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Volumn 7, Issue SUPPL 5, 2013, Pages

PREAL: Prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection

Author keywords

[No Author keywords available]

Indexed keywords

ALLERGEN; PROTEIN;

EID: 84889677044     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-S5-S9     Document Type: Article
Times cited : (39)

References (50)
  • 2
    • 0033753014 scopus 로고    scopus 로고
    • Signal transduction by the high-affinity immunoglobulin E receptor Fc epsilon RI: coupling form to function
    • Nadler MJ, Matthews SA, Turner H, Kinet JP. Signal transduction by the high-affinity immunoglobulin E receptor Fc epsilon RI: coupling form to function. Adv Immunol 2000, 76:325-355.
    • (2000) Adv Immunol , vol.76 , pp. 325-355
    • Nadler, M.J.1    Matthews, S.A.2    Turner, H.3    Kinet, J.P.4
  • 3
    • 0025778431 scopus 로고
    • The high affinity receptor for IgE on mast cells
    • 10.1111/j.1365-2222.1991.tb01658.x, 1830826
    • Metzger H. The high affinity receptor for IgE on mast cells. Clin Exp Allergy 1991, 21(3):269-279. 10.1111/j.1365-2222.1991.tb01658.x, 1830826.
    • (1991) Clin Exp Allergy , vol.21 , Issue.3 , pp. 269-279
    • Metzger, H.1
  • 5
    • 0033064254 scopus 로고    scopus 로고
    • Food allergy. Part 1: immunopathogenesis and clinical disorders
    • Sampson HA. Food allergy. Part 1: immunopathogenesis and clinical disorders. J Allergy Clin Immunol 1999, 103(5 Pt 1):717-728.
    • (1999) J Allergy Clin Immunol , vol.103 , Issue.5 PART 1 , pp. 717-728
    • Sampson, H.A.1
  • 6
    • 0032813419 scopus 로고    scopus 로고
    • Food allergy. Part 2: diagnosis and management
    • 10.1016/S0091-6749(99)70167-3, 10359874
    • Sampson HA. Food allergy. Part 2: diagnosis and management. J Allergy Clin Immunol 1999, 103(6):981-989. 10.1016/S0091-6749(99)70167-3, 10359874.
    • (1999) J Allergy Clin Immunol , vol.103 , Issue.6 , pp. 981-989
    • Sampson, H.A.1
  • 7
    • 11344294345 scopus 로고    scopus 로고
    • Food allergy: when mucosal immunity goes wrong
    • 10.1016/j.jaci.2004.11.003, 15637560
    • Sampson HA. Food allergy: when mucosal immunity goes wrong. J Allergy Clin Immunol 2005, 115(1):139-141. 10.1016/j.jaci.2004.11.003, 15637560.
    • (2005) J Allergy Clin Immunol , vol.115 , Issue.1 , pp. 139-141
    • Sampson, H.A.1
  • 8
    • 0036171720 scopus 로고    scopus 로고
    • Protein allergenicity assessment of foods produced through agricultural biotechnology
    • 10.1146/annurev.pharmtox.42.082401.130208, 11807166
    • Taylor SL. Protein allergenicity assessment of foods produced through agricultural biotechnology. Annu Rev Pharmacol Toxicol 2002, 42:99-112. 10.1146/annurev.pharmtox.42.082401.130208, 11807166.
    • (2002) Annu Rev Pharmacol Toxicol , vol.42 , pp. 99-112
    • Taylor, S.L.1
  • 9
    • 0034739238 scopus 로고    scopus 로고
    • Oral delivery of salmon calcitonin
    • 10.1016/S0169-409X(00)00063-6, 10963837
    • Lee YH, Sinko PJ. Oral delivery of salmon calcitonin. Adv Drug Deliv Rev 2000, 42(3):225-238. 10.1016/S0169-409X(00)00063-6, 10963837.
    • (2000) Adv Drug Deliv Rev , vol.42 , Issue.3 , pp. 225-238
    • Lee, Y.H.1    Sinko, P.J.2
  • 11
    • 0347208143 scopus 로고    scopus 로고
    • Report of the fourth session of the codex ad hoc intergovernmental task force on foods derived from biotechnology
    • FAO/WHO
    • FAO/WHO Report of the fourth session of the codex ad hoc intergovernmental task force on foods derived from biotechnology. 2003, FAO/WHO.
    • (2003)
  • 13
    • 12744279638 scopus 로고    scopus 로고
    • Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins
    • 10.1093/bioinformatics/bth477, 15319257
    • Bjorklund AK, Soeria-Atmadja D, Zorzet A, Hammerling U, Gustafsson MG. Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins. Bioinformatics 2005, 21(1):39-50. 10.1093/bioinformatics/bth477, 15319257.
    • (2005) Bioinformatics , vol.21 , Issue.1 , pp. 39-50
    • Bjorklund, A.K.1    Soeria-Atmadja, D.2    Zorzet, A.3    Hammerling, U.4    Gustafsson, M.G.5
  • 14
    • 0036260304 scopus 로고    scopus 로고
    • Sequence analysis for assessing potential allergenicity
    • Gendel SM. Sequence analysis for assessing potential allergenicity. Ann N Y Acad Sci 2002, 964:87-98.
