메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

PKIS: Computational identification of protein kinases for experimentally discovered protein phosphorylation sites

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS TOOLS; COMPUTATIONAL IDENTIFICATION; PHOSPHORYLATED PROTEINS; PHOSPHORYLATION SITES; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION NETWORKS; SIGNAL TRANSDUCTION PATHWAYS; SUPPORT VECTOR MACHINE (SVMS);

EID: 84881277095     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-247     Document Type: Article
Times cited : (45)

References (34)
  • 1
    • 79958034385 scopus 로고    scopus 로고
    • Protein phosphorylation and prevention of cytochrome oxidase inhibition by ATP: coupled mechanisms of energy metabolism regulation
    • 10.1016/j.cmet.2011.03.024, 3118639, 21641552
    • Acin-Perez R, Gatti DL, Bai Y, Manfredi G. Protein phosphorylation and prevention of cytochrome oxidase inhibition by ATP: coupled mechanisms of energy metabolism regulation. Cell Metab 2011, 13(6):712-719. 10.1016/j.cmet.2011.03.024, 3118639, 21641552.
    • (2011) Cell Metab , vol.13 , Issue.6 , pp. 712-719
    • Acin-Perez, R.1    Gatti, D.L.2    Bai, Y.3    Manfredi, G.4
  • 2
    • 70249090092 scopus 로고    scopus 로고
    • Nuclear localization of p38 MAPK in response to DNA damage
    • 2702826, 19564926
    • Wood CD, Thornton TM, Sabio G, Davis RA, Rincon M. Nuclear localization of p38 MAPK in response to DNA damage. Int J Biol Sci 2009, 5(5):428-437. 2702826, 19564926.
    • (2009) Int J Biol Sci , vol.5 , Issue.5 , pp. 428-437
    • Wood, C.D.1    Thornton, T.M.2    Sabio, G.3    Davis, R.A.4    Rincon, M.5
  • 3
    • 77953040994 scopus 로고    scopus 로고
    • The role of YAP transcription coactivator in regulating stem cell self-renewal and differentiation
    • 10.1101/gad.1903310, 2878649, 20516196
    • Lian I, Kim J, Okazawa H, Zhao J, Zhao B, Yu J, Chinnaiyan A, Israel MA, Goldstein LS, Abujarour R, et al. The role of YAP transcription coactivator in regulating stem cell self-renewal and differentiation. Genes Dev 2010, 24(11):1106-1118. 10.1101/gad.1903310, 2878649, 20516196.
    • (2010) Genes Dev , vol.24 , Issue.11 , pp. 1106-1118
    • Lian, I.1    Kim, J.2    Okazawa, H.3    Zhao, J.4    Zhao, B.5    Yu, J.6    Chinnaiyan, A.7    Israel, M.A.8    Goldstein, L.S.9    Abujarour, R.10
  • 4
    • 0036605185 scopus 로고    scopus 로고
    • Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome
    • 10.1016/S0167-7799(02)01944-3, 12007495
    • Mann M, Ong SE, Gronborg M, Steen H, Jensen ON, Pandey A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 2002, 20(6):261-268. 10.1016/S0167-7799(02)01944-3, 12007495.
    • (2002) Trends Biotechnol , vol.20 , Issue.6 , pp. 261-268
    • Mann, M.1    Ong, S.E.2    Gronborg, M.3    Steen, H.4    Jensen, O.N.5    Pandey, A.6
  • 5
    • 68849084400 scopus 로고    scopus 로고
    • Signal transduction cross talk mediated by Jun N-terminal kinase-interacting protein and insulin receptor substrate scaffold protein complexes
    • 10.1128/MCB.00155-09, 2725725, 19564410
    • Standen CL, Kennedy NJ, Flavell RA, Davis RJ. Signal transduction cross talk mediated by Jun N-terminal kinase-interacting protein and insulin receptor substrate scaffold protein complexes. Mol Cell Biol 2009, 29(17):4831-4840. 10.1128/MCB.00155-09, 2725725, 19564410.
    • (2009) Mol Cell Biol , vol.29 , Issue.17 , pp. 4831-4840
    • Standen, C.L.1    Kennedy, N.J.2    Flavell, R.A.3    Davis, R.J.4
  • 6
    • 78649723147 scopus 로고    scopus 로고
    • Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling
    • 10.1371/journal.pone.0013926, 2978091, 21085658
    • Tasaki S, Nagasaki M, Kozuka-Hata H, Semba K, Gotoh N, Hattori S, Inoue J, Yamamoto T, Miyano S, Sugano S, et al. Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS One 2010, 5(11):e13926. 10.1371/journal.pone.0013926, 2978091, 21085658.
