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Volumn 6, Issue , 2012, Pages

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks

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[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN;

EID: 84867613437     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-87     Document Type: Article
Times cited : (139)

References (50)
  • 1
    • 71449100299 scopus 로고    scopus 로고
    • A systems biology tour de force for a near-minimal bacterium
    • 2824490, 19953084
    • Glass JI, Hutchison CA, Smith HO, Venter JC. A systems biology tour de force for a near-minimal bacterium. Mol Syst Biol 2009, 5:330. 2824490, 19953084.
    • (2009) Mol Syst Biol , vol.5 , pp. 330
    • Glass, J.I.1    Hutchison, C.A.2    Smith, H.O.3    Venter, J.C.4
  • 2
    • 34548108138 scopus 로고    scopus 로고
    • Targeting virulence: a new paradigm for antimicrobial therapy
    • 10.1038/nchembio.2007.24, 17710100
    • Clatworthy AE, Pierson E, Hung DT. Targeting virulence: a new paradigm for antimicrobial therapy. Nat Chem Biol 2007, 3:541-548. 10.1038/nchembio.2007.24, 17710100.
    • (2007) Nat Chem Biol , vol.3 , pp. 541-548
    • Clatworthy, A.E.1    Pierson, E.2    Hung, D.T.3
  • 3
    • 33747019241 scopus 로고    scopus 로고
    • Differences in the evolutionary history of disease genes affected by dominant or recessive mutations
    • 10.1186/1471-2164-7-165, 1534034, 16817963
    • Furney SJ, Alba MM, Lopez-Bigas N. Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics 2006, 7:165. 10.1186/1471-2164-7-165, 1534034, 16817963.
    • (2006) BMC Genomics , vol.7 , pp. 165
    • Furney, S.J.1    Alba, M.M.2    Lopez-Bigas, N.3
  • 5
    • 20444424942 scopus 로고    scopus 로고
    • Genome-wide screening for gene function using RNAi in mammalian cells
    • 10.1111/j.1440-1711.2005.01332.x, 15877598
    • Cullen LM, Arndt GM. Genome-wide screening for gene function using RNAi in mammalian cells. Immunol Cell Biol 2005, 83:217-223. 10.1111/j.1440-1711.2005.01332.x, 15877598.
    • (2005) Immunol Cell Biol , vol.83 , pp. 217-223
    • Cullen, L.M.1    Arndt, G.M.2
  • 6
    • 0141818929 scopus 로고    scopus 로고
    • Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery
    • 10.1046/j.1365-2958.2003.03697.x, 14507372
    • Roemer T, Jiang B, Davison J, Ketela T, Veillette K, Breton A, Tandia F, Linteau A, Sillaots S, Marta C, et al. Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol 2003, 50:167-181. 10.1046/j.1365-2958.2003.03697.x, 14507372.
    • (2003) Mol Microbiol , vol.50 , pp. 167-181
    • Roemer, T.1    Jiang, B.2    Davison, J.3    Ketela, T.4    Veillette, K.5    Breton, A.6    Tandia, F.7    Linteau, A.8    Sillaots, S.9    Marta, C.10
  • 7
    • 0037177560 scopus 로고    scopus 로고
    • Evolutionary rate in the protein interaction network
    • 10.1126/science.1068696, 11976460
    • Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science 2002, 296:750-752. 10.1126/science.1068696, 11976460.
    • (2002) Science , vol.296 , pp. 750-752
    • Fraser, H.B.1    Hirsh, A.E.2    Steinmetz, L.M.3    Scharfe, C.4    Feldman, M.W.5
  • 8
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • 1383730, 12045149
    • Jordan IK, Rogozin IB, Wolf YI, Koonin EV. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12:962-968. 1383730, 12045149.
    • (2002) Genome Res , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 9
    • 33746631391 scopus 로고    scopus 로고
    • Evolutionary and physiological importance of hub proteins
    • 10.1371/journal.pcbi.0020088, 1500817, 16839197
    • Batada NN, Hurst LD, Tyers M. Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2006, 2:e88. 10.1371/journal.pcbi.0020088, 1500817, 16839197.
    • (2006) PLoS Comput Biol , vol.2
    • Batada, N.N.1    Hurst, L.D.2    Tyers, M.3
  • 10
    • 33750488443 scopus 로고    scopus 로고
    • Towards the identification of essential genes using targeted genome sequencing and comparative analysis
    • 10.1186/1471-2164-7-265, 1624830, 17052348
    • Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 2006, 7:265. 10.1186/1471-2164-7-265, 1624830, 17052348.
