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Volumn 28, Issue 12, 2012, Pages 1562-1570

MMFPH: A maximal motif finder for phosphoproteomics datasets

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEOME;

EID: 84863515374     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts195     Document Type: Article
Times cited : (29)

References (47)
  • 1
    • 77956285101 scopus 로고    scopus 로고
    • Understanding the role of PknJ in mycobacterium tuberculosis: biochemical characterization and identification of novel substrate Pyruvate Kinase A
    • Arora, G. et al. (2010) Understanding the role of PknJ in mycobacterium tuberculosis: biochemical characterization and identification of novel substrate Pyruvate Kinase A. PLoS ONE, 5, e10772.
    • (2010) PLoS ONE , vol.5
    • Arora, G.1
  • 2
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphrylation of proteins from the amino acid sequence
    • Blom, N. et al. (2004) Prediction of post-translational glycosylation and phosphrylation of proteins from the amino acid sequence. Proteomics, 4, 1633-1649.
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1
  • 3
    • 0037005887 scopus 로고    scopus 로고
    • Differing substrate specificities of members of the DYRK family of arginine-directed protein kinases
    • Campbell, L.E. and Proud, C.G. (2002) Differing substrate specificities of members of the DYRK family of arginine-directed protein kinases. FEBS Lett., 510, 31-36.
    • (2002) FEBS Lett. , vol.510 , pp. 31-36
    • Campbell, L.E.1    Proud, C.G.2
  • 4
    • 0033014180 scopus 로고    scopus 로고
    • The mood-stabilizing agent valproate inhibits the activity of glycogen synthase kinase-3
    • Chen, G. et al. (1999) The mood-stabilizing agent valproate inhibits the activity of glycogen synthase kinase-3. J. Neurochem., 72, 1327-1330.
    • (1999) J. Neurochem. , vol.72 , pp. 1327-1330
    • Chen, G.1
  • 5
    • 79957443956 scopus 로고    scopus 로고
    • Discovery of protein phosphorylation motifs through exploratory data analysis
    • Chen, Y. et al. (2011) Discovery of protein phosphorylation motifs through exploratory data analysis. PLoS ONE, 6, e2002.
    • (2011) PLoS ONE , vol.6
    • Chen, Y.1
  • 6
    • 0034383949 scopus 로고    scopus 로고
    • The regulation of protein function by multisite phosphorylation-a 25 year update
    • Cohen, P. (2000) The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem. Sci., 25, 596-601.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 596-601
    • Cohen, P.1
  • 7
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: a sequence logo generator
    • Crooks, G. et al. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
    • (2004) Genome Res. , vol.14 , pp. 1188-1190
    • Crooks, G.1
  • 8
    • 38549092088 scopus 로고    scopus 로고
    • Phospho ELM: a database of phosphorylation sites - update 2011
    • Dinkel, H. et al. (2010) Phospho.ELM: a database of phosphorylation sites - update 2011. Nucleic Acids Res., 36, 240-244.
    • (2010) Nucleic Acids Res. , vol.36 , pp. 240-244
    • Dinkel, H.1
  • 9
    • 0036198435 scopus 로고    scopus 로고
    • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
    • Ficarro, S. et al. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol., 20, 301-305.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 301-305
    • Ficarro, S.1
  • 10
    • 0023656594 scopus 로고
    • Formation of protein kinase recognition sites by covalent modi{thorn}cation of the substrate. Molecular mechanism for the synergistic action of casein kinase II and glycogen synthase kinase 3
    • Fiol, C.J. et al. (1987) Formation of protein kinase recognition sites by covalent modi{thorn}cation of the substrate. Molecular mechanism for the synergistic action of casein kinase II and glycogen synthase kinase 3. J. Biol. Chem., 262, 14042-14048.
    • (1987) J. Biol. Chem. , vol.262 , pp. 14042-14048
    • Fiol, C.J.1
  • 11
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    • Gnad, F. et al. (2007) PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol., 8, R250.
