메뉴 건너뛰기




Volumn 9, Issue 20, 2009, Pages 4799-4811

Interaction networks: Lessons from large-scale studies in yeast

Author keywords

Genetic interaction; Network; Protein interaction; Systems biology; Yeast

Indexed keywords

COMPUTER ANALYSIS; CYTOLOGY; FUNGAL GENE; FUNGAL STRAIN; GENE INTERACTION; GENETIC EPISTASIS; GENETIC MANIPULATION; HIGH THROUGHPUT SCREENING; MASS SPECTROMETRY; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MICROARRAY; PROTEIN MOTIF; PROTEIN PURIFICATION; QUALITY CONTROL; REVIEW; SACCHAROMYCES CEREVISIAE;

EID: 70350235043     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200900177     Document Type: Review
Times cited : (6)

References (116)
  • 3
    • 0031832544 scopus 로고    scopus 로고
    • The yeast protein database (YPD): A curated proteome database for Saccharomyces cerevisiae
    • DOI 10.1093/nar/26.1.68
    • Hodges, P. E., Payne, W. E., Garrels, J. I., The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae. Nucleic Acids Res. 1998, 26, 68-72. (Pubitemid 28295264)
    • (1998) Nucleic Acids Research , vol.26 , Issue.1 , pp. 68-72
    • Hodges, P.E.1    Payne, W.E.2    Garrels, J.I.3
  • 7
    • 33644875537 scopus 로고    scopus 로고
    • MIPS: Analysis and annotation of proteins from whole genomes in 2005
    • Mewes, H. W., Frishman, D., Mayer, K. F., Munsterkotter, M. et al., MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 2006, 34, D169-D172.
    • Nucleic Acids Res. , vol.2006 , Issue.34
    • Mewes, H.W.1    Frishman, D.2    Mayer, K.F.3    Munsterkotter, M.4
  • 11
    • 34548573170 scopus 로고    scopus 로고
    • Why are there still over 1000 uncharacterized yeast genes?
    • DOI 10.1534/genetics.107.074468
    • Peña-Castillo, L., Hughes, T. R., Why are there still over 1000 uncharacterized yeast genes? Genetics 2007, 176, 7-14. (Pubitemid 350021004)
    • (2007) Genetics , vol.176 , Issue.1 , pp. 7-14
    • Pena-Castillo, L.1    Hughes, T.R.2
  • 12
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe, K. H., Shields, D. C., Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997, 387, 708-713.
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 16
    • 0038680253 scopus 로고    scopus 로고
    • Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo
    • DOI 10.1038/nature01692
    • Kanemaki, M., Sanchez-Diaz, A., Gambus, A., Labib, K., Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo. Nature 2003, 423, 720-724. (Pubitemid 36735689)
    • (2003) Nature , vol.423 , Issue.6941 , pp. 720-724
    • Kanemaki, M.1    Sanchez-Diaz, A.2    Gambus, A.3    Labib, K.4
  • 20
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • DOI 10.1038/nature01771
    • Papp, B., Pal, C., Hurst, L. D., Dosage sensitivity and the evolution of gene families in yeast. Nature 2003, 424, 194-197. (Pubitemid 36858686)
    • (2003) Nature , vol.424 , Issue.6945 , pp. 194-197
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 21
    • 0037087575 scopus 로고    scopus 로고
    • Subcellular localization of the yeast proteome
    • Kumar, A., Agarwal, S., Heyman, J. A., Matson, S. et al., Subcellular localization of the yeast proteome. Genes Dev. 2002, 16, 707-719.
    • (2002) Genes Dev. , vol.16 , pp. 707-719
    • Kumar, A.1    Agarwal, S.2    Heyman, J.A.3    Matson, S.4
  • 24
    • 51549087123 scopus 로고    scopus 로고
    • Probing nucleosome function: A highly versatile library of synthetic histone H3 and H4 mutants
    • Dai, J., Hyland, E. M., Yuan, D. S., Huang, H., Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell 2008, 134, 1066-1078.
    • (2008) Cell , vol.134 , pp. 1066-1078
    • Dai, J.1    Hyland, E.M.2    Yuan, D.S.3    Huang, H.4
  • 28
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin, A. C., Bosche, M., Krause, R., Grandi, P. et al., Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440, 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4
  • 29
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan, N. J., Cagney, G., Yu, H., Zhong, G. et al., Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440, 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4
  • 31
    • 0242298316 scopus 로고    scopus 로고
    • DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray
    • Ooi, S. L., Shoemaker, D. D., Boeke, J. D. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat. Genet. 2003, 35, 277-286.
    • (2003) Nat. Genet. , vol.35 , pp. 277-286
    • Ooi, S.L.1    Shoemaker, D.D.2    Boeke, J.D.3
  • 33
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • DOI 10.1038/340245a0
    • Fields, S., Song, O., A novel genetic system to detect protein-protein interactions. Nature 1989, 340, 245-246. (Pubitemid 19171591)
    • (1989) Nature , vol.340 , Issue.6230 , pp. 245-246
    • Fields, S.1    Song, O.-K.2
  • 34
    • 45949100254 scopus 로고    scopus 로고
    • Improving yeast two-hybrid screening systems
    • DOI 10.1093/bfgp/elm035
    • Koegl, M., Uetz, P., Improving yeast two-hybrid screening systems. Brief. Funct. Genomic. Proteomic. 2007, 6, 302-312. (Pubitemid 351890477)
    • (2007) Briefings in Functional Genomics and Proteomics , vol.6 , Issue.4 , pp. 302-312
