메뉴 건너뛰기




Volumn 17, Issue 6, 2012, Pages 645-658

Prediction of essential proteins using topological properties in GO-pruned PPI network based on machine learning methods

Author keywords

CENT ING GO; centrality algorithm; essential protein; gene ontology; machine learning; motif centrality GO; network motif; Protein Protein Interaction (PPI)

Indexed keywords

CENT-ING-GO; ESSENTIAL PROTEINS; GENE ONTOLOGY; MOTIF CENTRALITY GO; NETWORK MOTIF; PROTEIN-PROTEIN INTERACTIONS;

EID: 84876375322     PISSN: 10070214     EISSN: None     Source Type: Journal    
DOI: 10.1109/TST.2012.6374366     Document Type: Article
Times cited : (51)

References (54)
  • 1
    • 0033910576 scopus 로고    scopus 로고
    • TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes
    • Judson N, Mekalanos J J. TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes. Nat Biotechnol,, 2000, 18(7): 740-745.
    • (2000) Nat Biotechnol , vol.18 , Issue.7 , pp. 740-745
    • Judson, N.1    Mekalanos, J.J.2
  • 2
    • 0036632847 scopus 로고    scopus 로고
    • Comparative mycobacterial genomics as a tool for drug target and antigen discovery
    • Cole S T. Comparative mycobacterial genomics as a tool for drug target and antigen discovery. European Respiratory Journal, 2002, 20(36 suppl): 78s-86s.
    • (2002) European Respiratory Journal , vol.20 , Issue.36 SUPPL.
    • Cole, S.T.1
  • 4
    • 20444424942 scopus 로고    scopus 로고
    • Genome-wide screening for gene function using RNAi in mammalian cells
    • Cullen L M, Arndt G M. Genome-wide screening for gene function using RNAi in mammalian cells. Immunology and CellBiology, 2005, 83(3): 217-223.
    • (2005) Immunology and CellBiology , vol.83 , Issue.3 , pp. 217-223
    • Cullen, L.M.1    Arndt, G.M.2
  • 9
    • 84876371950 scopus 로고    scopus 로고
    • SGDP. Saccharomyces genome deletion project
    • SGDP. Saccharomyces genome deletion project. http:// www-sequence. stanford.edu/group/yeast-deletion-project/ deletions3.html, 2012.
    • (2012)
  • 10
    • 0029789824 scopus 로고    scopus 로고
    • A minimal gene set for cellular life derived by comparison of complete bacterial genomes
    • Mushegian A R, Koonin E V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proceedings of the National Academy ofSciences, 1996, 93(19): 10 268-10 273.
    • (1996) Proceedings of the National Academy OfSciences , vol.93 , Issue.19 , pp. 10268-10273
    • Mushegian, A.R.1    Koonin, E.V.2
  • 15
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics ofcentrality and essentiality in three eukaryotic protein-interaction networks
    • Hahn M W, Kern A D. Comparative genomics ofcentrality and essentiality in three eukaryotic protein-interaction networks. MolecularBiology and Evolution, 2005, 22(4): 803-806.
    • (2005) MolecularBiology and Evolution , vol.22 , Issue.4 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 16
    • 34447624151 scopus 로고    scopus 로고
    • Gene essentiality, gene duplicability and protein connectivity in human and mouse
    • Liang H, Li W-H. Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends in Genetics, 2007,23(8): 375-378.
    • (2007) Trends in Genetics , vol.23 , Issue.8 , pp. 375-378
    • Liang, H.1    Li, W.-H.2
  • 17
    • 84865730611 scopus 로고
    • A set of measures of centrality based on betweenness
    • Freeman L C. A set of measures of centrality based on betweenness. Sociometry, 1977, 40(1): 35-41.
    • (1977) Sociometry , vol.40 , Issue.1 , pp. 35-41
    • Freeman, L.C.1
  • 18
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • Joy M P P, Brock A, Ingber D E, Huang S. High-betweenness proteins in the yeast protein interaction network. JBiomed. Biotechnol., 2005,2005(2): 96-103.
    • (2005) JBiomed. Biotechnol. , vol.2005 , Issue.2 , pp. 96-103
    • Joy, M.P.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 19
    • 0038700482 scopus 로고    scopus 로고
    • Centers of complex networks
    • Wuchty S, Stadler P F. Centers of complex networks. J. Theor. Biol., 2003, 223(1): 45-53.
    • (2003) J. Theor. Biol. , vol.223 , Issue.1 , pp. 45-53
    • Wuchty, S.1    Stadler, P.F.2
  • 21
    • 84936824655 scopus 로고
    • Power and centrality: A family of measures
    • Bonacich P. Power and centrality: A family of measures. The American Journal ofSociology, 1987, 92(5): 1170-1182
    • (1987) The American Journal OfSociology , vol.92 , Issue.5 , pp. 1170-1182
    • Bonacich, P.1
  • 22
    • 31344478575 scopus 로고    scopus 로고
    • Virtual identification of essential proteins within the protein interaction network of yeast
