    • Bodenmiller, B., Campbell, D., Gerrits, B., Lam, H. et al., PhosphoPep - a database of protein phosphorylation sites in model organisms. Nat. Biotechnol. 2008, 26, 1339-1340.
    • (2008) Nat. Biotechnol , vol.26 , pp. 1339-1340
    • Bodenmiller, B.1    Campbell, D.2    Gerrits, B.3    Lam, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.