    • (2002) Ann N Y Acad Sci , vol.964 , pp. 87-98
    • Gendel, S.M.1
  • 15
    • 25444518424 scopus 로고    scopus 로고
    • Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE - binding linear epitopes of allergens
    • 10.1186/1472-6807-2-8, 139984, 12477382
    • Kleter GA, Peijnenburg AA. Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE - binding linear epitopes of allergens. BMC Struct Biol 2002, 2:8. 10.1186/1472-6807-2-8, 139984, 12477382.
    • (2002) BMC Struct Biol , vol.2 , pp. 8
    • Kleter, G.A.1    Peijnenburg, A.A.2
  • 16
    • 8844259689 scopus 로고    scopus 로고
    • Predicting allergenic proteins using wavelet transform
    • 10.1093/bioinformatics/bth286, 15117757
    • Li KB, Issac P, Krishnan A. Predicting allergenic proteins using wavelet transform. Bioinformatics 2004, 20(16):2572-2578. 10.1093/bioinformatics/bth286, 15117757.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2572-2578
    • Li, K.B.1    Issac, P.2    Krishnan, A.3
  • 17
    • 33144474710 scopus 로고    scopus 로고
    • The value of short amino acid sequence matches for prediction of protein allergenicity
    • Silvanovich A, Nemeth MA, Song P, Herman R, Tagliani L, Bannon GA. The value of short amino acid sequence matches for prediction of protein allergenicity. Toxicol Sci 2006, 90(1):252-258.
    • (2006) Toxicol Sci , vol.90 , Issue.1 , pp. 252-258
    • Silvanovich, A.1    Nemeth, M.A.2    Song, P.3    Herman, R.4    Tagliani, L.5    Bannon, G.A.6
  • 18
    • 0038380463 scopus 로고    scopus 로고
    • Allergenicity prediction by protein sequence
    • Stadler MB, Stadler BM. Allergenicity prediction by protein sequence. FASEB 2003,
    • (2003) FASEB
    • Stadler, M.B.1    Stadler, B.M.2
  • 19
    • 0033836431 scopus 로고    scopus 로고
    • Structural biology of allergens
    • 10.1067/mai.2000.108434, 10932064
    • Aalberse RC. Structural biology of allergens. J Allergy Clin Immunol 2000, 106(2):228-238. 10.1067/mai.2000.108434, 10932064.
    • (2000) J Allergy Clin Immunol , vol.106 , Issue.2 , pp. 228-238
    • Aalberse, R.C.1
  • 20
    • 33747871140 scopus 로고    scopus 로고
    • AlgPred: prediction of allergenic proteins and mapping of IgE epitopes
    • 10.1093/nar/gkl343, 1538830, 16844994, Web Server
    • Saha S, Raghava GPS. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Research 2006, 34(Web Server):W202-W209. 10.1093/nar/gkl343, 1538830, 16844994.
    • (2006) Nucleic Acids Research , vol.34
    • Saha, S.1    Raghava, G.P.S.2
  • 21
    • 67649219008 scopus 로고    scopus 로고
    • AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins
    • 10.1371/journal.pone.0005861, 2689655, 19516900
    • Muh HC, Tong JC, Tammi MT. AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins. PLoS One 2009, 4(6):e5861. 10.1371/journal.pone.0005861, 2689655, 19516900.
    • (2009) PLoS One , vol.4 , Issue.6
    • Muh, H.C.1    Tong, J.C.2    Tammi, M.T.3
  • 23
    • 33748199236 scopus 로고    scopus 로고
    • Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties
    • 10.1016/j.molimm.2006.02.010, 16563508
    • Cui J, Han LY, Li H, Ung CY, Tang ZQ, Zheng CJ, Cao ZW, Chen YZ. Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Molecular Immunology 2007, 44(4):514-520. 10.1016/j.molimm.2006.02.010, 16563508.
    • (2007) Molecular Immunology , vol.44 , Issue.4 , pp. 514-520
    • Cui, J.1    Han, L.Y.2    Li, H.3    Ung, C.Y.4    Tang, Z.Q.5    Zheng, C.J.6    Cao, Z.W.7    Chen, Y.Z.8
  • 24
    • 33748672467 scopus 로고    scopus 로고
    • Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning
    • 10.1093/nar/gkl467, 1540723, 16977698
    • Soeria-Atmadja D. Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning. Nucleic Acids Research 2006, 34(13):3779-3793. 10.1093/nar/gkl467, 1540723, 16977698.
    • (2006) Nucleic Acids Research , vol.34 , Issue.13 , pp. 3779-3793
    • Soeria-Atmadja, D.1
  • 25
    • 59249105533 scopus 로고    scopus 로고
    • The property distance index PD predicts peptides that cross-react with IgE antibodies
    • 10.1016/j.molimm.2008.09.004, 2651743, 18950868
