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Volumn 12, Issue 7, 2011, Pages 591-601

Computational analysis of phosphoproteomics: Progresses and perspectives

Author keywords

PhosGV; Phosphorylation; Phosphorylation evolution; Phosphorylation motif; Phosphorylation network; Post translational modification

Indexed keywords

GENETIC VARIABILITY; INTRACELLULAR SIGNALING; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; REVIEW;

EID: 80055071246     PISSN: 13892037     EISSN: 18755550     Source Type: Journal    
DOI: 10.2174/1389203711109070591     Document Type: Review
Times cited : (14)

References (120)
  • 1
    • 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(6), 286-290
    • (2005) Trends Biochem. Sci , vol.30 , Issue.6 , pp. 286-290
    • Pawson, T.1    Scott, J.D.2
  • 2
    • 63749113783 scopus 로고    scopus 로고
    • Tyrosine phosphorylation: Thirty years and counting
    • Hunter, T. Tyrosine phosphorylation: thirty years and counting. Curr. Opin. Cell Biol., 2009, 21(2), 140-146
    • (2009) Curr. Opin. Cell Biol , vol.21 , Issue.2 , pp. 140-146
    • Hunter, T.1
  • 3
    • 70349330577 scopus 로고    scopus 로고
    • The regulation of protein phosphorylation
    • Johnson, L.N. The regulation of protein phosphorylation. Biochem. Soc. Trans., 2009, 37(Pt 4), 627-641
    • (2009) Biochem. Soc. Trans , vol.37 , Issue.Pt 4 , pp. 627-641
    • Johnson, L.N.1
  • 4
    • 0034383949 scopus 로고    scopus 로고
    • The regulation of protein function by multisite phosphorylation-a 25 year update
    • Cohen, P. The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem. Sci., 2000, 25(12), 596-601
    • (2000) Trends Biochem. Sci , vol.25 , Issue.12 , pp. 596-601
    • Cohen, P.1
  • 5
    • 72849127628 scopus 로고    scopus 로고
    • Kinase mutations in human disease: Interpreting genotype-phenotype relationships
    • Lahiry, P.; Torkamani, A.; Schork, N.J.; Hegele, R.A. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat. Rev. Genet., 2009, 11(1), 60-74
    • (2009) Nat. Rev. Genet , vol.11 , Issue.1 , pp. 60-74
    • Lahiry, P.1    Torkamani, A.2    Schork, N.J.3    Hegele, R.A.4
  • 6
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • Manning, G.; Whyte, D.B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome. Science, 2002, 298(5600), 1912-1934
    • (2002) Science , vol.298 , Issue.5600 , pp. 1912-1934
    • Manning, G.1    Whyte, D.B.2    Martinez, R.3    Hunter, T.4    Sudarsanam, S.5
  • 7
    • 0032922002 scopus 로고    scopus 로고
    • PhosphoBase, a database of phosphorylation sites: Release 2.0
    • Kreegipuu, A.; Blom, N.; Brunak, S. PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic. Acids Res., 1999, 27(1), 237-239
    • (1999) Nucleic. Acids Res , vol.27 , Issue.1 , pp. 237-239
    • Kreegipuu, A.1    Blom, N.2    Brunak, S.3
  • 9
    • 63049113651 scopus 로고    scopus 로고
    • Analytical strategies for phosphoproteomics
    • Thingholm, T.E.; Jensen, O.N.; Larsen, M.R. Analytical strategies for phosphoproteomics. Proteomics, 2009, 9(6), 1451-1468
    • (2009) Proteomics , vol.9 , Issue.6 , pp. 1451-1468
    • Thingholm, T.E.1    Jensen, O.N.2    Larsen, M.R.3
  • 10
    • 63049127416 scopus 로고    scopus 로고
    • Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics
    • Tedford, N.C.; Hall, A.B.; Graham, J.R.; Murphy, C.E.; Gordon, N.F.; Radding, J.A. Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics. Proteomics, 2009, 9(6), 1469-1487
    • (2009) Proteomics , vol.9 , Issue.6 , pp. 1469-1487
    • Tedford, N.C.1    Hall, A.B.2    Graham, J.R.3    Murphy, C.E.4    Gordon, N.F.5    Radding, J.A.6
  • 11
    • 70349131530 scopus 로고    scopus 로고
    • The phosphoproteomics data explosion
    • Lemeer, S.; Heck, A.J. The phosphoproteomics data explosion. Curr. Opin. Chem. Biol., 2009, 13(4), 414-420