    • (2006) BMC Genomics , vol.7 , pp. 265
    • Gustafson, A.M.1    Snitkin, E.S.2    Parker, S.C.3    DeLisi, C.4    Kasif, S.5
  • 11
    • 72949094885 scopus 로고    scopus 로고
    • Predicting essential genes based on network and sequence analysis
    • 10.1039/b900611g, 19452048
    • Hwang YC, Lin CC, Chang JY, Mori H, Juan HF, Huang HC. Predicting essential genes based on network and sequence analysis. Mol Biosyst 2009, 5:1672-1678. 10.1039/b900611g, 19452048.
    • (2009) Mol Biosyst , vol.5 , pp. 1672-1678
    • Hwang, Y.C.1    Lin, C.C.2    Chang, J.Y.3    Mori, H.4    Juan, H.F.5    Huang, H.C.6
  • 12
    • 79951573994 scopus 로고    scopus 로고
    • Investigating the predictability of essential genes across distantly related organisms using an integrative approach
    • 10.1093/nar/gkq784, 3035443, 20870748
    • Deng J, Deng L, Su S, Zhang M, Lin X, Wei L, Minai AA, Hassett DJ, Lu LJ. Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res 2011, 39:795-807. 10.1093/nar/gkq784, 3035443, 20870748.
    • (2011) Nucleic Acids Res , vol.39 , pp. 795-807
    • Deng, J.1    Deng, L.2    Su, S.3    Zhang, M.4    Lin, X.5    Wei, L.6    Minai, A.A.7    Hassett, D.J.8    Lu, L.J.9
  • 13
    • 70449369491 scopus 로고    scopus 로고
    • Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
    • 10.1186/1471-2105-10-290, 2753850, 19758426
    • Acencio ML, Lemke N. Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics 2009, 10:290. 10.1186/1471-2105-10-290, 2753850, 19758426.
    • (2009) BMC Bioinformatics , vol.10 , pp. 290
    • Acencio, M.L.1    Lemke, N.2
  • 14
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • 10.1038/35075138, 11333967
    • Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 15
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • 10.1093/molbev/msi072, 15616139
    • Hahn MW, Kern AD. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 2005, 22:803-806. 10.1093/molbev/msi072, 15616139.
    • (2005) Mol Biol Evol , vol.22 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 16
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • Joy MP, Brock A, Ingber DE, Huang S. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005, 2:96-103.
    • (2005) J Biomed Biotechnol , vol.2 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 17
    • 0038700482 scopus 로고    scopus 로고
    • Centers of complex networks
    • 10.1016/S0022-5193(03)00071-7, 12782116
    • Wuchty S, Stadler PF. Centers of complex networks. J Theor Biol 2003, 223:45-53. 10.1016/S0022-5193(03)00071-7, 12782116.
    • (2003) J Theor Biol , vol.223 , pp. 45-53
    • Wuchty, S.1    Stadler, P.F.2
  • 18
  • 19
    • 84936824655 scopus 로고
    • Power and centrality: A family of measures
    • Bonacich P. Power and centrality: A family of measures. Am J Sociol 1987, 92:12.
    • (1987) Am J Sociol , vol.92 , pp. 12
    • Bonacich, P.1
  • 20
    • 84867619810 scopus 로고    scopus 로고
    • Rethinking centrality: Methods and examples
    • Karen S, Zelen M. Rethinking centrality: Methods and examples. Social Networks 2002, 11:37.
    • (2002) Social Networks , vol.11 , pp. 37
    • Karen, S.1    Zelen, M.2
  • 22
    • 77953785685 scopus 로고    scopus 로고
    • Essential Proteins Discovery from Weighted Protein Interaction Networks
    • Li M, Wang JX, Wang H, Pan Y. Essential Proteins Discovery from Weighted Protein Interaction Networks. Proc Bioinform Res Appl 2010, 6053:89-100.
    • (2010) Proc Bioinform Res Appl , vol.6053 , pp. 89-100
    • Li, M.1    Wang, J.X.2    Wang, H.3    Pan, Y.4
  • 23
    • 84862787765 scopus 로고    scopus 로고
    • A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
    • 10.1186/1752-0509-6-15, 3325894, 22405054
    • 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. BMC Syst Biol 2012, 6:15-23. 10.1186/1752-0509-6-15, 3325894, 22405054.