    • Ivanciuc O, Midoro-Horiuti T, Schein CH, Xie L, Hillman GR, Goldblum RM, Braun W. The property distance index PD predicts peptides that cross-react with IgE antibodies. Mol Immunol 2009, 46(5):873-883. 10.1016/j.molimm.2008.09.004, 2651743, 18950868.
    • (2009) Mol Immunol , vol.46 , Issue.5 , pp. 873-883
    • Ivanciuc, O.1    Midoro-Horiuti, T.2    Schein, C.H.3    Xie, L.4    Hillman, G.R.5    Goldblum, R.M.6    Braun, W.7
  • 26
    • 33846586517 scopus 로고    scopus 로고
    • Structural Database of Allergenic Proteins (SDAP)
    • Edited by SJ M. Washington D.C: ASM Press
    • Schein CH, Ivanciuc O, Braun W. Structural Database of Allergenic Proteins (SDAP). Food Allergy 2006, 257-283. Edited by SJ M. Washington D.C: ASM Press.
    • (2006) Food Allergy , pp. 257-283
    • Schein, C.H.1    Ivanciuc, O.2    Braun, W.3
  • 27
    • 84865097794 scopus 로고    scopus 로고
    • SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides
    • 10.1093/bioinformatics/bts326, 22692221
    • Zhang L, Huang Y, Zou Z, He Y, Chen X, Tao A. SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides. Bioinformatics 2012, 28(16):2178-2179. 10.1093/bioinformatics/bts326, 22692221.
    • (2012) Bioinformatics , vol.28 , Issue.16 , pp. 2178-2179
    • Zhang, L.1    Huang, Y.2    Zou, Z.3    He, Y.4    Chen, X.5    Tao, A.6
  • 28
    • 84879520811 scopus 로고    scopus 로고
    • Evaluation and integration of existing methods for computational prediction of allergens
    • Wang J, Yu Y, Zhao Y, Zhang D, Li J. Evaluation and integration of existing methods for computational prediction of allergens. BMC Bioinformatics 2013, (14 Suppl 4):S1.
    • (2013) BMC Bioinformatics , Issue.14 SUPPL. 4
    • Wang, J.1    Yu, Y.2    Zhao, Y.3    Zhang, D.4    Li, J.5
  • 29
    • 33644504193 scopus 로고    scopus 로고
    • [Development of Allergen Database for Food Safety (ADFS): an integrated database to search allergens and predict allergenicity]
    • Nakamura R, Teshima R, Takagi K, Sawada J. [Development of Allergen Database for Food Safety (ADFS): an integrated database to search allergens and predict allergenicity]. Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku 2005, (123):32-36.
    • (2005) Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku , Issue.123 , pp. 32-36
    • Nakamura, R.1    Teshima, R.2    Takagi, K.3    Sawada, J.4
  • 30
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 31
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • 10.1002/prot.10082, 11933069
    • Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002, 47(2):228-235. 10.1002/prot.10082, 11933069.
    • (2002) Proteins , vol.47 , Issue.2 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 32
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • 10.1002/prot.10069, 11933061
    • Pollastri G, Baldi P, Fariselli P, Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins 2002, 47(2):142-153. 10.1002/prot.10069, 11933061.
    • (2002) Proteins , vol.47 , Issue.2 , pp. 142-153
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 34
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy
    • Peng H, Long F, Ding C. Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 2005, 27(8):1226-1238.
    • (2005) IEEE Trans Pattern Anal Mach Intell , vol.27 , Issue.8 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 35
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • 10.1093/nar/25.24.4876, 147148, 9396791
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25(24):4876-4882. 10.1093/nar/25.24.4876, 147148, 9396791.
    • (1997) Nucleic Acids Res , vol.25 , Issue.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 36
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • 10.1093/nar/gkh340, 390337, 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 37
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • 10.1093/molbev/msr121, 3203626, 21546353
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
    • (2011) Mol Biol Evol , vol.28 , Issue.10 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 38
    • 0025120203 scopus 로고
    • Members of the alpha-amylase inhibitors family from wheat endosperm are major allergens associated with baker's asthma
    • 10.1016/0014-5793(90)80642-V, 2307238
