메뉴 건너뛰기




Volumn 15, Issue 5, 2013, Pages 839-855

Data construction for phosphorylation site prediction

Author keywords

Classification; Friedman test; Generalization performance; Phosphorylation site prediction; Wilcoxon signed ranks test

Indexed keywords

PROTEIN;

EID: 84883188502     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbt012     Document Type: Article
Times cited : (13)

References (36)
  • 1
    • 34250878954 scopus 로고    scopus 로고
    • Mechanisms of specificity in protein phosphorylation
    • Ubersax JA, Ferrell JEJr. Mechanisms of specificity in protein phosphorylation. Nat RevMol Cell Biol 2007;8:530-41.
    • (2007) Nat RevMol Cell Biol , vol.8 , pp. 530-541
    • Ubersax, J.A.1    Ferrell, J.E.2
  • 2
    • 0030581751 scopus 로고    scopus 로고
    • How do protein kinases recognize their substrates?
    • Pinna LA, Ruzzene M. How do protein kinases recognize their substrates? Biochim Biophys Acta 1996;1314:191-225.
    • (1996) Biochim Biophys Acta , vol.1314 , pp. 191-225
    • Pinna, L.A.1    Ruzzene, M.2
  • 3
    • 65349140628 scopus 로고    scopus 로고
    • Kinase-specific prediction of protein phosphorylation sites
    • Miller ML, Blom N. Kinase-specific prediction of protein phosphorylation sites. MethodsMol Biol 2009;527:299-310.
    • (2009) MethodsMol Biol , vol.527 , pp. 299-310
    • Miller, M.L.1    Blom, N.2
  • 4
    • 78651317205 scopus 로고    scopus 로고
    • A summary of computational resources for protein phosphorylation
    • Xue Y, Gao X, Cao J, et al. A summary of computational resources for protein phosphorylation. Curr Protein Pept Sci 2010;11:485-96.
    • (2010) Curr Protein Pept Sci , vol.11 , pp. 485-496
    • Xue, Y.1    Gao, X.2    Cao, J.3
  • 5
    • 80054937592 scopus 로고    scopus 로고
    • Computational prediction of eukaryotic phosphorylation sites
    • Trost B, Kusalik A. Computational prediction of eukaryotic phosphorylation sites. Bioinformatics 2011;27:2927-35.
    • (2011) Bioinformatics , vol.27 , pp. 2927-2935
    • Trost, B.1    Kusalik, A.2
  • 6
    • 76749092270 scopus 로고    scopus 로고
    • The WEKA data mining software: an update
    • Hall M, Frank E, Holmes G, et al. The WEKA data mining software: an update. SIGKDD Explor. Newsl. 2009;11:10-18.
    • (2009) SIGKDD Explor. Newsl. , vol.11 , pp. 10-18
    • Hall, M.1    Frank, E.2    Holmes, G.3
  • 7
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom N, Gammeltoft S, Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. JMol Biol 1999;294:1351-62.
    • (1999) JMol Biol , vol.294 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 8
    • 0842301301 scopus 로고    scopus 로고
    • Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms
    • Berry EA, Dalby AR, Yang ZR. Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. Comput Biol Chem 2004;28:75-85.
    • (2004) Comput Biol Chem , vol.28 , pp. 75-85
    • Berry, E.A.1    Dalby, A.R.2    Yang, Z.R.3
  • 9
    • 2342473198 scopus 로고    scopus 로고
    • The importance of intrinsic disorder for protein phosphorylation
    • Iakoucheva LM, Radivojac P, Brown CJ, et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 2004;32:1037-49.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1037-1049
    • Iakoucheva, L.M.1    Radivojac, P.2    Brown, C.J.3
  • 10
    • 34248576306 scopus 로고    scopus 로고
    • NetPhosYeast:prediction of protein phosphorylation sites in yeast
    • Ingrell CR, Miller ML, Jensen ON, et al. NetPhosYeast:prediction of protein phosphorylation sites in yeast. Bioinformatics 2007;23:895-7.
    • (2007) Bioinformatics , vol.23 , pp. 895-897
    • Ingrell, C.R.1    Miller, M.L.2    Jensen, O.N.3
  • 11
    • 34548770172 scopus 로고    scopus 로고
    • GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network
    • Tang YR, Chen YZ, Canchaya CA, et al. GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network. Protein Eng Des Sel 2007;20:405-12.
    • (2007) Protein Eng Des Sel , vol.20 , pp. 405-412