    • (2010) PLoS One , vol.5 , Issue.11
    • Tasaki, S.1    Nagasaki, M.2    Kozuka-Hata, H.3    Semba, K.4    Gotoh, N.5    Hattori, S.6    Inoue, J.7    Yamamoto, T.8    Miyano, S.9    Sugano, S.10
  • 7
    • 77953252823 scopus 로고    scopus 로고
    • Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates
    • Sobolev B, Filimonov D, Lagunin A, Zakharov A, Koborova O, Kel A, Poroikov V. Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. BMC Bioinforma 2010, 11:313.
    • (2010) BMC Bioinforma , vol.11 , pp. 313
    • Sobolev, B.1    Filimonov, D.2    Lagunin, A.3    Zakharov, A.4    Koborova, O.5    Kel, A.6    Poroikov, V.7
  • 8
    • 80054937592 scopus 로고    scopus 로고
    • Computational prediction of eukaryotic phosphorylation sites
    • 10.1093/bioinformatics/btr525, 21926126
    • Trost B, Kusalik A. Computational prediction of eukaryotic phosphorylation sites. Bioinformatics 2011, 27(21):2927-2935. 10.1093/bioinformatics/btr525, 21926126.
    • (2011) Bioinformatics , vol.27 , Issue.21 , pp. 2927-2935
    • Trost, B.1    Kusalik, A.2
  • 10
    • 0028540405 scopus 로고
    • Use of an oriented peptide library to determine the optimal substrates of protein kinases
    • 10.1016/S0960-9822(00)00221-9, 7874496
    • Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica-Worms H, Cantley LC. Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 1994, 4(11):973-982. 10.1016/S0960-9822(00)00221-9, 7874496.
    • (1994) Curr Biol , vol.4 , Issue.11 , pp. 973-982
    • Songyang, Z.1    Blechner, S.2    Hoagland, N.3    Hoekstra, M.F.4    Piwnica-Worms, H.5    Cantley, L.C.6
  • 11
    • 77954565509 scopus 로고    scopus 로고
    • Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology
    • 10.1021/pr1002214, 20415495
    • Wisniewski JR, Nagaraj N, Zougman A, Gnad F, Mann M. Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology. J Proteome Res 2010, 9(6):3280-3289. 10.1021/pr1002214, 20415495.
    • (2010) J Proteome Res , vol.9 , Issue.6 , pp. 3280-3289
    • Wisniewski, J.R.1    Nagaraj, N.2    Zougman, A.3    Gnad, F.4    Mann, M.5
  • 14
    • 33645758540 scopus 로고    scopus 로고
    • PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory
    • Xue Y, Li A, Wang L, Feng H, Yao X. PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinforma 2006, 7:163.
    • (2006) BMC Bioinforma , vol.7 , pp. 163
    • Xue, Y.1    Li, A.2    Wang, L.3    Feng, H.4    Yao, X.5
  • 15
    • 34547555987 scopus 로고    scopus 로고
    • KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
    • 1933228, 17517770
    • Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, Yang YH, Chu CH, Huang HD, Ko MT, Hwang JK. KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res 2007, 35(Web Server issue):W588-W594. 1933228, 17517770.
    • (2007) Nucleic Acids Res , vol.35 , Issue.WEB SERVER ISSUE
    • Wong, Y.H.1    Lee, T.Y.2    Liang, H.K.3    Huang, C.M.4    Wang, T.Y.5    Yang, Y.H.6    Chu, C.H.7    Huang, H.D.8    Ko, M.T.9    Hwang, J.K.10
  • 16
    • 78650153738 scopus 로고    scopus 로고
    • Musite, a tool for global prediction of general and kinase-specific phosphorylation sites
    • 10.1074/mcp.M110.001388, 3101956, 20702892
    • Gao J, Thelen JJ, Dunker AK, Xu D. Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics 2010, 9(12):2586-2600. 10.1074/mcp.M110.001388, 3101956, 20702892.
    • (2010) Mol Cell Proteomics , vol.9 , Issue.12 , pp. 2586-2600
    • Gao, J.1    Thelen, J.J.2    Dunker, A.K.3    Xu, D.4
  • 17
    • 79951859645 scopus 로고    scopus 로고
    • GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection
    • 10.1093/protein/gzq094, 21062758
    • Xue Y, Liu Z, Cao J, Ma Q, Gao X, Wang Q, Jin C, Zhou Y, Wen L, Ren J. GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel 2011, 24(3):255-260. 10.1093/protein/gzq094, 21062758.