    • Gomez L, Martin E, Hernandez D, Sanchez-Monge R, Barber D, del Pozo V, de Andres B, Armentia A, Lahoz C, Salcedo G, et al. Members of the alpha-amylase inhibitors family from wheat endosperm are major allergens associated with baker's asthma. FEBS Lett 1990, 261(1):85-88. 10.1016/0014-5793(90)80642-V, 2307238.
    • (1990) FEBS Lett , vol.261 , Issue.1 , pp. 85-88
    • Gomez, L.1    Martin, E.2    Hernandez, D.3    Sanchez-Monge, R.4    Barber, D.5    del Pozo, V.6    de Andres, B.7    Armentia, A.8    Lahoz, C.9    Salcedo, G.10
  • 41
    • 0036864268 scopus 로고    scopus 로고
    • Pathogenesis-related (PR)-proteins identified as allergens
    • Hoffmann-Sommergruber K. Pathogenesis-related (PR)-proteins identified as allergens. Biochem Soc Trans 2002, 30(Pt 6):930-935.
    • (2002) Biochem Soc Trans , vol.30 , Issue.PART 6 , pp. 930-935
    • Hoffmann-Sommergruber, K.1
  • 42
    • 2342578126 scopus 로고    scopus 로고
    • Thaumatin-like proteins -- a new family of pollen and fruit allergens
    • 10.1046/j.1398-9995.2003.00421.x, 15080826
    • Breiteneder H. Thaumatin-like proteins -- a new family of pollen and fruit allergens. Allergy 2004, 59(5):479-481. 10.1046/j.1398-9995.2003.00421.x, 15080826.
    • (2004) Allergy , vol.59 , Issue.5 , pp. 479-481
    • Breiteneder, H.1
  • 43
    • 77955199287 scopus 로고    scopus 로고
    • Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
    • 10.1371/journal.pone.0010972, 2881046, 20532046
    • Huang T, Shi XH, Wang P, He Z, Feng KY, Hu L, Kong X, Li YX, Cai YD, Chou KC. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 2010, 5(6):e10972. 10.1371/journal.pone.0010972, 2881046, 20532046.
    • (2010) PLoS One , vol.5 , Issue.6
    • Huang, T.1    Shi, X.H.2    Wang, P.3    He, Z.4    Feng, K.Y.5    Hu, L.6    Kong, X.7    Li, Y.X.8    Cai, Y.D.9    Chou, K.C.10
  • 44
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • 10.1146/annurev.bi.59.070190.005043, 2197975
    • Chothia C, Finkelstein AV. The classification and origins of protein folding patterns. Annu Rev Biochem 1990, 59:1007-1039. 10.1146/annurev.bi.59.070190.005043, 2197975.
    • (1990) Annu Rev Biochem , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.V.2
  • 45
    • 0023731964 scopus 로고
    • Amino acid side chain parameters for correlation studies in biology and pharmacology
    • Fauchere JL, Charton M, Kier LB, Verloop A, Pliska V. Amino acid side chain parameters for correlation studies in biology and pharmacology. Int J Pept Protein Res 1988, 32(4):269-278.
    • (1988) Int J Pept Protein Res , vol.32 , Issue.4 , pp. 269-278
    • Fauchere, J.L.1    Charton, M.2    Kier, L.B.3    Verloop, A.4    Pliska, V.5
  • 46
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • 10.1126/science.185.4154.862, 4843792
    • Grantham R. Amino acid difference formula to help explain protein evolution. Science 1974, 185(4154):862-864. 10.1126/science.185.4154.862, 4843792.
    • (1974) Science , vol.185 , Issue.4154 , pp. 862-864
    • Grantham, R.1
  • 47
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • 10.1016/j.ab.2007.07.006, 17698024
    • Chou KC, Shen HB. Recent progress in protein subcellular location prediction. Anal Biochem 2007, 370(1):1-16. 10.1016/j.ab.2007.07.006, 17698024.
    • (2007) Anal Biochem , vol.370 , Issue.1 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 48
    • 39449105071 scopus 로고    scopus 로고
    • Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
    • 10.1038/nprot.2007.494, 18274516
    • Chou KC, Shen HB. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc 2008, 3(2):153-162. 10.1038/nprot.2007.494, 18274516.
    • (2008) Nat Protoc , vol.3 , Issue.2 , pp. 153-162
    • Chou, K.C.1    Shen, H.B.2
  • 49
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • 2808944, 19843607, Database
    • The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010, 38(Database):D142-148. 2808944, 19843607.
    • (2010) Nucleic Acids Res , vol.38
  • 50
    • 70149113077 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • Vienna, Austria: R Foundation for Statistical Computing, Team RDC
    • Team RDC R: A language and environment for statistical computing. 2009, Vienna, Austria: R Foundation for Statistical Computing, Team RDC.
    • (2009)


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