    • Tang, Y.R.1    Chen, Y.Z.2    Canchaya, C.A.3
  • 12
    • 68249084742 scopus 로고    scopus 로고
    • A new machine learning approach for protein phosphorylation site prediction in plants
    • Gao J, Agrawal G, Thelen J, et al. A new machine learning approach for protein phosphorylation site prediction in plants. LectNotes Comput Sci 2009;5462:18-29.
    • (2009) LectNotes Comput Sci , vol.5462 , pp. 18-29
    • Gao, J.1    Agrawal, G.2    Thelen, J.3
  • 13
    • 77952464216 scopus 로고    scopus 로고
    • Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information
    • Biswas A, Noman N, Sikder A. Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. BMCBioinformatics 2010;11:273.
    • (2010) BMCBioinformatics , vol.11 , pp. 273
    • Biswas, A.1    Noman, N.2    Sikder, A.3
  • 14
    • 79959469922 scopus 로고    scopus 로고
    • PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity
    • Lee TY, Bretana N, Lu CT. PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. BMCBioinformatics 2011; 12:261.
    • (2011) BMCBioinformatics , vol.12 , pp. 261
    • Lee, T.Y.1    Bretana, N.2    Lu, C.T.3
  • 15
    • 78650153738 scopus 로고    scopus 로고
    • Musite, a tool for global prediction of general and kinase-specific phosphorylation sites
    • Gao J, Thelen JJ, Dunker AK, et al. Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics 2010;9:2586-600.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2586-2600
    • Gao, J.1    Thelen, J.J.2    Dunker, A.K.3
  • 16
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    • Gnad F, Ren S, Cox J, 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 , pp. R250
    • Gnad, F.1    Ren, S.2    Cox, J.3
  • 17
    • 52649145895 scopus 로고    scopus 로고
    • GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy
    • Xue Y, Ren J, Gao X, et al. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics 2008;7:1598-608.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 1598-1608
    • Xue, Y.1    Ren, J.2    Gao, X.3
  • 18
    • 55949104581 scopus 로고    scopus 로고
    • Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom
    • Gao X, Jin C, Ren J, et al. Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom. Genomics 2008;92:457-63.
    • (2008) Genomics , vol.92 , pp. 457-463
    • Gao, X.1    Jin, C.2    Ren, J.3
  • 19
    • 57249105125 scopus 로고    scopus 로고
    • Prediction of kinase-specific phosphorylation sites using conditional random fields
    • Dang TH, Van Leemput K, Verschoren A, et al. Prediction of kinase-specific phosphorylation sites using conditional random fields. Bioinformatics 2008;24:2857-64.
    • (2008) Bioinformatics , vol.24 , pp. 2857-2864
    • Dang, T.H.1    Van Leemput, K.2    Verschoren, A.3
  • 20
    • 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 TE, et al. Identification of phosphorylation sites in protein kinase a substrates using artificial neural networks and mass spectrometry. J Proteome Res 2004;3:426-33.
    • (2004) J Proteome Res , vol.3 , pp. 426-433
    • Hjerrild, M.1    Stensballe, A.2    Rasmussen, T.E.3
  • 21
    • 12344288032 scopus 로고    scopus 로고
    • Highly specific prediction of phosphorylation sites in proteins
    • Koenig M, Grabe N. Highly specific prediction of phosphorylation sites in proteins. Bioinformatics 2004;20:3620-7.
    • (2004) Bioinformatics , vol.20 , pp. 3620-3627
    • Koenig, M.1    Grabe, N.2
  • 22
    • 75149118340 scopus 로고    scopus 로고
    • PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship
    • Jung I, Matsuyama A, Yoshida M, et al. PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. BMC Bioinformatics 2010; 11(Suppl 1):S10.
    • (2010) BMC Bioinformatics , vol.11 , pp. S10
    • Jung, I.1    Matsuyama, A.2    Yoshida, M.3
  • 23
    • 56349090571 scopus 로고    scopus 로고
    • Active learning for the prediction of phosphorylation sites. In: Liu, Derong (eds)
    • Piscataway, N.J.: IEEE