    • (2007) Genome Biol. , vol.8
    • Gnad, F.1
  • 12
    • 78651277460 scopus 로고    scopus 로고
    • Phosida 2011: the posttranslational modification database
    • Gnad, F. et al. (2011) Phosida 2011: the posttranslational modification database. Nucleic Acids Res., 39, 253-260.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 253-260
    • Gnad, F.1
  • 13
    • 0026487365 scopus 로고
    • Glycogen synthase kinase-3 induces Alzheimer's disease-like phosphorylation of tau: generation of paired helical filament epitopes and neuronal localisation of the kinase
    • Hanger, D. et al. (1992) Glycogen synthase kinase-3 induces Alzheimer's disease-like phosphorylation of tau: generation of paired helical filament epitopes and neuronal localisation of the kinase. Neurosci. Lett., 147, 58-62.
    • (1992) Neurosci. Lett. , vol.147 , pp. 58-62
    • Hanger, D.1
  • 14
    • 0037205315 scopus 로고    scopus 로고
    • Glycogen synthase kinase-3?: a novel regulator of cardiac hypertrophy and development
    • Hardt, S. and Sadoshima, J. (2002) Glycogen synthase kinase-3?: a novel regulator of cardiac hypertrophy and development. Circ. Res., 90, 1055-1063.
    • (2002) Circ. Res. , vol.90 , pp. 1055-1063
    • Hardt, S.1    Sadoshima, J.2
  • 15
    • 38549127781 scopus 로고    scopus 로고
    • Phosphat: a database of phosphorylation sites in arabidopsis thaliana and a plant-specific phosphorylation site predictor
    • Heazlewood, J. et al. (2008) Phosphat: a database of phosphorylation sites in arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res., 36, 1015-1021.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 1015-1021
    • Heazlewood, J.1
  • 16
    • 79951784508 scopus 로고    scopus 로고
    • Motif-All: discovering all phosphorylation motifs
    • He, Z. et al. (2011) Motif-All: discovering all phosphorylation motifs. BMC Bioinform., 12 (Suppl. 1), S22.
    • (2011) BMC Bioinform , vol.12 , Issue.SUPPL. 1
    • He, Z.1
  • 17
    • 0034723403 scopus 로고    scopus 로고
    • Specificity determinants of substrate recognition by the protein kinase DYRK1A
    • Himpel, S. et al. (2000) Specificity determinants of substrate recognition by the protein kinase DYRK1A. J. Biol. Chem. Meth., 275, 2431-2438.
    • (2000) J. Biol. Chem. Meth. , vol.275 , pp. 2431-2438
    • Himpel, S.1
  • 18
    • 70349546862 scopus 로고    scopus 로고
    • Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
    • Holt, L. et al. (2009) Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science, 325, 1682-1686.
    • (2009) Science , vol.325 , pp. 1682-1686
    • Holt, L.1
  • 19
    • 17644391197 scopus 로고    scopus 로고
    • A rapid method for determining protein kinase phosphorylation specificity
    • Hutti, J. et al. (2004) A rapid method for determining protein kinase phosphorylation specificity. Nat. Meth., 1, 27-29.
    • (2004) Nat. Meth. , vol.1 , pp. 27-29
    • Hutti, J.1
  • 20
    • 80054698820 scopus 로고    scopus 로고
    • Rapid and reproducible single-stage phosphopeptide enrichment of complex peptide mixtures: application to general and phosphotyrosine-specific phosphoproteomics experiments
    • Kettenbach, A. and Gerber, S. (2011) Rapid and reproducible single-stage phosphopeptide enrichment of complex peptide mixtures: application to general and phosphotyrosine-specific phosphoproteomics experiments. Anal. Chem. 83, 7635-7644. http://www.ncbi.nlm.nih.gov/pubmed/21899308.
    • (2011) Anal. Chem. , vol.83 , pp. 7635-7644
    • Kettenbach, A.1    Gerber, S.2
  • 21
    • 79959735228 scopus 로고    scopus 로고
    • Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells
    • Kettenbach, A. et al. (2011) Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells. Sci. Signal, 4, rs5.