    • (2009) Curr. Opin. Chem. Biol , vol.13 , Issue.4 , pp. 414-420
    • Lemeer, S.1    Heck, A.J.2
  • 12
    • 75749099733 scopus 로고    scopus 로고
    • Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides
    • Song, C.; Ye, M.; Han, G.; Jiang, X.; Wang, F.; Yu, Z.; Chen, R.; Zou, H. Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides. Anal. Chem., 2010, 82(1), 53-56
    • (2010) Anal. Chem , vol.82 , Issue.1 , pp. 53-56
    • Song, C.1    Ye, M.2    Han, G.3    Jiang, X.4    Wang, F.5    Yu, Z.6    Chen, R.7    Zou, H.8
  • 15
    • 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.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell, 2006, 127(3), 635-648
    • (2006) Cell , vol.127 , Issue.3 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5    Mortensen, P.6    Mann, M.7
  • 16
    • 71049118572 scopus 로고    scopus 로고
    • SysPTM a systematic resource for proteomic research of posttranslational modifications
    • Li, H.; Xing, X.; Ding, G.; Li, Q.; Wang, C.; Xie, L.; Zeng, R.; Li, Y. SysPTM a systematic resource for proteomic research of posttranslational modifications. Mol. Cell. Proteomics, 2009, 8(8), 1839-1849
    • (2009) Mol. Cell. Proteomics , vol.8 , Issue.8 , pp. 1839-1849
    • Li, H.1    Xing, X.2    Ding, G.3    Li, Q.4    Wang, C.5    Xie, L.6    Zeng, R.7    Li, Y.8
  • 18
    • 33747836005 scopus 로고    scopus 로고
    • Phosphoproteomics toolbox: Computational biology, protein chemistry and mass spectrometry
    • Hjerrild, M.; Gammeltoft, S. Phosphoproteomics toolbox: computational biology, protein chemistry and mass spectrometry. FEBS Lett., 2006, 580(20), 4764-4770
    • (2006) FEBS Lett , vol.580 , Issue.20 , pp. 4764-4770
    • Hjerrild, M.1    Gammeltoft, S.2
  • 19
    • 29144510554 scopus 로고    scopus 로고
    • Substrate specificity of protein kinases and computational prediction of substrates
    • Kobe, B.; Kampmann, T.; Forwood, J.K.; Listwan, P.; Brinkworth, R.I. Substrate specificity of protein kinases and computational prediction of substrates. Biochim. Biophys. Acta., 2005, 1754(1-2), 200-209
    • (2005) Biochim. Biophys. Acta , vol.1754 , Issue.1-2 , pp. 200-209
    • Kobe, B.1    Kampmann, T.2    Forwood, J.K.3    Listwan, P.4    Brinkworth, R.I.5
  • 20
    • 65349140628 scopus 로고    scopus 로고
    • Kinase-specific prediction of protein phosphorylation sites
    • Miller, M.L.; Blom, N. Kinase-specific prediction of protein phosphorylation sites. Methods Mol. Biol., 2009, 527, 299-310
    • (2009) Methods Mol. Biol , vol.527 , pp. 299-310
    • Miller, M.L.1    Blom, N.2
  • 21
    • 34250878954 scopus 로고    scopus 로고
    • Mechanisms of specificity in protein phosphorylation
    • Ubersax, J.A., Ferrell, J.E., Jr. Mechanisms of specificity in protein phosphorylation. Nat. Rev. Mol. Cell Biol., 2007, 8(7), 530-541
    • (2007) Nat. Rev. Mol. Cell Biol , vol.8 , Issue.7 , pp. 530-541
    • Ubersax, J.A.1    Ferrell Jr., J.E.2
  • 22
    • 15444372337 scopus 로고    scopus 로고
    • Protein kinase specificity. A strategic collaboration between kinase peptide specificity and substrate recruitment
    • Zhu, G.; Liu, Y.; Shaw, S. Protein kinase specificity. A strategic collaboration between kinase peptide specificity and substrate recruitment. Cell Cycle, 2005, 4(1), 52-56
    • (2005) Cell Cycle , vol.4 , Issue.1 , pp. 52-56
    • Zhu, G.1    Liu, Y.2    Shaw, S.3
  • 23
    • 77950361921 scopus 로고    scopus 로고
    • Understanding protein phosphorylation on a systems level
    • Lin, J.; Xie, Z.; Zhu, H.; Qian, J. Understanding protein phosphorylation on a systems level. Brief. Funct. Genomics, 2010, 9(1), 3242
    • (2010) Brief. Funct. Genomics , vol.9 , Issue.1 , pp. 3242
    • Lin, J.1    Xie, Z.2    Zhu, H.3    Qian, J.4
  • 24
    • 0030581751 scopus 로고    scopus 로고
    • How do protein kinases recognize their substrates?