    • (2012) BMC Syst Biol , vol.6 , pp. 15-23
    • Li, M.1    Zhang, H.2    Wang, J.3    Pan, Y.4
  • 25
    • 79955856339 scopus 로고    scopus 로고
    • Describing the Orthology Signal in a PPI Network at a Functional, Complex Level
    • Jancura P, Mavridou E, Pontes B, Marchiori E. Describing the Orthology Signal in a PPI Network at a Functional, Complex Level. Lect N Bioinformat 2011, 6674:209-226.
    • (2011) Lect N Bioinformat , vol.6674 , pp. 209-226
    • Jancura, P.1    Mavridou, E.2    Pontes, B.3    Marchiori, E.4
  • 26
    • 33644931696 scopus 로고    scopus 로고
    • Stable evolutionary signal in a Yeast protein interaction network
    • 10.1186/1471-2148-6-8, 1395346, 16441898
    • Wuchty S, Barabasi AL, Ferdig MT. Stable evolutionary signal in a Yeast protein interaction network. BMC Evol Biol 2006, 6:8. 10.1186/1471-2148-6-8, 1395346, 16441898.
    • (2006) BMC Evol Biol , vol.6 , pp. 8
    • Wuchty, S.1    Barabasi, A.L.2    Ferdig, M.T.3
  • 27
    • 0037177560 scopus 로고    scopus 로고
    • Evolutionary rate in the protein interaction network
    • 10.1126/science.1068696, 11976460
    • Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science 2002, 296:750-752. 10.1126/science.1068696, 11976460.
    • (2002) Science , vol.296 , pp. 750-752
    • Fraser, H.B.1    Hirsh, A.E.2    Steinmetz, L.M.3    Scharfe, C.4    Feldman, M.W.5
  • 28
    • 3543099834 scopus 로고    scopus 로고
    • Evolution and topology in the yeast protein interaction network
    • 10.1101/gr.2300204, 442146, 15231746
    • Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res 2004, 14:1310-1314. 10.1101/gr.2300204, 442146, 15231746.
    • (2004) Genome Res , vol.14 , pp. 1310-1314
    • Wuchty, S.1
  • 29
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • 1383730, 12045149
    • Jordan IK, Rogozin IB, Wolf YI, Koonin EV. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12:962-968. 1383730, 12045149.
    • (2002) Genome Res , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 30
    • 66349108229 scopus 로고    scopus 로고
    • IsoRankN: spectral methods for global alignment of multiple protein networks
    • 10.1093/bioinformatics/btp203, 2687957, 19477996
    • Liao CS, Lu KH, Baym M, Singh R, Berger B. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 2009, 25:I253-I258. 10.1093/bioinformatics/btp203, 2687957, 19477996.
    • (2009) Bioinformatics , vol.25
    • Liao, C.S.1    Lu, K.H.2    Baym, M.3    Singh, R.4    Berger, B.5
  • 31
    • 34547416529 scopus 로고    scopus 로고
    • Pairwise global alignment of protein interaction networks by matching neighborhood topology
    • Singh R, Xu JB, Berger B. Pairwise global alignment of protein interaction networks by matching neighborhood topology. Lect Notes Comput Sci 2007, 4453:16-31.
    • (2007) Lect Notes Comput Sci , vol.4453 , pp. 16-31
    • Singh, R.1    Xu, J.B.2    Berger, B.3
  • 33
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • 10.1101/gr.1224503, 403725, 12952885
    • Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 34
    • 78651316211 scopus 로고    scopus 로고
    • OMA 2011: orthology inference among 1000 complete genomes
    • 10.1093/nar/gkq1238, 3013747, 21113020
    • Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 2011, 39:D289-D294. 10.1093/nar/gkq1238, 3013747, 21113020.
    • (2011) Nucleic Acids Res , vol.39
    • Altenhoff, A.M.1    Schneider, A.2    Gonnet, G.H.3    Dessimoz, C.4
  • 35
    • 78651317907 scopus 로고    scopus 로고
    • IsoBase: a database of functionally related proteins across PPI networks
    • 10.1093/nar/gkq1234, 3013743, 21177658
    • Park D, Singh R, Baym M, Liao CS, Berger B. IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res 2011, 39:D295-D300. 10.1093/nar/gkq1234, 3013743, 21177658.