    • (2011) Sci. Signal , vol.4
    • Kettenbach, A.1
  • 23
    • 0023645087 scopus 로고
    • Substrate specificity determinants for casein kinase I1 as deduced from studies with synthetic peptides
    • Kuenzel, E. et al. (1987) Substrate specificity determinants for casein kinase I1 as deduced from studies with synthetic peptides. J. Biol. Chem., 262, 9136-9140.
    • (1987) J. Biol. Chem. , vol.262 , pp. 9136-9140
    • Kuenzel, E.1
  • 24
    • 0029899091 scopus 로고    scopus 로고
    • Tau protein is phosphorylated by cyclic AMP-dependent protein kinase and calcium/calmodulin-dependent protein kinase II within its microtubulebinding domains at Ser-262 and Ser-35
    • Litersky, J. et al. (1996) Tau protein is phosphorylated by cyclic AMP-dependent protein kinase and calcium/calmodulin-dependent protein kinase II within its microtubulebinding domains at Ser-262 and Ser-35. J. Biochem., 316, 655-660.
    • (1996) J. Biochem. , vol.316 , pp. 655-660
    • Litersky, J.1
  • 25
    • 0036806311 scopus 로고    scopus 로고
    • Evolution of protein kinase signaling from yeast to man
    • Manning, G. et al. (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci., 27, 514-520.
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 514-520
    • Manning, G.1
  • 26
    • 34249947699 scopus 로고    scopus 로고
    • ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    • Matsuoka, S. et al. (2007) ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science, 316, 1160-1166.
    • (2007) Science , vol.316 , pp. 1160-1166
    • Matsuoka, S.1
  • 27
    • 70350462371 scopus 로고    scopus 로고
    • Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions
    • Mayya, V. et al. (2009) Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci. Signal, 2, ra46.
    • (2009) Sci. Signal , vol.2
    • Mayya, V.1
  • 28
    • 55749111058 scopus 로고    scopus 로고
    • Linear motif atlas for phosphorylation-dependent signaling
    • Miller, M.L. et al. (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal, 1, ra2.
    • (2008) Sci. Signal , vol.1
    • Miller, M.L.1
  • 29
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S. and Wunsch, C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 30
    • 0031012892 scopus 로고    scopus 로고
    • Determination of the specific substrate sequence motifs of protein kinase C isozymes
    • Nishikawa, K. et al. (1997) Determination of the specific substrate sequence motifs of protein kinase C isozymes. J. Biol. Chem., 272, 952-960.
    • (1997) J. Biol. Chem. , vol.272 , pp. 952-960
    • Nishikawa, K.1
  • 31
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer, J. et al. (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res., 31, 3635-3641.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3635-3641
    • Obenauer, J.1
  • 32
    • 0033104986 scopus 로고    scopus 로고
    • Optimal sequences for non-phosphate-directed phoshorylation by protein kinase CK1 (casein kinase-1) - a re-evaluation
    • Pulgar, V. et al. (1999) Optimal sequences for non-phosphate-directed phoshorylation by protein kinase CK1 (casein kinase-1) - a re-evaluation. Eur. J. Biochem., 260, 520-526.
    • (1999) Eur. J. Biochem. , vol.260 , pp. 520-526
    • Pulgar, V.1
  • 33
    • 58049204428 scopus 로고    scopus 로고
    • Discovery of phosphorylation motif mixtures in phosphoproteomics data
    • Ritz, A. et al. (2009) Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics, 25, 14-21.
    • (2009) Bioinformatics , vol.25 , pp. 14-21
    • Ritz, A.1
  • 34
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider, T. and Stephens, R. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.1    Stephens, R.2
  • 35
    • 27944499451 scopus 로고    scopus 로고
    • An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets
    • Schwartz, D. and Gygi, S. (2005) An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat. Biotechnol., 23, 1391-1398.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 1391-1398
    • Schwartz, D.1    Gygi, S.2
  • 36
    • 0035413602 scopus 로고    scopus 로고
    • Physiological substrates of cAMP-dependent protein kinase
    • Shabb, J. (2001) Physiological substrates of cAMP-dependent protein kinase. Chem. Rev., 101, 2381-2411.