    • Pinna, L.A.; Ruzzene, M. How do protein kinases recognize their substrates? Biochim. Biophys. Acta., 1996, 1314(3), 191-225
    • (1996) Biochim. Biophys. Acta , vol.1314 , Issue.3 , pp. 191-225
    • Pinna, L.A.1    Ruzzene, M.2
  • 25
    • 0037954572 scopus 로고    scopus 로고
    • Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions
    • Biondi, R.M.; Nebreda, A.R. Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions. Biochem. J., 2003, 372(Pt 1), 1-13
    • (2003) Biochem. J , vol.372 , Issue.Pt 1 , pp. 1-13
    • Biondi, R.M.1    Nebreda, A.R.2
  • 26
    • 0033529034 scopus 로고    scopus 로고
    • Protein modification: Docking sites for kinases
    • Holland, P.M.; Cooper, J.A. Protein modification: docking sites for kinases. Curr. Biol., 1999, 9(9), 329-331
    • (1999) Curr. Biol , vol.9 , Issue.9 , pp. 329-331
    • Holland, P.M.1    Cooper, J.A.2
  • 27
    • 0035313699 scopus 로고    scopus 로고
    • Phosphoserine/threonine-binding domains
    • Yaffe, M.B.; Elia, A.E. Phosphoserine/threonine-binding domains. Curr. Opin. Cell Biol., 2001, 13(2), 131-138
    • (2001) Curr. Opin. Cell Biol , vol.13 , Issue.2 , pp. 131-138
    • Yaffe, M.B.1    Elia, A.E.2
  • 28
    • 0036518996 scopus 로고    scopus 로고
    • Phosphotyrosine-binding domains in signal transduction
    • Yaffe, M.B. Phosphotyrosine-binding domains in signal transduction. Nat. Rev. Mol. Cell Biol., 2002, 3(3), 177-186
    • (2002) Nat. Rev. Mol. Cell Biol , vol.3 , Issue.3 , pp. 177-186
    • Yaffe, M.B.1
  • 29
    • 33745813187 scopus 로고    scopus 로고
    • Reading protein modifications with interaction domains
    • Seet, B.T.; Dikic, I.; Zhou, M.M.; Pawson, T. Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol., 2006, 7(7), 473-483
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , Issue.7 , pp. 473-483
    • Seet, B.T.1    Dikic, I.2    Zhou, M.M.3    Pawson, T.4
  • 31
    • 0842346438 scopus 로고    scopus 로고
    • Specificity in signal transduction: From phosphotyrosine-SH2 domain interactions to complex cellular systems
    • Pawson, T. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell, 2004, 116(2), 191-203
    • (2004) Cell , vol.116 , Issue.2 , pp. 191-203
    • Pawson, T.1
  • 32
    • 0142240342 scopus 로고    scopus 로고
    • BRCT repeats as phosphopeptide-binding modules involved in protein targeting
    • Manke, I.A.; Lowery, D.M.; Nguyen, A.; Yaffe, M.B. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science, 2003, 302(5645), 636-639
    • (2003) Science , vol.302 , Issue.5645 , pp. 636-639
    • Manke, I.A.1    Lowery, D.M.2    Nguyen, A.3    Yaffe, M.B.4
  • 33
    • 69449099036 scopus 로고    scopus 로고
    • Zhang, C. Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome
    • Zhang, X.; Chen, Q.; Feng, J.; Hou, J.; Yang, F.; Liu, J.; Jiang, Q.; Zhang, C. Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome. J. Cell Sci., 2009, 122(Pt 13), 2240-2251
    • (2009) J. Cell Sci , vol.122 , Issue.Pt 13 , pp. 2240-2251
    • Zhang, X.1    Chen, Q.2    Feng, J.3    Hou, J.4    Yang, F.5    Liu, J.6    Jiang, Q.7
  • 35
    • 0031012892 scopus 로고    scopus 로고
    • Determination of the specific substrate sequence motifs of protein kinase C isozymes
    • Nishikawa, K.; Toker, A.; Johannes, F.J.; Songyang, Z.; Cantley, L.C. Determination of the specific substrate sequence motifs of protein kinase C isozymes. J. Biol. Chem., 1997, 272(2), 952-960
    • (1997) J. Biol. Chem , vol.272 , Issue.2 , pp. 952-960
    • Nishikawa, K.1    Toker, A.2    Johannes, F.J.3    Songyang, Z.4    Cantley, L.C.5
  • 39
    • 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(11), 1391-1398
    • (2005) Nat. Biotechnol , vol.23 , Issue.11 , pp. 1391-1398
    • Schwartz, D.1    Gygi, S.P.2
  • 41
    • 44449132255 scopus 로고    scopus 로고
    • Phosphoproteome analysis of fission yeast
    • Wilson-Grady, J.T.; Villen, J.; Gygi, S.P. Phosphoproteome analysis of fission yeast. J. Proteome Res., 2008, 7(3), 1088-1097
    • (2008) J. Proteome Res , vol.7 , Issue.3 , pp. 1088-1097
    • Wilson-Grady, J.T.1    Villen, J.2    Gygi, S.P.3
  • 44
    • 61649126270 scopus 로고    scopus 로고
    • Predicting protein posttranslational modifications using meta-analysis of proteome scale data sets
    • Schwartz, D.; Chou, M.F.; Church, G.M. Predicting protein posttranslational modifications using meta-analysis of proteome scale data sets. Mol. Cell. Proteomics, 2009, 8(2), 365-379
    • (2009) Mol. Cell. Proteomics , vol.8 , Issue.2 , pp. 365-379
    • Schwartz, D.1    Chou, M.F.2    Church, G.M.3
  • 45
    • 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(1), 14-21
    • (2009) Bioinformatics , vol.25 , Issue.1 , pp. 14-21
    • Ritz, A.1    Shakhnarovich, G.2    Salomon, A.R.3    Raphael, B.J.4
  • 48
    • 11144245309 scopus 로고    scopus 로고
    • A computational method for the analysis and prediction of protein:Phosphopeptide-binding sites
    • Joughin, B.A.; Tidor, B.; Yaffe, M.B. A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci., 2005, 14(1), 131-139
    • (2005) Protein Sci , vol.14 , Issue.1 , pp. 131-139
    • Joughin, B.A.1    Tidor, B.2    Yaffe, M.B.3
  • 49
    • 45549090122 scopus 로고    scopus 로고
    • Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach
    • Li, L.; Wu, C.; Huang, H.; Zhang, K.; Gan, J.; Li, S.S. Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. Nucleic. Acids Res., 2008, 36(10), 3263-3273
    • (2008) Nucleic. Acids Res , vol.36 , Issue.10 , pp. 3263-3273
    • Li, L.1    Wu, C.2    Huang, H.3    Zhang, K.4    Gan, J.5    Li, S.S.6
  • 50
    • 0035072833 scopus 로고    scopus 로고
    • motif-based profile scanning approach for genome-wide prediction of signaling pathways
    • Yaffe, M.B.; Leparc, G.G.; Lai, J.; Obata, T.; Volinia, S.; Cantley, L.C. A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat. Biotechnol., 2001, 19(4), 348-353
    • (2001) Nat. Biotechnol , vol.19 , Issue.4 , pp. 348-353
    • Yaffe, M.B.1    Leparc, G.G.2    Lai, J.3    Obata, T.4    Volinia, S.5    Cantley, L.C.A.6
  • 52
    • 33748325681 scopus 로고    scopus 로고
    • Identification of 14-3-3epsilon substrates from embryonic murine brain
    • Ballif, B.A.; Cao, Z.; Schwartz, D.; Carraway, K.L., 3rd; Gygi, S.P. Identification of 14-3-3epsilon substrates from embryonic murine brain. J. Proteome Res., 2006, 5(9), 2372-2379
    • (2006) J. Proteome Res , vol.5 , Issue.9 , pp. 2372-2379
    • Ballif, B.A.1    Cao, Z.2    Schwartz, D.3    Carraway III, K.L.4    Gygi, S.P.5
  • 53
    • 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.; Brunak, S.; Mann, M.; Blom, N. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2. Mol. Cell. Proteomics, 2008, 7(1), 181-192
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.1 , pp. 181-192
    • Miller, M.L.1    Hanke, S.2    Hinsby, A.M.3    Friis, C.4    Brunak, S.5    Mann, M.6    Blom, N.7
  • 54
    • 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(1), 1726
    • (2008) Brief. Funct. Genomic. Proteomic , vol.7 , Issue.1 , pp. 1726
    • Jorgensen, C.1    Linding, R.2
  • 55
    • 41149167511 scopus 로고    scopus 로고
    • Network medicine
    • Pawson, T.; Linding, R. Network medicine. FEBS Lett., 2008, 582(8), 1266-1270
    • (2008) FEBS Lett , vol.582 , Issue.8 , pp. 1266-1270
    • Pawson, T.1    Linding, R.2
  • 56
    • 65349100540 scopus 로고    scopus 로고
    • Reconstructing regulatory kinase pathways from phosphopeptide data: A bioinformatics approach
    • Puente, L.G.; Lee, R.E.; Megeney, L.A. Reconstructing regulatory kinase pathways from phosphopeptide data: a bioinformatics approach. Methods Mol. Biol., 2009, 527:311-319
    • (2009) Methods Mol. Biol , vol.527 , pp. 311-319
    • Puente, L.G.1    Lee, R.E.2    Megeney, L.A.3
  • 57
    • 73249115991 scopus 로고    scopus 로고
    • Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks
    • Tan, C.S.; Linding, R. Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks. Proteomics, 2009, 9(23); 5233-5242
    • (2009) Proteomics , vol.9 , Issue.23 , pp. 5233-5242
    • Tan, C.S.1    Linding, R.2
  • 58
    • 33144465579 scopus 로고    scopus 로고
    • Protein kinases associated with the yeast phosphoproteome
    • Brinkworth, R.I.; Munn, A.L.; Kobe, B. Protein kinases associated with the yeast phosphoproteome. BMC Bioinformatics, 2006, 7, 47
