메뉴 건너뛰기




Volumn 6, Issue 5, 2011, Pages

Discovery of protein Phosphorylation motifs through exploratory data analysis

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE; PEPTIDE FRAGMENT; PHOSPHOPROTEIN;

EID: 79957443956     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020025     Document Type: Article
Times cited : (22)

References (44)
  • 1
    • 0030581751 scopus 로고    scopus 로고
    • How do protein kinases recognize their substrates?
    • Pinna LA, Ruzzene M, (1996) How do protein kinases recognize their substrates? Biochim Biophys Acta 1314: 191-225.
    • (1996) Biochim Biophys Acta , vol.1314 , pp. 191-225
    • Pinna, L.A.1    Ruzzene, M.2
  • 3
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • Blom N, Sicheritz-Pontén T, Gupta R, Gammeltoft S, Brunak S, (2004) Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4: 1633-1649.
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Pontén, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 4
    • 20444383859 scopus 로고    scopus 로고
    • Protein phosphorylation in signaling-50 years and counting
    • Pawson T, Scott JD, (2005) Protein phosphorylation in signaling-50 years and counting. Trends Biochem Sci 30: 286-290.
    • (2005) Trends Biochem Sci , vol.30 , pp. 286-290
    • Pawson, T.1    Scott, J.D.2
  • 5
    • 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 JV, Macek B, 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    Ren, S.2    Cox, J.3    Olsen, J.V.4    Macek, B.5
  • 7
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer JC, Cantley LC, Yaffe MB, (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.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 8
    • 33646358251 scopus 로고    scopus 로고
    • Minimotif miner: a tool for investigating protein function
    • Balla S, Thapar V, Verma S, Luong T, Faghri T, et al. (2006) Minimotif miner: a tool for investigating protein function. Nat Methods 3: 175-177.
    • (2006) Nat Methods , vol.3 , pp. 175-177
    • Balla, S.1    Thapar, V.2    Verma, S.3    Luong, T.4    Faghri, T.5
  • 10
    • 47849125967 scopus 로고    scopus 로고
    • A multidimensional chromatography technology for in-depth phosphoproteome analysis
    • Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, et al. (2008) A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 7: 1389-1396.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 1389-1396
    • Albuquerque, C.P.1    Smolka, M.B.2    Payne, S.H.3    Bafna, V.4    Eng, J.5
  • 11
    • 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, Tomita M, et al. (2008) Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol 4: 193.
    • (2008) Mol Syst Biol , vol.4 , pp. 193
    • Sugiyama, N.1    Nakagami, H.2    Mochida, K.3    Daudi, A.4    Tomita, M.5
  • 13
    • 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, (2007) pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol Direct 2: 1.
    • (2007) Biol Direct , vol.2 , pp. 1
    • Neuberger, G.1    Schneider, G.2    Eisenhaber, F.3
  • 14
    • 46649097611 scopus 로고    scopus 로고
    • SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles
    • Yoo PD, Ho YS, Zhou BB, Zomaya AY, (2008) SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles. BMC Bioinformatics 9: 272.
    • (2008) BMC Bioinformatics , vol.9 , pp. 272
    • Yoo, P.D.1    Ho, Y.S.2    Zhou, B.B.3    Zomaya, A.Y.4
  • 15
    • 61649126270 scopus 로고    scopus 로고
    • Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets
    • Schwartz D, Chou MF, Church GM, (2009) Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets. Mol Cell Proteomics 8: 365-379.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 365-379
    • Schwartz, D.1    Chou, M.F.2    Church, G.M.3
  • 16
    • 27944499451 scopus 로고    scopus 로고
    • An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets
    • Schwartz D, Gygi SP, (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.P.2
  • 17
    • 58049204428 scopus 로고    scopus 로고
    • Discovery of phosphorylation motif mixtures in phosphoproteomics data
    • Ritz A, Shakhnarovich G, Salomon AR, Raphael BJ, (2009) Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics 25: 14-21.
    • (2009) Bioinformatics , vol.25 , pp. 14-21
    • Ritz, A.1    Shakhnarovich, G.2    Salomon, A.R.3    Raphael, B.J.4
  • 18
    • 23144434356 scopus 로고    scopus 로고
    • KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
    • Huang HD, Lee TY, Tzeng SW, Horng JT, (2005) KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 33: W226-W229.