    • Estrada E. Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics, 2006, 6(1): 35-40.
    • (2006) Proteomics , vol.6 , Issue.1 , pp. 35-40
    • Estrada, E.1
  • 23
  • 24
    • 79959695371 scopus 로고    scopus 로고
    • A local average connectivity-based method for identifying essential proteins from the network level
    • Li M, Wang J, Chen X, Wang H, Pan Y A local average connectivity-based method for identifying essential proteins from the network level. Computational BiologyandChemistry, 2011: 35(3): 143-150.
    • (2011) Computational BiologyandChemistry , vol.35 , Issue.3 , pp. 143-150
    • Li, M.1    Wang, J.2    Chen, X.3    Wang, H.4    Pan, Y.5
  • 25
    • 84862787765 scopus 로고    scopus 로고
    • A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
    • Li M, Zhang H, Wang J, Pan Y A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. BMCSystems Biology, 2012, 6(1): 15.
    • (2012) BMCSystems Biology , vol.6 , Issue.1 , pp. 15
    • Li, M.1    Zhang, H.2    Wang, J.3    Pan, Y.4
  • 27
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart G T, Ramani A, Marcotte E. How complete are current yeast and human protein-interaction networks? Genome Biology, 2006, 7(11): 120.
    • (2006) Genome Biology , vol.7 , Issue.11 , pp. 120
    • Hart, G.T.1    Ramani, A.2    Marcotte, E.3
  • 30
    • 0012624911 scopus 로고    scopus 로고
    • Prediction of protein essentiality based on genomic data
    • Jeong H, Oltvai Z N, Barabasi A L. Prediction of protein essentiality based on genomic data. Complexus, 2003, 1(1): 19-28.
    • (2003) Complexus , vol.1 , Issue.1 , pp. 19-28
    • Jeong, H.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 31
    • 70449369491 scopus 로고    scopus 로고
    • Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
    • Acencio M, Lemke N. Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics, 2009,10(1): 290.
    • (2009) BMC Bioinformatics , vol.10 , Issue.1 , pp. 290
    • Acencio, M.1    Lemke, N.2
  • 32
    • 50949092459 scopus 로고    scopus 로고
    • Why do Hubs in the yeast protein interaction network tend to be essential: Reexaming the connection between the network topology and essentiality
    • Zotenko E, Mestre J, O'Leary D P, Przytycka T M. Why do Hubs in the yeast protein interaction network tend to be essential: Reexaming the connection between the network topology and essentiality. PLoS Compu. Biol., 2008, 4: e1000140.
    • (2008) PLoS Compu. Biol. , vol.4
    • Zotenko, E.1    Mestre, J.2    O'Leary, D.P.3    Przytycka, T.M.4
  • 33
    • 0023710206 scopus 로고
    • Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach
    • DeLong E R, DeLong D M, Clarke-Pearson D L. Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach. Biometrics, 1988, 44(3): 837-845.
    • (1988) Biometrics , vol.44 , Issue.3 , pp. 837-845
    • Delong, E.R.1    Delong, D.M.2    Clarke-Pearson, D.L.3
  • 36
    • 70949096921 scopus 로고    scopus 로고
    • Localized network centrality and essentiality in the yeast-protein interaction network
    • Park K, Kim D. Localized network centrality and essentiality in the yeast-protein interaction network. Proteomics, 2009, 9(22): 5143-5154.
    • (2009) Proteomics , vol.9 , Issue.22 , pp. 5143-5154
    • Park, K.1    Kim, D.2
  • 37
    • 70449647110 scopus 로고    scopus 로고
    • How to identify essential genes from molecular networks?
    • del Rio G, Koschutzki D, Coello G. How to identify essential genes from molecular networks? BMC Systems Biology, 2009,3(1): 102.
    • (2009) BMC Systems Biology , vol.3 , Issue.1 , pp. 102
    • Del Rio, G.1    Koschutzki, D.2    Coello, G.3
  • 38
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio A, Collado-Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria. Current Opinion in Microbiology, 2003, 6(5): 482-489.
    • (2003) Current Opinion in Microbiology , vol.6 , Issue.5 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 44
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Machine Learning, 2001, 45(1): 5-32.
    • (2001) Machine Learning , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 48
    • 0006452367 scopus 로고    scopus 로고
    • The alternating decision tree learning algorithm
    • San Francisco, CA, USA: Morgan Kaufmann
    • Freund Y, Mason L. The alternating decision tree learning algorithm,. In: Proc. 16th International Conf. on Machine Learning. San Francisco, CA, USA: Morgan Kaufmann, 1999: 124-133.
    • (1999) Proc. 16th International Conf. on Machine Learning , pp. 124-133
    • Freund, Y.1    Mason, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.