    • (2006) BMC Bioinformatics , vol.7 , pp. 47
    • Brinkworth, R.I.1    Munn, A.L.2    Kobe, B.3
  • 59
    • 84879798456 scopus 로고    scopus 로고
    • Prediction of cyclin-dependent kinase phosphorylation substrates
    • Chang, E.J.; Begum, R.; Chait, B.T.; Gaasterland, T. Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One, 2007, 2(7), e656
    • (2007) PLoS One , vol.2 , Issue.7
    • Chang, E.J.1    Begum, R.2    Chait, B.T.3    Gaasterland, T.4
  • 60
    • 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.; Wen, L.; Yao, X. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol. Cell. Proteomics, 2008, 7(9) 1598-1608
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.9 , pp. 1598-1608
    • Xue, Y.1    Ren, J.2    Gao, X.3    Jin, C.4    Wen, L.5    Yao, X.6
  • 62
    • 61449203001 scopus 로고    scopus 로고
    • KEA: Kinase enrichment analysis
    • Lachmann, A.; Ma'ayan, A. KEA: kinase enrichment analysis. Bioinformatics, 2009, 25(5), 684-686
    • (2009) Bioinformatics , vol.25 , Issue.5 , pp. 684-686
    • Lachmann, A.1    Ma'ayan, A.2
  • 64
    • 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(6), 1633-1649
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Ponten, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 65
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteomewide prediction of cell signaling interactions using short sequence motifs
    • Obenauer, J.C.; Cantley, L.C.; Yaffe, M.B. Scansite 2.0: Proteomewide prediction of cell signaling interactions using short sequence motifs. Nucleic. Acids Res., 2003, 31(13), 3635-3641
    • (2003) Nucleic. Acids Res , vol.31 , Issue.13 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 67
    • 34547112520 scopus 로고    scopus 로고
    • Cell signalling: The power of NetworKIN
    • Kritikou, E. Cell signalling: The power of NetworKIN. Nat. Rev. Mol. Cell Biol., 2007, 8, 598-599
    • (2007) Nat. Rev. Mol. Cell Biol , vol.8 , pp. 598-599
    • Kritikou, E.1
  • 68
    • 80055067317 scopus 로고    scopus 로고
    • NetworKIN in context-casting a net for kinases
    • Rusk, N. NetworKIN in context-casting a net for kinases. Nat. Methods., 2007, 4, 604-605
    • (2007) Nat. Methods , vol.4 , pp. 604-605
    • Rusk, N.1
  • 71
  • 73
    • 77951963192 scopus 로고    scopus 로고
    • Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data
    • Imamura, H.; Yachie, N.; Saito, R.; Ishihama, Y.; Tomita, M. Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics, 2010, 11, 232
    • (2010) BMC Bioinformatics , vol.11 , pp. 232
    • Imamura, H.1    Yachie, N.2    Saito, R.3    Ishihama, Y.4    Tomita, M.5
  • 77
    • 55949104581 scopus 로고    scopus 로고
    • Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom
    • Gao, X.; Jin, C.; Ren, J.; Yao, X.; Xue, Y. Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom. Genomics, 2008, 92(6), 457-463
    • (2008) Genomics , vol.92 , Issue.6 , pp. 457-463
    • Gao, X.1    Jin, C.2    Ren, J.3    Yao, X.4    Xue, Y.5
  • 78
    • 70350462371 scopus 로고    scopus 로고
    • Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions
    • Mayya, V.; Lundgren, D.H.; Hwang, S.I.; Rezaul, K.; Wu, L.; Eng, J.K.; Rodionov, V.; Han, D.K. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci. Signal., 2009, 2(84), ra46
    • (2009) Sci. Signal , vol.2 , Issue.84
    • Mayya, V.1    Lundgren, D.H.2    Hwang, S.I.3    Rezaul, K.4    Wu, L.5    Eng, J.K.6    Rodionov, V.7    Han, D.K.8
  • 82
    • 77953936773 scopus 로고    scopus 로고
    • Identifying differentially regulated subnetworks from phosphoproteomic data
    • Klammer, M.; Godl, K.; Tebbe, A.; Schaab, C. Identifying differentially regulated subnetworks from phosphoproteomic data. BMC Bioinformatics, 2010, 11, 351
    • (2010) BMC Bioinformatics , vol.11 , pp. 351
    • Klammer, M.1    Godl, K.2    Tebbe, A.3    Schaab, C.4
  • 83
    • 72849144434 scopus 로고    scopus 로고
    • Metzker, M.L. Sequencing technologies the next generation. Nat
    • Metzker, M.L. Sequencing technologies the next generation. Nat. Rev. Genet., 2009, 11(1), 31-46
    • (2009) Rev. Genet , vol.11 , Issue.1 , pp. 31-46