    • Koegl, M.1    Uetz, P.2
  • 37
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • DOI 10.1038/nbt924
    • Bader, J. S., Chaudhuri, A., Rothberg, J. M., Chant, J., Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 2004, 22, 78-85. (Pubitemid 38057960)
    • (2004) Nature Biotechnology , vol.22 , Issue.1 , pp. 78-85
    • Bader, J.S.1    Chaudhuri, A.2    Rothberg, J.M.3    Chant, J.4
  • 40
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • DOI 10.1038/13732
    • Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 1999, 17, 1030-1032. (Pubitemid 29474865)
    • (1999) Nature Biotechnology , vol.17 , Issue.10 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6
  • 41
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440, 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4
  • 42
    • 33645453254 scopus 로고    scopus 로고
    • Global land-scape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan, N, J., Cagney, G., Yu, H., Zhong, G., Global land-scape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440, 637-643
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4
  • 43
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 44
    • 4444335470 scopus 로고    scopus 로고
    • The ABC's and XYZ's, of peptide sequencing
    • Steen, H., Mann, M., The ABC's and XYZ's, of peptide sequencing. Nat. Rev. Mol. Cell. Biol. 2004, 5, 699-711.
    • (2004) Nat. Rev. Mol. Cell. Biol. , vol.5 , pp. 699-711
    • Steen, H.1    Mann, M.2
  • 51
    • 58149306033 scopus 로고    scopus 로고
    • The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71
    • Ester, C., Uetz, P., The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71. BMC Biochem. 2008, 9, 29.
    • (2008) BMC Biochem. , vol.9 , pp. 29
    • Ester, C.1    Uetz, P.2
  • 52
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M. et al., Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417, 399-403. (Pubitemid 34563526)
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 53
    • 0028926048 scopus 로고
    • Protein-protein interactions: Methods for detection and analysis
    • Phizicky, E. M., Fields, S., Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 1995, 59, 94-123.
    • (1995) Microbiol. Rev. , vol.59 , pp. 94-123
    • Phizicky, E.M.1    Fields, S.2
  • 54
    • 34548418142 scopus 로고    scopus 로고
    • Methods for the detection and analysis of protein-protein interactions
    • DOI 10.1002/pmic.200700131
    • Berggård, T., Linse, S., James, P., Methods for the detection and analysis of protein-protein interactions. Proteomics 2007, 7, 2833-2842. (Pubitemid 47359924)
    • (2007) Proteomics , vol.7 , Issue.16 , pp. 2833-2842
    • Berggard, T.1    Linse, S.2    James, P.3
  • 55
    • 0036276974 scopus 로고    scopus 로고
    • Synthetic dosage lethality
    • Measday, V., Hieter, P., Synthetic dosage lethality. Methods Enzymol. 2002, 350, 316-326.
    • (2002) Methods Enzymol. , vol.350 , pp. 316-326
    • Measday, V.1    Hieter, P.2
  • 56
    • 34249041230 scopus 로고    scopus 로고
    • Exploring genetic interactions and networks with yeast
    • DOI 10.1038/nrg2085, PII NRG2085
    • Boone, C., Bussey, H., Andrews, B. J., Exploring genetic interactions and networks in yeast. Nat. Rev. Genet. 2007, 8, 437-449. (Pubitemid 46789246)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.6 , pp. 437-449
    • Boone, C.1    Bussey, H.2    Andrews, B.J.3
  • 57
    • 54149088214 scopus 로고    scopus 로고
    • Epistasis - The essential role of gene interactions in the structure and evolution of genetic systems
    • Phillips, P. C., Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat. Rev. Genet. 2008, 9, 855-867.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 855-867
    • Phillips, P.C.1
  • 59
    • 1642499365 scopus 로고    scopus 로고
    • The ctf13-30/CTF13 Genomic Haploinsufficiency Modifier Screen Identifies the Yeast Chromatin Remodeling Complex RSC, Which Is Required for the Establishment of Sister Chromatid Cohesion
    • DOI 10.1128/MCB.24.3.1232-1244.2003
    • Baetz, K. K., Krogan, N. J., Emili, A., Greenblatt, J., Hieter, P., The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion. Mol. Cell. Biol. 2004, 24, 1232-1244. (Pubitemid 38112185)
    • (2004) Molecular and Cellular Biology , vol.24 , Issue.3 , pp. 1232-1244
    • Baetz, K.K.1    Krogan, N.J.2    Emili, A.3    Greenblatt, J.4    Hieter, P.5
  • 60
    • 33846528944 scopus 로고    scopus 로고
    • Modeling complex genetic interactions in a simple eukaryotic genome: Actin displays a rich spectrum of complex haploinsufficiencies
    • DOI 10.1101/gad.1477507
    • Haarer, B., Viggiano, S., Hibbs, M. A., Troyanskya, O. G., Amberg, D. C., Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev. 2007, 21, 148-159. (Pubitemid 46155809)
    • (2007) Genes and Development , vol.21 , Issue.2 , pp. 148-159
    • Haarer, B.1    Viggiano, S.2    Hibbs, M.A.3    Troyanskaya, O.G.4    Amberg, D.C.5
  • 61
    • 0024024370 scopus 로고
    • Unlinked noncomplementation: Isolation of new conditional lethal mutations in each of the tubulin genes of Saccharomyces cerevisiae
    • