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Volumn 6, Issue 3, 2011, Pages

Predicting protein phenotypes based on protein-protein interaction network

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 79952509639     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017668     Document Type: Article
Times cited : (46)

References (55)
  • 1
    • 69949166547 scopus 로고    scopus 로고
    • A comparison of HIV-1 drug susceptibility as provided by conventional phenotyping and by a phenotype prediction tool based on viral genotype
    • Van Houtte M, Picchio G, Van Der Borght K, Pattery T, Lecocq P, et al. (2009) A comparison of HIV-1 drug susceptibility as provided by conventional phenotyping and by a phenotype prediction tool based on viral genotype. Journal of medical virology 81: 1702-1709.
    • (2009) Journal of Medical Virology , vol.81 , pp. 1702-1709
    • van Houtte, M.1    Picchio, G.2    van der Borght, K.3    Pattery, T.4    Lecocq, P.5
  • 2
    • 67949115746 scopus 로고    scopus 로고
    • [Prediction of phenotype R5/X4 of HIV-1 variants circulating in Russia, by using computer methods]
    • Vasil'ev AV, Kazennova EV, Bobkova MR, (2009) [Prediction of phenotype R5/X4 of HIV-1 variants circulating in Russia, by using computer methods]. Voprosy virusologii 54: 17-21.
    • (2009) Voprosy Virusologii , vol.54 , pp. 17-21
    • Vasil'ev, A.V.1    Kazennova, E.V.2    Bobkova, M.R.3
  • 3
    • 35648983524 scopus 로고    scopus 로고
    • Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest
    • Xu S, Huang X, Xu H, Zhang C, (2007) Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest. Journal of microbiology 45: 441-446.
    • (2007) Journal of Microbiology , vol.45 , pp. 441-446
    • Xu, S.1    Huang, X.2    Xu, H.3    Zhang, C.4
  • 4
    • 34547841291 scopus 로고    scopus 로고
    • Prediction of HIV-1 drug susceptibility phenotype from the viral genotype using linear regression modeling
    • Vermeiren H, Van Craenenbroeck E, Alen P, Bacheler L, Picchio G, et al. (2007) Prediction of HIV-1 drug susceptibility phenotype from the viral genotype using linear regression modeling. Journal of virological methods 145: 47-55.
    • (2007) Journal of Virological Methods , vol.145 , pp. 47-55
    • Vermeiren, H.1    Van Craenenbroeck, E.2    Alen, P.3    Bacheler, L.4    Picchio, G.5
  • 5
    • 0036189326 scopus 로고    scopus 로고
    • Characterizing the relationship between HIV-1 genotype and phenotype: prediction-based classification
    • Foulkes AS, De GV, (2002) Characterizing the relationship between HIV-1 genotype and phenotype: prediction-based classification. Biometrics 58: 145-156.
    • (2002) Biometrics , vol.58 , pp. 145-156
    • Foulkes, A.S.1    De, G.V.2
  • 6
    • 77955923224 scopus 로고    scopus 로고
    • Proteomics of the Radioresistant Phenotype in Head-and-Neck Cancer: Gp96 as a Novel Prediction Marker and Sensitizing Target for Radiotherapy
    • Lin TY, Chang JT, Wang HM, Chan SH, Chiu CC, et al. (2010) Proteomics of the Radioresistant Phenotype in Head-and-Neck Cancer: Gp96 as a Novel Prediction Marker and Sensitizing Target for Radiotherapy. International journal of radiation oncology, biology, physics 78: 246-256.
    • (2010) International Journal of Radiation Oncology, Biology, Physics , vol.78 , pp. 246-256
    • Lin, T.Y.1    Chang, J.T.2    Wang, H.M.3    Chan, S.H.4    Chiu, C.C.5
  • 7
    • 34447639457 scopus 로고    scopus 로고
    • MR-determined metabolic phenotype of breast cancer in prediction of lymphatic spread, grade, and hormone status
    • Bathen TF, Jensen LR, Sitter B, Fjosne HE, Halgunset J, et al. (2007) MR-determined metabolic phenotype of breast cancer in prediction of lymphatic spread, grade, and hormone status. Breast cancer research and treatment 104: 181-189.