  • 84
    • 33947188719 scopus 로고    scopus 로고
    • Cancer: Drivers and passengers
    • Haber, D.A.; Settleman, J. Cancer: drivers and passengers. Nature, 2007, 446(7132), 145-146
    • (2007) Nature , vol.446 , Issue.7132 , pp. 145-146
    • Haber, D.A.1    Settleman, J.2
  • 86
    • 77950644139 scopus 로고    scopus 로고
    • PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation
    • Ren, J.; Jiang, C.; Gao, X.; Liu, Z.; Yuan, Z.; Jin, C.; Wen, L.; Zhang, Z.; Xue, Y.; Yao, X. PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Mol. Cell. Proteomics, 2010, 9(4), 623-634
    • (2010) Mol. Cell. Proteomics , vol.9 , Issue.4 , pp. 623-634
    • Ren, J.1    Jiang, C.2    Gao, X.3    Liu, Z.4    Yuan, Z.5    Jin, C.6    Wen, L.7    Zhang, Z.8    Xue, Y.9    Yao, X.10
  • 89
    • 33644870558 scopus 로고    scopus 로고
    • Cyclosporin and Timothy syndrome increase mode 2 gating of CaV1.2 calcium channels through aberrant phosphorylation of S6 helices
    • Erxleben, C.; Liao, Y.; Gentile, S.; Chin, D.; Gomez-Alegria, C.; Mori, Y.; Birnbaumer, L.; Armstrong, D.L. Cyclosporin and Timothy syndrome increase mode 2 gating of CaV1.2 calcium channels through aberrant phosphorylation of S6 helices. Proc. Natl. Acad. Sci. USA, 2006, 103(10), 3932-3937
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , Issue.10 , pp. 3932-3937
    • Erxleben, C.1    Liao, Y.2    Gentile, S.3    Chin, D.4    Gomez-Alegria, C.5    Mori, Y.6    Birnbaumer, L.7    Armstrong, D.L.8
  • 90
    • 55749095403 scopus 로고    scopus 로고
    • The human ERG1 channel polymorphism, K897T, creates a phosphorylation site that inhibits channel activity
    • Gentile, S.; Martin, N.; Scappini, E.; Williams, J.; Erxleben, C.; Armstrong, D.L. The human ERG1 channel polymorphism, K897T, creates a phosphorylation site that inhibits channel activity. Proc. Natl. Acad. Sci. USA, 2008, 105(38), 14704-14708
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , Issue.38 , pp. 14704-14708
    • Gentile, S.1    Martin, N.2    Scappini, E.3    Williams, J.4    Erxleben, C.5    Armstrong, D.L.6
  • 92
    • 77957875163 scopus 로고    scopus 로고
    • Moving from transcriptional to phospho-evolution: Generalizing regulatory evolution?
    • Moses, A.M.; Landry, C.R. Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends Genet., 2010, 26(11), 462-467
    • (2010) Trends Genet , vol.26 , Issue.11 , pp. 462-467
    • Moses, A.M.1    Landry, C.R.2
  • 93
    • 33749535603 scopus 로고    scopus 로고
    • Co-evolution of transcriptional and post-translational cell-cycle regulation
    • Jensen, L.J.; Jensen, T.S.; de Lichtenberg, U.; Brunak, S.; Bork, P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature, 2006, 443(7111), 594-597
    • (2006) Nature , vol.443 , Issue.7111 , pp. 594-597
    • Jensen, L.J.1    Jensen, T.S.2    de Lichtenberg, U.3    Brunak, S.4    Bork, P.5
  • 94
    • 34548222737 scopus 로고    scopus 로고
    • Evolution of cell cycle control: Same molecular machines, different regulation
    • de Lichtenberg, U.; Jensen, T.S.; Brunak, S.; Bork, P.; Jensen, L.J. Evolution of cell cycle control: same molecular machines, different regulation. Cell Cycle, 2007, 6(15), 1819-1825
    • (2007) Cell Cycle , vol.6 , Issue.15 , pp. 1819-1825
    • de Lichtenberg, U.1    Jensen, T.S.2    Brunak, S.3    Bork, P.4    Jensen, L.J.5
  • 95
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
    • Gnad, F.; Ren, S.; Cox, J.; Olsen, J.V.; Macek, B.; Oroshi, M.; Mann, M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol., 2007, 8(11), R250
    • (2007) Genome Biol , vol.8 , Issue.11
    • Gnad, F.1    Ren, S.2    Cox, J.3    Olsen, J.V.4    Macek, B.5    Oroshi, M.6    Mann, M.7
  • 96
    • 75849140545 scopus 로고    scopus 로고
    • Evidence for the concerted evolution between short linear protein motifs and their flanking regions
    • Chica, C.; Diella, F.; Gibson, T.J. Evidence for the concerted evolution between short linear protein motifs and their flanking regions. PLoS One, 2009, 4(7), e6052
    • (2009) PLoS One , vol.4 , Issue.7
    • Chica, C.1    Diella, F.2    Gibson, T.J.3
  • 97