    • (2011) Protein Eng Des Sel , vol.24 , Issue.3 , pp. 255-260
    • Xue, Y.1    Liu, Z.2    Cao, J.3    Ma, Q.4    Gao, X.5    Wang, Q.6    Jin, C.7    Zhou, Y.8    Wen, L.9    Ren, J.10
  • 18
    • 79953768199 scopus 로고    scopus 로고
    • Support vector machine-based mucin-type o-linked glycosylation site prediction using enhanced sequence feature encoding
    • 2815398, 20351933
    • Torii M, Liu H, Hu ZZ. Support vector machine-based mucin-type o-linked glycosylation site prediction using enhanced sequence feature encoding. AMIA Annu Symp Proc 2009, 2009:640-644. 2815398, 20351933.
    • (2009) AMIA Annu Symp Proc , vol.2009 , pp. 640-644
    • Torii, M.1    Liu, H.2    Hu, Z.Z.3
  • 19
    • 38049063206 scopus 로고    scopus 로고
    • Prediction of PK-specific phosphorylation site based on information entropy
    • 10.1007/s11427-008-0012-1, 18176786
    • Wang M, Li C, Chen W, Wang C. Prediction of PK-specific phosphorylation site based on information entropy. Sci China C Life Sci 2008, 51(1):12-20. 10.1007/s11427-008-0012-1, 18176786.
    • (2008) Sci China C Life Sci , vol.51 , Issue.1 , pp. 12-20
    • Wang, M.1    Li, C.2    Chen, W.3    Wang, C.4
  • 20
    • 51849134550 scopus 로고    scopus 로고
    • Neurofilament tail phosphorylation: identity of the RT-97 phosphoepitope and regulation in neurons by cross-talk among proline-directed kinases
    • 2941900, 18715269
    • Veeranna, Lee JH, Pareek TK, Jaffee H, Boland B, Vinod KY, Amin N, Kulkarni AB, Pant HC, Nixon RA. Neurofilament tail phosphorylation: identity of the RT-97 phosphoepitope and regulation in neurons by cross-talk among proline-directed kinases. J Neurochem 2008, 107(1):35-49. 2941900, 18715269.
    • (2008) J Neurochem , vol.107 , Issue.1 , pp. 35-49
    • Veeranna1    Lee, J.H.2    Pareek, T.K.3    Jaffee, H.4    Boland, B.5    Vinod, K.Y.6    Amin, N.7    Kulkarni, A.B.8    Pant, H.C.9    Nixon, R.A.10
  • 21
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • 10.1126/science.1075762, 12471243
    • Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002, 298(5600):1912-1934. 10.1126/science.1075762, 12471243.
    • (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
  • 23
    • 0032055484 scopus 로고    scopus 로고
    • Phosphatidylinositol-3,4,5-trisphosphate (PtdIns-3,4,5-P3)/Tec kinase-dependent calcium signaling pathway: a target for SHIP-mediated inhibitory signals
    • 10.1093/emboj/17.7.1961, 1170542, 9524119
    • Scharenberg AM, El-Hillal O, Fruman DA, Beitz LO, Li Z, Lin S, Gout I, Cantley LC, Rawlings DJ, Kinet JP. Phosphatidylinositol-3,4,5-trisphosphate (PtdIns-3,4,5-P3)/Tec kinase-dependent calcium signaling pathway: a target for SHIP-mediated inhibitory signals. EMBO J 1998, 17(7):1961-1972. 10.1093/emboj/17.7.1961, 1170542, 9524119.
    • (1998) EMBO J , vol.17 , Issue.7 , pp. 1961-1972
    • Scharenberg, A.M.1    El-Hillal, O.2    Fruman, D.A.3    Beitz, L.O.4    Li, Z.5    Lin, S.6    Gout, I.7    Cantley, L.C.8    Rawlings, D.J.9    Kinet, J.P.10
  • 24
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for Annotation, Visualization, and Integrated Discovery
    • 10.1186/gb-2003-4-5-p3, 3720094, 12734009
    • Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 3720094, 12734009.