    • (2005) Nucleic Acids Res , vol.33 , pp. 226-229
    • Huang, H.D.1    Lee, T.Y.2    Tzeng, S.W.3    Horng, J.T.4
  • 19
    • 0029197507 scopus 로고
    • The value of prior knowledge in discovering motifs with MEME
    • Bailey TL, Elkan C, (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3: 21-29.
    • (1995) Proc Int Conf Intell Syst Mol Biol , vol.3 , pp. 21-29
    • Bailey, T.L.1    Elkan, C.2
  • 20
    • 0029159799 scopus 로고
    • Finding flexible patterns in unaligned protein sequences
    • Jonassen I, Collins JF, Higgins DG, (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci 4: 1587-1595.
    • (1995) Protein Sci , vol.4 , pp. 1587-1595
    • Jonassen, I.1    Collins, J.F.2    Higgins, D.G.3
  • 21
    • 0031684427 scopus 로고    scopus 로고
    • Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm
    • Rigoutsos I, Floratos A, (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14: 55-67.
    • (1998) Bioinformatics , vol.14 , pp. 55-67
    • Rigoutsos, I.1    Floratos, A.2
  • 22
    • 61349150575 scopus 로고    scopus 로고
    • Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry
    • Zanivan S, Gnad F, Wickstrom SA, Geiger T, Macek B, et al. (2008) Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry. J Proteome Res 7: 5314-5326.
    • (2008) J Proteome Res , vol.7 , pp. 5314-5326
    • Zanivan, S.1    Gnad, F.2    Wickstrom, S.A.3    Geiger, T.4    Macek, B.5
  • 23
    • 33747823564 scopus 로고    scopus 로고
    • MEME: discovering and analyzing DNA and protein sequence motifs
    • Bailey TL, Williams N, Misleh C, Li WW, (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369-W373.
    • (2006) Nucleic Acids Res , vol.34 , pp. 369-373
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 24
    • 33645748095 scopus 로고    scopus 로고
    • What are DNA sequence motifs?
    • D'haeseleer P, (2006) What are DNA sequence motifs? Nat Biotechnol 24: 423-425.
    • (2006) Nat Biotechnol , vol.24 , pp. 423-425
    • D'haeseleer, P.1
  • 26
    • 3343003521 scopus 로고    scopus 로고
    • Hepatitis C virus whole genome position weight matrix and robust primer design
    • Qiu P, Cai XY, Wang L, Greene JR, Malcolm B, (2002) Hepatitis C virus whole genome position weight matrix and robust primer design. BMC Microbiol 2: 29.
    • (2002) BMC Microbiol , vol.2 , pp. 29
    • Qiu, P.1    Cai, X.Y.2    Wang, L.3    Greene, J.R.4    Malcolm, B.5
  • 27
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • Das MK, Dai HK, (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics 8: S21.
    • (2007) BMC Bioinformatics , vol.8
    • Das, M.K.1    Dai, H.K.2
  • 28
    • 0028502095 scopus 로고
    • Some useful statistical properties of position-weight matrices
    • Claverie JM, (1994) Some useful statistical properties of position-weight matrices. Comput Chem 18: 287-294.
    • (1994) Comput Chem , vol.18 , pp. 287-294
    • Claverie, J.M.1
  • 29
    • 0030449157 scopus 로고    scopus 로고
    • The statistical significance of nucleotide position-weight matrix matches
    • Claverie JM, Audic S, (1996) The statistical significance of nucleotide position-weight matrix matches. Comput Appl Biosci 12: 431-439.
    • (1996) Comput Appl Biosci , vol.12 , pp. 431-439
    • Claverie, J.M.1    Audic, S.2
  • 30
    • 63349083142 scopus 로고    scopus 로고
    • Pseudocounts for transcription factor binding sites
    • Nishida K, Frith MC, Nakai K, (2009) Pseudocounts for transcription factor binding sites. Nucleic Acids Res 37: 939-944.
    • (2009) Nucleic Acids Res , vol.37 , pp. 939-944
    • Nishida, K.1    Frith, M.C.2    Nakai, K.3
  • 31
    • 0029360028 scopus 로고
    • On cluster validity for the fuzzy c-means model
    • Pal NR, Bezdek JC, (1995) On cluster validity for the fuzzy c-means model. IEEE Trans Fuzzy Systs 3: 370-379.
    • (1995) IEEE Trans Fuzzy Systs , vol.3 , pp. 370-379
    • Pal, N.R.1    Bezdek, J.C.2
  • 33
    • 0025888298 scopus 로고
    • Identification of substrate recognition determinants for human ERK1 and ERK2 protein kinases
    • Gonzalez FA, Raden DL, Davis RJ, (1991) Identification of substrate recognition determinants for human ERK1 and ERK2 protein kinases. J Biol Chem 266: 22159-22163.
    • (1991) J Biol Chem , vol.266 , pp. 22159-22163
    • Gonzalez, F.A.1    Raden, D.L.2    Davis, R.J.3
  • 34
    • 12644284504 scopus 로고    scopus 로고
    • The consensus motif for phosphorylation by cyclin D1-Cdk4 is different from that for phosphorylation by cyclin A/E-Cdk2