    • 39049129309 scopus 로고    scopus 로고
    • PhosphoBlast, a computational tool for comparing phosphoprotein signatures among large datasets. Mol. Cell
    • Wang, Y.; Klemke, R.L. PhosphoBlast, a computational tool for comparing phosphoprotein signatures among large datasets. Mol. Cell. Proteomics, 2008, 7(1), 145-162
    • (2008) Proteomics , vol.7 , Issue.1 , pp. 145-162
    • Wang, Y.1    Klemke, R.L.2
  • 98
    • 45449101679 scopus 로고    scopus 로고
    • Comparative conservation analysis of the human mitotic phosphoproteome
    • Malik, R.; Nigg, E.A.; Korner, R. Comparative conservation analysis of the human mitotic phosphoproteome. Bioinformatics, 2008, 24(12), 1426-1432
    • (2008) Bioinformatics , vol.24 , Issue.12 , pp. 1426-1432
    • Malik, R.1    Nigg, E.A.2    Korner, R.3
  • 99
    • 65349155149 scopus 로고    scopus 로고
    • Weak functional constraints on phosphoproteomes
    • Landry, C.R.; Levy, E.D.; Michnick, S.W. Weak functional constraints on phosphoproteomes. Trends Genet., 2009, 25(5), 193197
    • (2009) Trends Genet , vol.25 , Issue.5 , pp. 193197
    • Landry, C.R.1    Levy, E.D.2    Michnick, S.W.3
  • 100
    • 77955957347 scopus 로고    scopus 로고
    • Evolution of characterized phosphorylation sites in budding yeast. Mol. Biol
    • Ba, A.N.; Moses, A.M. Evolution of characterized phosphorylation sites in budding yeast. Mol. Biol. Evol., 2010, 27(9), 2027-2037
    • (2010) Evol , vol.27 , Issue.9 , pp. 2027-2037
    • Ba, A.N.1    Moses, A.M.2
  • 101
    • 77958118308 scopus 로고    scopus 로고
    • Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals
    • Chen, S.C.; Chen, F.C.; Li, W.H. Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals. Mol. Biol. Evol., 2010, 27(11), 2548-2554
    • (2010) Mol. Biol. Evol , vol.27 , Issue.11 , pp. 2548-2554
    • Chen, S.C.1    Chen, F.C.2    Li, W.H.3
  • 102
    • 39749166860 scopus 로고    scopus 로고
    • Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    • Macek, B.; Gnad, F.; Soufi, B.; Kumar, C.; Olsen, J.V.; Mijakovic, I.; Mann, M. Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell. Proteomics, 2008, 7(2), 299-307
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.2 , pp. 299-307
    • Macek, B.1    Gnad, F.2    Soufi, B.3    Kumar, C.4    Olsen, J.V.5    Mijakovic, I.6    Mann, M.7
  • 103
    • 38649139336 scopus 로고    scopus 로고
    • Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain
    • Ballif, B.A.; Carey, G.R.; Sunyaev, S.R.; Gygi, S.P. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J. Proteome Res., 2008, 7(1), 311-318
    • (2008) J. Proteome Res , vol.7 , Issue.1 , pp. 311-318
    • Ballif, B.A.1    Carey, G.R.2    Sunyaev, S.R.3    Gygi, S.P.4
  • 104
    • 68549085023 scopus 로고    scopus 로고
    • High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
    • Gnad, F.; de Godoy, L.M.; Cox, J.; Neuhauser, N.; Ren, S.; Olsen, J.V.; Mann, M. High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics, 2009, 9(20), 4642-4652
    • (2009) Proteomics , vol.9 , Issue.20 , pp. 4642-4652
    • Gnad, F.1    de Godoy, L.M.2    Cox, J.3    Neuhauser, N.4    Ren, S.5    Olsen, J.V.6    Mann, M.7
  • 105
    • 85038514669 scopus 로고    scopus 로고
    • Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes
    • epub ahead of print
    • Wang, Z.; Ding, G.; Geistlinger, L.; Hong, L.; Liu, L.; Zeng, R.; Tateno, Y.; Li, Y. Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. Mol. Biol. Evol., 2010, epub ahead of print
    • (2010) Mol. Biol. Evol
    • Wang, Z.1    Ding, G.2    Geistlinger, L.3    Hong, L.4    Liu, L.5    Zeng, R.6    Tateno, Y.7    Li, Y.8
  • 106
    • 54549123613 scopus 로고    scopus 로고
    • Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes
    • Boekhorst, J.; van Breukelen, B.; Heck, A., Jr.; Snel, B. Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol., 2008, 9(10), R144
    • (2008) Genome Biol , vol.9 , Issue.10
    • Boekhorst, J.1    van Breukelen, B.2    Heck Jr., A.3    Snel, B.4
  • 107
    • 77953563038 scopus 로고    scopus 로고
    • Roles of junk phosphorylation in modulating biomolecular association of phosphorylated proteins?