    • (2011) Nucleic Acids Res , vol.39
    • Park, D.1    Singh, R.2    Baym, M.3    Liao, C.S.4    Berger, B.5
  • 37
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    • 10.1093/nar/30.1.303, 99070, 11752321
    • Xenarios I, Salwinski L, Duan XQJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305. 10.1093/nar/30.1.303, 99070, 11752321.
    • (2002) Nucleic Acids Res , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.Q.J.3    Higney, P.4    Kim, S.M.5    Eisenberg, D.6
  • 39
    • 0031858914 scopus 로고    scopus 로고
    • SGD: Saccharomyces Genome Database
    • Cherry JM. SGD: Saccharomyces Genome Database. Nucleic Acids Res 1998, 26:9.
    • (1998) Nucleic Acids Res , vol.26 , pp. 9
    • Cherry, J.M.1
  • 40
    • 58149197597 scopus 로고    scopus 로고
    • DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    • 10.1093/nar/gkn858, 2686491, 18974178
    • Zhang R, Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 2009, 37:D455-D458. 10.1093/nar/gkn858, 2686491, 18974178.
    • (2009) Nucleic Acids Res , vol.37
    • Zhang, R.1    Lin, Y.2
  • 42
    • 31344478575 scopus 로고    scopus 로고
    • Virtual identification of essential proteins within the protein interaction network of yeast
    • 10.1002/pmic.200500209, 16281187
    • Estrada E. Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 2006, 6:35-40. 10.1002/pmic.200500209, 16281187.
    • (2006) Proteomics , vol.6 , pp. 35-40
    • Estrada, E.1
  • 43
    • 34547787599 scopus 로고    scopus 로고
    • A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
    • 10.1186/1471-2105-8-236, 1940025, 17605818
    • Hart GT, Lee I, Marcotte E. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 2007, 8:236. 10.1186/1471-2105-8-236, 1940025, 17605818.
    • (2007) BMC Bioinformatics , vol.8 , pp. 236
    • Hart, G.T.1    Lee, I.2    Marcotte, E.3
  • 44
    • 1542357701 scopus 로고    scopus 로고
    • Defining and identifying communities in networks
    • 10.1073/pnas.0400054101, 365677, 14981240
    • Radicchi F, Castellano C, Cecconi F, Loreto V, Parisi D. Defining and identifying communities in networks. Proc Natl Acad Sci U S A 2004, 101:2658-2663. 10.1073/pnas.0400054101, 365677, 14981240.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 2658-2663
    • Radicchi, F.1    Castellano, C.2    Cecconi, F.3    Loreto, V.4    Parisi, D.5
  • 45
    • 53749105832 scopus 로고    scopus 로고
    • Clustering coefficient and community structure of bipartite networks
    • Zhang P, Wang J, Li X, Li M, Di Z, Fan Y. Clustering coefficient and community structure of bipartite networks. Physica A 2008, 387:6869-6875.
    • (2008) Physica A , vol.387 , pp. 6869-6875
    • Zhang, P.1    Wang, J.2    Li, X.3    Li, M.4    Di, Z.5    Fan, Y.6
  • 46
    • 73849107815 scopus 로고    scopus 로고
    • Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi
    • 10.1186/1471-2180-9-243, 2794283, 19943957
    • Holman A, Davis P, Foster J, Carlow C, Kumar S. Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi. BMC Microbiol 2009, 9:243. 10.1186/1471-2180-9-243, 2794283, 19943957.
    • (2009) BMC Microbiol , vol.9 , pp. 243
    • Holman, A.1    Davis, P.2    Foster, J.3    Carlow, C.4    Kumar, S.5
  • 47
    • 63349085550 scopus 로고    scopus 로고
    • Up-to-date catalogues of yeast protein complexes
    • 10.1093/nar/gkn1005, 2647312, 19095691
    • Pu S, Wong J, Turner B, Cho E, Wodak SJ. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res 2009, 37:825-831. 10.1093/nar/gkn1005, 2647312, 19095691.
    • (2009) Nucleic Acids Res , vol.37 , pp. 825-831
    • Pu, S.1    Wong, J.2    Turner, B.3    Cho, E.4    Wodak, S.J.5
  • 48
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: new features for data integration and network visualization
    • 10.1093/bioinformatics/btq675, 3031041, 21149340
    • Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432. 10.1093/bioinformatics/btq675, 3031041, 21149340.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.-L.4    Ideker, T.5
  • 49


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