    • (2003) Genome Biol , vol.4 , Issue.5
    • Dennis, G.1    Sherman, B.T.2    Hosack, D.A.3    Yang, J.4    Gao, W.5    Lane, H.C.6    Lempicki, R.A.7
  • 25
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 26
    • 0035496603 scopus 로고    scopus 로고
    • Natural killer cells, viruses and cancer
    • 10.1038/35095564, 11905813
    • Cerwenka A, Lanier LL. Natural killer cells, viruses and cancer. Nat Rev Immunol 2001, 1(1):41-49. 10.1038/35095564, 11905813.
    • (2001) Nat Rev Immunol , vol.1 , Issue.1 , pp. 41-49
    • Cerwenka, A.1    Lanier, L.L.2
  • 27
    • 0037470034 scopus 로고    scopus 로고
    • The chaperone protein 14-3-3 interacts with 3BP2/SH3BP2 and regulates its adapter function
    • 10.1074/jbc.M209509200, 12501243
    • Foucault I, Liu YC, Bernard A, Deckert M. The chaperone protein 14-3-3 interacts with 3BP2/SH3BP2 and regulates its adapter function. J Biol Chem 2003, 278(9):7146-7153. 10.1074/jbc.M209509200, 12501243.
    • (2003) J Biol Chem , vol.278 , Issue.9 , pp. 7146-7153
    • Foucault, I.1    Liu, Y.C.2    Bernard, A.3    Deckert, M.4
  • 28
    • 12844271053 scopus 로고    scopus 로고
    • The adaptor protein 3BP2 associates with VAV guanine nucleotide exchange factors to regulate NFAT activation by the B-cell antigen receptor
    • Foucault I, Le Bras S, Charvet C, Moon C, Altman A, Deckert M. The adaptor protein 3BP2 associates with VAV guanine nucleotide exchange factors to regulate NFAT activation by the B-cell antigen receptor. Blood 2005, 105(3):1106-1113.
    • (2005) Blood , vol.105 , Issue.3 , pp. 1106-1113
    • Foucault, I.1    Le Bras, S.2    Charvet, C.3    Moon, C.4    Altman, A.5    Deckert, M.6
  • 29
    • 79960380134 scopus 로고    scopus 로고
    • Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav
    • 10.1128/MCB.05043-11, 3133406, 21606197
    • Chen CH, Martin VA, Gorenstein NM, Geahlen RL, Post CB. Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav. Mol Cell Biol 2011, 31(14):2984-2996. 10.1128/MCB.05043-11, 3133406, 21606197.
    • (2011) Mol Cell Biol , vol.31 , Issue.14 , pp. 2984-2996
    • Chen, C.H.1    Martin, V.A.2    Gorenstein, N.M.3    Geahlen, R.L.4    Post, C.B.5
  • 30
    • 0029867911 scopus 로고    scopus 로고
    • Syk, activated by cross-linking the B-cell antigen receptor, localizes to the cytosol where it interacts with and phosphorylates alpha-tubulin on tyrosine
    • 10.1074/jbc.271.9.4755, 8617742
    • Peters JD, Furlong MT, Asai DJ, Harrison ML, Geahlen RL. Syk, activated by cross-linking the B-cell antigen receptor, localizes to the cytosol where it interacts with and phosphorylates alpha-tubulin on tyrosine. J Biol Chem 1996, 271(9):4755-4762. 10.1074/jbc.271.9.4755, 8617742.
    • (1996) J Biol Chem , vol.271 , Issue.9 , pp. 4755-4762
    • Peters, J.D.1    Furlong, M.T.2    Asai, D.J.3    Harrison, M.L.4    Geahlen, R.L.5
  • 31
    • 70350356241 scopus 로고    scopus 로고
    • Autoinhibition and adapter function of Syk
    • 10.1111/j.1600-065X.2009.00837.x, 19909371
    • Kulathu Y, Grothe G, Reth M. Autoinhibition and adapter function of Syk. Immunol Rev 2009, 232(1):286-299. 10.1111/j.1600-065X.2009.00837.x, 19909371.
    • (2009) Immunol Rev , vol.232 , Issue.1 , pp. 286-299
    • Kulathu, Y.1    Grothe, G.2    Reth, M.3
  • 33
    • 84883188502 scopus 로고    scopus 로고
    • Data construction for phosphorylation site prediction
    • Gong H, Liu X, Wu J, He Z. Data construction for phosphorylation site prediction. Brief Bioinform 2013,
    • (2013) Brief Bioinform
    • Gong, H.1    Liu, X.2    Wu, J.3    He, Z.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.