    • (2007) Breast Cancer Research and Treatment , vol.104 , pp. 181-189
    • Bathen, T.F.1    Jensen, L.R.2    Sitter, B.3    Fjosne, H.E.4    Halgunset, J.5
  • 9
    • 2342583510 scopus 로고    scopus 로고
    • Does the addition of information on genotype improve prediction of the risk of melanoma and nonmelanoma skin cancer beyond that obtained from skin phenotype?
    • Dwyer T, Stankovich JM, Blizzard L, FitzGerald LM, Dickinson JL, et al. (2004) Does the addition of information on genotype improve prediction of the risk of melanoma and nonmelanoma skin cancer beyond that obtained from skin phenotype? American journal of epidemiology 159: 826-833.
    • (2004) American Journal of Epidemiology , vol.159 , pp. 826-833
    • Dwyer, T.1    Stankovich, J.M.2    Blizzard, L.3    FitzGerald, L.M.4    Dickinson, J.L.5
  • 11
    • 18544382242 scopus 로고    scopus 로고
    • Correlation among genotype, phenotype, and biochemical markers in Gaucher disease: implications for the prediction of disease severity
    • Whitfield PD, Nelson P, Sharp PC, Bindloss CA, Dean C, et al. (2002) Correlation among genotype, phenotype, and biochemical markers in Gaucher disease: implications for the prediction of disease severity. Molecular genetics and metabolism 75: 46-55.
    • (2002) Molecular Genetics and Metabolism , vol.75 , pp. 46-55
    • Whitfield, P.D.1    Nelson, P.2    Sharp, P.C.3    Bindloss, C.A.4    Dean, C.5
  • 14
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5
  • 15
    • 0034566789 scopus 로고    scopus 로고
    • Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization
    • discussion 109-111
    • Winzeler EA, Liang H, Shoemaker DD, Davis RW, (2000) Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization. Novartis Foundation symposium 229: 105-109; discussion 109-111.
    • (2000) Novartis Foundation Symposium , vol.229 , pp. 105-109
    • Winzeler, E.A.1    Liang, H.2    Shoemaker, D.D.3    Davis, R.W.4
  • 17
    • 4344592252 scopus 로고    scopus 로고
    • The uses of genome-wide yeast mutant collections
    • Scherens B, Goffeau A, (2004) The uses of genome-wide yeast mutant collections. Genome biology 5: 229.
    • (2004) Genome Biology , vol.5 , pp. 229
    • Scherens, B.1    Goffeau, A.2
  • 18
    • 40449107017 scopus 로고    scopus 로고
    • Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes
    • McGary KL, Lee I, Marcotte EM, (2007) Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome biology 8: R258.
    • (2007) Genome Biology , vol.8
    • McGary, K.L.1    Lee, I.2    Marcotte, E.M.3
  • 19
  • 20
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo-amino acid composition
    • Chou KC, (2001) Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 43: 246-255.
    • (2001) Proteins , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 21
    • 0035884899 scopus 로고    scopus 로고
    • Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks
    • Resch W, Hoffman N, Swanstrom R, (2001) Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 288: 51-62.
    • (2001) Virology , vol.288 , pp. 51-62
    • Resch, W.1    Hoffman, N.2    Swanstrom, R.3
  • 25
    • 0026588787 scopus 로고
    • Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS
    • Gimeno CJ, Ljungdahl PO, Styles CA, Fink GR, (1992) Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68: 1077-1090.
    • (1992) Cell , vol.68 , pp. 1077-1090
    • Gimeno, C.J.1    Ljungdahl, P.O.2    Styles, C.A.3    Fink, G.R.4
  • 28
    • 58149193234 scopus 로고    scopus 로고
    • STRING 8-a global view on proteins and their functional interactions in 630 organisms
    • Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic acids research 37: D412-416.
    • (2009) Nucleic Acids Research , vol.37
    • Jensen, L.J.1    Kuhn, M.2    Stark, M.3    Chaffron, S.4    Creevey, C.5
  • 31
    • 39449105071 scopus 로고    scopus 로고
    • Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
    • Chou KC, Shen HB, (2008) Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nature protocols 3: 153-162.
    • (2008) Nature Protocols , vol.3 , pp. 153-162
    • Chou, K.C.1    Shen, H.B.2
  • 32
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou KC, Shen HB, (2007) Recent progress in protein subcellular location prediction. Analytical biochemistry 370: 1-16.