    • (2001) Chem. Rev. , vol.101 , pp. 2381-2411
    • Shabb, J.1
  • 37
    • 0026039891 scopus 로고
    • Casein kinase I and II-multipotential serine protein kinases: structure, function, and regulation
    • Tuazon, P. and Traugh, J. (1991) Casein kinase I and II-multipotential serine protein kinases: structure, function, and regulation. Adv. Second Messenger Phosphoprotein Res., 23, 123-164.
    • (1991) Adv. Second Messenger Phosphoprotein Res. , vol.23 , pp. 123-164
    • Tuazon, P.1    Traugh, J.2
  • 38
    • 40849119616 scopus 로고    scopus 로고
    • Understanding and exploiting substrate recognition by protein kinases
    • Turk, B. (2008) Understanding and exploiting substrate recognition by protein kinases. Curr. Opin. Chem. Biol., 12, 4-10.
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 4-10
    • Turk, B.1
  • 39
    • 33846785485 scopus 로고    scopus 로고
    • Large-scale phosphorylation analysis of mouse liver
    • Villen, J. et al. (2007) Large-scale phosphorylation analysis of mouse liver. PNAS, 104, 1488-1493.
    • (2007) PNAS , vol.104 , pp. 1488-1493
    • Villen, J.1
  • 40
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2 - a multiple sequence alignment editor and analysis workbench
    • Waterhouse, A. et al. (2009) Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.1
  • 41
    • 44449132255 scopus 로고    scopus 로고
    • Phosphoproteome analysis of fission yeast
    • Wilson-Grady, J. et al. (2008) Phosphoproteome analysis of fission yeast. J. Proteome Res., 7, 1088-1097.
    • (2008) J. Proteome Res. , vol.7 , pp. 1088-1097
    • Wilson-Grady, J.1
  • 42
    • 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. et al. (2007) KinasePhos 2.0 - a web server for identifying protein kinasespecific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res., 35, 588-594.
    • (2007) Nucleic Acids Res , vol.35 , pp. 588-594
    • Wong, Y.1
  • 43
    • 23144452431 scopus 로고    scopus 로고
    • GPS: a comprehensive www server for phosphorylation sites prediction
    • Xue, Y. et al. (2005) GPS: a comprehensive www server for phosphorylation sites prediction. Nucleic Acids Res., 33, 184-187.
    • (2005) Nucleic Acids Res , vol.33 , pp. 184-187
    • Xue, Y.1
  • 44
    • 33747838835 scopus 로고    scopus 로고
    • SUMOsp: a web server for sumoylation site prediction
    • Xue, Y. et al. (2006) SUMOsp: a web server for sumoylation site prediction. Nucleic Acids Res., 34, 254-257.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 254-257
    • Xue, Y.1
  • 45
    • 0027340541 scopus 로고
    • Protein kinase FA/GSK-3 phosphorylates tau on Ser235-Pro and Ser404-Pro that are abnormally phosphorylated in Alzheimer's disease brain
    • Yang, S. et al. (1993) Protein kinase FA/GSK-3 phosphorylates tau on Ser235-Pro and Ser404-Pro that are abnormally phosphorylated in Alzheimer's disease brain. J. Neurochem., 61, 1742-1747.
    • (1993) J. Neurochem. , vol.61 , pp. 1742-1747
    • Yang, S.1
  • 46
    • 79958696336 scopus 로고    scopus 로고
    • Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling
    • Yu, Y. et al. (2011) Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science, 332, 1322-1326.
    • (2011) Science , vol.332 , pp. 1322-1326
    • Yu, Y.1
  • 47
    • 45549086908 scopus 로고    scopus 로고
    • Phosphoproteome analysis of Drosophila melanogaster embryos
    • Zhai, B. et al. (2008) Phosphoproteome analysis of Drosophila melanogaster embryos. J. Proteome Res., 7, 1675-1682.
    • (2008) J. Proteome Res. , vol.7 , pp. 1675-1682
    • Zhai, B.1


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