    • [Epub ahead of print]
    • Tan, C.S., Jorgensen, C., Linding, R. Roles of junk phosphorylation in modulating biomolecular association of phosphorylated proteins? Cell Cycle, 2010, 9(7). [Epub ahead of print]
    • (2010) Cell Cycle , vol.9 , Issue.7
    • Tan, C.S.1    Jorgensen, C.2    Linding, R.3
  • 108
    • 67449104195 scopus 로고    scopus 로고
    • In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution
    • Yachie, N.; Saito, R.; Sugahara, J.; Tomita, M.; Ishihama, Y. In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Mol. Cell. Proteomics, 2009, 8(5), 1061-1071
    • (2009) Mol. Cell. Proteomics , vol.8 , Issue.5 , pp. 1061-1071
    • Yachie, N.1    Saito, R.2    Sugahara, J.3    Tomita, M.4    Ishihama, Y.5
  • 109
    • 36749051222 scopus 로고    scopus 로고
    • Regulatory evolution in proteins by turnover and lineage-specific changes of cyclindependent kinase consensus sites
    • Moses, A.M.; Liku, M.E.; Li, J.J.; Durbin, R. Regulatory evolution in proteins by turnover and lineage-specific changes of cyclindependent kinase consensus sites. Proc. Natl. Acad. Sci. USA, 2007, 104(45), 17713-17718
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , Issue.45 , pp. 17713-17718
    • Moses, A.M.1    Liku, M.E.2    Li, J.J.3    Durbin, R.4
  • 110
    • 70349546862 scopus 로고    scopus 로고
    • Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
    • 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. Science, 2009, 325(5948), 1682-1686
    • (2009) Science , vol.325 , Issue.5948 , pp. 1682-1686
    • Holt, L.J.1    Tuch, B.B.2    Villen, J.3    Johnson, A.D.4    Gygi, S.P.5    Morgan, D.O.6
  • 111
    • 78650127368 scopus 로고    scopus 로고
    • Mann, M. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes and mitochondria
    • epub ahead of print
    • Gnad, F.; Forner, F.; Zielinska, D.F.; Birney, E.; Gunawardena, J.; Mann, M. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes and mitochondria. Mol. Cell. Proteomics, 2010, epub ahead of print
    • (2010) Mol. Cell. Proteomics
    • Gnad, F.1    Forner, F.2    Zielinska, D.F.3    Birney, E.4    Gunawardena, J.5
  • 114
    • 70349518562 scopus 로고    scopus 로고
    • Positive selection of tyrosine loss in metazoan evolution
    • Tan, C.S.; Pasculescu, A.; Lim, W.A.; Pawson, T.; Bader, G.D.; Linding, R. Positive selection of tyrosine loss in metazoan evolution. Science, 2009, 325(5948), 1686-1688
    • (2009) Science , vol.325 , Issue.5948 , pp. 1686-1688
    • Tan, C.S.1    Pasculescu, A.2    Lim, W.A.3    Pawson, T.4    Bader, G.D.5    Linding, R.6
  • 115
    • 53949103770 scopus 로고    scopus 로고
    • Evolution of phosphorylationdependent regulation of activation-induced cytidine deaminase
    • Basu, U.; Wang, Y.; Alt, F.W. Evolution of phosphorylationdependent regulation of activation-induced cytidine deaminase. Mol. Cell, 2008, 32(2), 285-291
    • (2008) Mol. Cell , vol.32 , Issue.2 , pp. 285-291
    • Basu, U.1    Wang, Y.2    Alt, F.W.3
  • 116
    • 14644392172 scopus 로고    scopus 로고
    • Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome. Mol. Cell
    • Wykoff, D.D.; O'Shea, E.K. Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome. Mol. Cell. Proteomics, 2005, 4(1), 73-83
    • (2005) Proteomics , vol.4 , Issue.1 , pp. 73-83
    • Wykoff, D.D.1    O'Shea, E.K.2
  • 118
    • 68949212379 scopus 로고    scopus 로고
    • Lysine acetylation targets protein complexes and co-regulates major cellular functions
    • Choudhary, C.; Kumar, C.; Gnad, F.; Nielsen, M.L.; Rehman, M.; Walther, T.C.; Olsen, J.V.; Mann, M. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science, 2009, 325(5942), 834-840
    • (2009) Science , vol.325 , Issue.5942 , pp. 834-840
    • Choudhary, C.1    Kumar, C.2    Gnad, F.3    Nielsen, M.L.4    Rehman, M.5    Walther, T.C.6    Olsen, J.V.7    Mann, M.8


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