    • (2007) Analytical Biochemistry , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 33
    • 61849153473 scopus 로고    scopus 로고
    • A novel computational approach to predict transcription factor DNA binding preference
    • Cai Y, He J, Li X, Lu L, Yang X, et al. (2009) A novel computational approach to predict transcription factor DNA binding preference. Journal of proteome research 8: 999-1003.
    • (2009) Journal of Proteome Research , vol.8 , pp. 999-1003
    • Cai, Y.1    He, J.2    Li, X.3    Lu, L.4    Yang, X.5
  • 34
    • 38449119746 scopus 로고    scopus 로고
    • Identification of enzymes and activity from two-dimensional gel electrophoresis
    • Afjehi-Sadat L, Lubec G, (2007) Identification of enzymes and activity from two-dimensional gel electrophoresis. Nature protocols 2: 2318-2324.
    • (2007) Nature Protocols , vol.2 , pp. 2318-2324
    • Afjehi-Sadat, L.1    Lubec, G.2
  • 35
    • 61549096128 scopus 로고    scopus 로고
    • Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine
    • Chen C, Chen L, Zou X, Cai P, (2009) Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine. Protein and peptide letters 16: 27-31.
    • (2009) Protein and Peptide Letters , vol.16 , pp. 27-31
    • Chen, C.1    Chen, L.2    Zou, X.3    Cai, P.4
  • 36
    • 67349244013 scopus 로고    scopus 로고
    • Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach
    • Zeng YH, Guo YZ, Xiao RQ, Yang L, Yu LZ, et al. (2009) Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. Journal of theoretical biology 259: 366-372.
    • (2009) Journal of Theoretical Biology , vol.259 , pp. 366-372
    • Zeng, Y.H.1    Guo, Y.Z.2    Xiao, R.Q.3    Yang, L.4    Yu, L.Z.5
  • 37
    • 65349165718 scopus 로고    scopus 로고
    • Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition
    • Ding H, Luo L, Lin H, (2009) Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition. Protein and peptide letters 16: 351-355.
    • (2009) Protein and Peptide Letters , vol.16 , pp. 351-355
    • Ding, H.1    Luo, L.2    Lin, H.3
  • 38
    • 34548439881 scopus 로고    scopus 로고
    • Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes
    • Zhou XB, Chen C, Li ZC, Zou XY, (2007) Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. Journal of theoretical biology 248: 546-551.
    • (2007) Journal of Theoretical Biology , vol.248 , pp. 546-551
    • Zhou, X.B.1    Chen, C.2    Li, Z.C.3    Zou, X.Y.4
  • 39
    • 52749089141 scopus 로고    scopus 로고
    • The prediction of interferon treatment effects based on time series microarray gene expression profiles
    • Huang T, Tu K, Shyr Y, Wei CC, Xie L, et al. (2008) The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med 6: 44.
    • (2008) J Transl Med , vol.6 , pp. 44
    • Huang, T.1    Tu, K.2    Shyr, Y.3    Wei, C.C.4    Xie, L.5
  • 40
    • 77949493376 scopus 로고    scopus 로고
    • Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles
    • Huang T, Cui W, Hu L, Feng K, Li YX, et al. (2009) Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS ONE 4: e8126.
    • (2009) PLoS ONE , vol.4
    • Huang, T.1    Cui, W.2    Hu, L.3    Feng, K.4    Li, Y.X.5
  • 41
    • 77955199287 scopus 로고    scopus 로고
    • Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
    • Huang T, Shi XH, Wang P, He Z, Feng KY, et al. (2010) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE 5: e10972.
    • (2010) PLoS ONE , vol.5
    • Huang, T.1    Shi, X.H.2    Wang, P.3    He, Z.4    Feng, K.Y.5
  • 42
    • 77955645823 scopus 로고    scopus 로고
    • Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties
    • Huang T, Wang P, Ye ZQ, Xu H, He Z, et al. (2010) Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties. PLoS ONE 5: e11900.