    • Kitagawa M, Higashi H, Jung HK, Suzuki-Takahashi I, Ikeda M, et al. (1996) The consensus motif for phosphorylation by cyclin D1-Cdk4 is different from that for phosphorylation by cyclin A/E-Cdk2. EMBO J 15: 7060-7069.
    • (1996) EMBO J , vol.15 , pp. 7060-7069
    • Kitagawa, M.1    Higashi, H.2    Jung, H.K.3    Suzuki-Takahashi, I.4    Ikeda, M.5
  • 35
    • 0030590875 scopus 로고    scopus 로고
    • Molecular basis for the substrate specificity of protein kinase B; comparison with MAPKAP kinase-1 and p70 S6 kinase
    • Alessi DR, Caudwell FB, Andjelkovic M, Hemmings BA, Cohen P, (1996) Molecular basis for the substrate specificity of protein kinase B; comparison with MAPKAP kinase-1 and p70 S6 kinase. FEBS Lett 399: 333-338.
    • (1996) FEBS Lett , vol.399 , pp. 333-338
    • Alessi, D.R.1    Caudwell, F.B.2    Andjelkovic, M.3    Hemmings, B.A.4    Cohen, P.5
  • 36
    • 0034680838 scopus 로고    scopus 로고
    • Peptide and protein library screening defines optimal substrate motifs for AKT/PKB
    • Obata T, Yaffe MB, Leparc GG, Piro ET, Maegawa H, et al. (2000) Peptide and protein library screening defines optimal substrate motifs for AKT/PKB. J Biol Chem 275: 36108-36115.
    • (2000) J Biol Chem , vol.275 , pp. 36108-36115
    • Obata, T.1    Yaffe, M.B.2    Leparc, G.G.3    Piro, E.T.4    Maegawa, H.5
  • 37
    • 33845708060 scopus 로고    scopus 로고
    • Protein kinase B/Akt phosphorylation of PDE3A and its role in mammalian oocyte maturation
    • Han SJ, Vaccari S, Nedachi T, Andersen CB, Kovacina KS, et al. (2006) Protein kinase B/Akt phosphorylation of PDE3A and its role in mammalian oocyte maturation. EMBO J 25: 5716-5725.
    • (2006) EMBO J , vol.25 , pp. 5716-5725
    • Han, S.J.1    Vaccari, S.2    Nedachi, T.3    Andersen, C.B.4    Kovacina, K.S.5
  • 38
    • 0026355413 scopus 로고
    • Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations
    • Pearson RB, Kemp BE, (1991) Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations. Methods Enzymol 200: 62-81.
    • (1991) Methods Enzymol , vol.200 , pp. 62-81
    • Pearson, R.B.1    Kemp, B.E.2
  • 39
    • 33745209672 scopus 로고    scopus 로고
    • Regulation of NR1/NR2C N-methyl-D-aspartate (NMDA) receptors by phosphorylation
    • Chen BS, Braud S, Badger JD II, Isaac JTR, Roche KW, (2006) Regulation of NR1/NR2C N-methyl-D-aspartate (NMDA) receptors by phosphorylation. J Biol Chem 281: 16583-16590.
    • (2006) J Biol Chem , vol.281 , pp. 16583-16590
    • Chen, B.S.1    Braud, S.2    Badger II, J.D.3    Isaac, J.T.R.4    Roche, K.W.5
  • 40
    • 41449093997 scopus 로고    scopus 로고
    • A short motif in Kir6.1 consisting of four phosphorylation repeats underlies the vascular KATP channel inhibition by protein kinase C
    • Shi Y, Cui N, Shi W, Jiang C, (2008) A short motif in Kir6.1 consisting of four phosphorylation repeats underlies the vascular KATP channel inhibition by protein kinase C. J Biol Chem 283: 2488-2494.
    • (2008) J Biol Chem , vol.283 , pp. 2488-2494
    • Shi, Y.1    Cui, N.2    Shi, W.3    Jiang, C.4
  • 41
    • 0022348840 scopus 로고
    • Studies on the phosphorylation of myelin basic protein by protein kinase C and adenosine 3′:5′-monophosphate-dependent protein kinase
    • Kishimoto A, Nishiyama K, Nakanishi H, Uratsuji Y, Nomura H, et al. (1985) Studies on the phosphorylation of myelin basic protein by protein kinase C and adenosine 3′:5′-monophosphate-dependent protein kinase. J Biol Chem 260: 12492-12499.
    • (1985) J Biol Chem , vol.260 , pp. 12492-12499
    • Kishimoto, A.1    Nishiyama, K.2    Nakanishi, H.3    Uratsuji, Y.4    Nomura, H.5
  • 42
    • 0028540405 scopus 로고
    • Use of an oriented peptide library to determine the optimal substrates of protein kinases
    • Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica-Worms H, et al. (1994) Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 4: 973-982.
    • (1994) Curr Biol , vol.4 , pp. 973-982
    • Songyang, Z.1    Blechner, S.2    Hoagland, N.3    Hoekstra, M.F.4    Piwnica-Worms, H.5
  • 43
    • 28644439005 scopus 로고    scopus 로고
    • A dual-kinase mechanism for Wnt co-receptor phosphorylation and activation
    • Zeng X, Tamai K, Doble B, Li S, Huang H, et al. (2005) A dual-kinase mechanism for Wnt co-receptor phosphorylation and activation. Nature 438: 873-877.
    • (2005) Nature , vol.438 , pp. 873-877
    • Zeng, X.1    Tamai, K.2    Doble, B.3    Li, S.4    Huang, H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.