    • Jiang J, Ip H. Active learning for the prediction of phosphorylation sites. In: Liu, Derong (eds). International Joint Conference on Neural Networks. Piscataway, N.J.: IEEE, 2008, 3158-65.
    • (2008) International Joint Conference on Neural Networks , pp. 3158-3165
    • Jiang, J.1    Ip, H.2
  • 24
    • 77951560949 scopus 로고    scopus 로고
    • AMS 3.0: prediction of post-translational modifications
    • Basu S, Plewczynski D. AMS 3.0: prediction of post-translational modifications. BMC Bioinformatics 2010; 11:210.
    • (2010) BMC Bioinformatics , vol.11 , pp. 210
    • Basu, S.1    Plewczynski, D.2
  • 25
    • 78649759348 scopus 로고    scopus 로고
    • Identifying human kinase-specific protein phosphorylation sites by integrating heterogeneous information from various sources
    • Li T, Du P, Xu N. Identifying human kinase-specific protein phosphorylation sites by integrating heterogeneous information from various sources. Plos One 2010;5:e15411.
    • (2010) Plos One , vol.5 , pp. e15411
    • Li, T.1    Du, P.2    Xu, N.3
  • 26
    • 8844219516 scopus 로고    scopus 로고
    • Prediction of phosphorylation sites using SVMs
    • Kim JH, Lee J, Oh B, et al. Prediction of phosphorylation sites using SVMs. Bioinformatics 2004;20:3179-84.
    • (2004) Bioinformatics , vol.20 , pp. 3179-3184
    • Kim, J.H.1    Lee, J.2    Oh, B.3
  • 27
    • 23144434356 scopus 로고    scopus 로고
    • KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
    • Huang HD, Lee TY, Tzeng SW, et al. KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 2005; 33(Suppl 2):W226-9.
    • (2005) Nucleic Acids Res , vol.33 , pp. W226-W229
    • Huang, H.D.1    Lee, T.Y.2    Tzeng, S.W.3
  • 28
    • 34547555987 scopus 로고    scopus 로고
    • KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
    • Wong YH, Lee TY, Liang HK, et al. KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res 2007; 35(Suppl 2):W588-94.
    • (2007) Nucleic Acids Res , vol.35 , pp. W588-W594
    • Wong, Y.H.1    Lee, T.Y.2    Liang, H.K.3
  • 29
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • Blom N, Sicheritz-Pontn T, Gupta R, et al. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004;4:1633-49.
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Pontn, T.2    Gupta, R.3
  • 30
    • 37849047943 scopus 로고    scopus 로고
    • Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach
    • Li T, Li F, Zhang X. Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach. Proteins 2008;70:404-14.
    • (2008) Proteins , vol.70 , pp. 404-414
    • Li, T.1    Li, F.2    Zhang, X.3
  • 31
    • 78651320816 scopus 로고    scopus 로고
    • Phospho.ELM: a database of phosphorylation site-supdate 2011
    • Dinkel H, Chica C, Via A, et al. Phospho.ELM: a database of phosphorylation site-supdate 2011. Nucleic Acids Res 2011; 39(Suppl 1):D261-7.
    • (2011) Nucleic Acids Res , vol.39 , pp. D261-D267
    • Dinkel, H.1    Chica, C.2    Via, A.3
  • 32
    • 2942557190 scopus 로고    scopus 로고
    • Annotation of post-translational modifications in the Swiss-Prot knowledge base
    • Farriol-Mathis N, Garavelli JS, Boeckmann B, et al. Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics 2004;4:1537-50.
    • (2004) Proteomics , vol.4 , pp. 1537-1550
    • Farriol-Mathis, N.1    Garavelli, J.S.2    Boeckmann, B.3
  • 33
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schffer, A.A.3
  • 34
    • 70350340056 scopus 로고    scopus 로고
    • Serine/Threonine phosphatases: mechanism through structure
    • Shi Y. Serine/Threonine phosphatases: mechanism through structure. Cell 2009;139:468-84.
    • (2009) Cell , vol.139 , pp. 468-484
    • Shi, Y.1
  • 35
    • 29644438050 scopus 로고    scopus 로고
    • Statistical comparisons of classifiers over multiple data sets
    • Demšar J. Statistical comparisons of classifiers over multiple data sets. JMach Learn Res 2006;7:1-30.
    • (2006) JMach Learn Res , vol.7 , pp. 1-30
    • Demšar, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.