    • (2010) PLoS ONE , vol.5
    • Huang, T.1    Wang, P.2    Ye, Z.Q.3    Xu, H.4    He, Z.5
  • 43
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4    Moore, L.5
  • 44
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28: 27-30.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 45
    • 57049095797 scopus 로고    scopus 로고
    • Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast
    • Sinha H, David L, Pascon RC, Clauder-Munster S, Krishnakumar S, et al. (2008) Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics 180: 1661-1670.
    • (2008) Genetics , vol.180 , pp. 1661-1670
    • Sinha, H.1    David, L.2    Pascon, R.C.3    Clauder-Munster, S.4    Krishnakumar, S.5
  • 46
    • 34447320461 scopus 로고    scopus 로고
    • An amphibian-derived, cationic, alpha-helical antimicrobial peptide kills yeast by caspase-independent but AIF-dependent programmed cell death
    • Morton CO, Dos Santos SC, Coote P, (2007) An amphibian-derived, cationic, alpha-helical antimicrobial peptide kills yeast by caspase-independent but AIF-dependent programmed cell death. Molecular microbiology 65: 494-507.
    • (2007) Molecular Microbiology , vol.65 , pp. 494-507
    • Morton, C.O.1    Dos Santos, S.C.2    Coote, P.3
  • 47
    • 68649089232 scopus 로고    scopus 로고
    • Comprehensive and quantitative analysis of yeast deletion mutants defective in apical and isotropic bud growth
    • Watanabe M, Watanabe D, Nogami S, Morishita S, Ohya Y, (2009) Comprehensive and quantitative analysis of yeast deletion mutants defective in apical and isotropic bud growth. Current genetics 55: 365-380.
    • (2009) Current Genetics , vol.55 , pp. 365-380
    • Watanabe, M.1    Watanabe, D.2    Nogami, S.3    Morishita, S.4    Ohya, Y.5
  • 48
    • 27644467457 scopus 로고    scopus 로고
    • Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae
    • Altmann K, Westermann B, (2005) Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae. Molecular biology of the cell 16: 5410-5417.
    • (2005) Molecular Biology of the Cell , vol.16 , pp. 5410-5417
    • Altmann, K.1    Westermann, B.2
  • 49
    • 67651171456 scopus 로고    scopus 로고
    • A genome-wide screen for essential yeast genes that affect telomere length maintenance
    • Ungar L, Yosef N, Sela Y, Sharan R, Ruppin E, et al. (2009) A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic acids research 37: 3840-3849.
    • (2009) Nucleic Acids Research , vol.37 , pp. 3840-3849
    • Ungar, L.1    Yosef, N.2    Sela, Y.3    Sharan, R.4    Ruppin, E.5
  • 50
    • 33645228980 scopus 로고    scopus 로고
    • Genomewide screen reveals a wide regulatory network for di/tripeptide utilization in Saccharomyces cerevisiae
    • Cai H, Kauffman S, Naider F, Becker JM, (2006) Genomewide screen reveals a wide regulatory network for di/tripeptide utilization in Saccharomyces cerevisiae. Genetics 172: 1459-1476.
    • (2006) Genetics , vol.172 , pp. 1459-1476
    • Cai, H.1    Kauffman, S.2    Naider, F.3    Becker, J.M.4
  • 51
    • 9144264169 scopus 로고    scopus 로고
    • A map of the interactome network of the metazoan C. elegans
    • Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543.
    • (2004) Science , vol.303 , pp. 540-543
    • Li, S.1    Armstrong, C.M.2    Bertin, N.3    Ge, H.4    Milstein, S.5
  • 52
    • 0345600247 scopus 로고    scopus 로고
    • A protein interaction map of Drosophila melanogaster
    • Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.
    • (2003) Science , vol.302 , pp. 1727-1736
    • Giot, L.1    Bader, J.S.2    Brouwer, C.3    Chaudhuri, A.4    Kuang, B.5
  • 53
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3    Hirozane-Kishikawa, T.4    Dricot, A.5
  • 54
    • 14744270216 scopus 로고    scopus 로고
    • A first-draft human protein-interaction map
    • Lehner B, Fraser AG, (2004) A first-draft human protein-interaction map. Genome biology 5: R63.
    • (2004) Genome Biology , vol.5
    • Lehner, B.1    Fraser, A.G.2
  • 55
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: a resource for annotating the proteome
    • Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1    Worm, U.2    Lalowski, M.3    Haenig, C.4    Brembeck, F.H.5


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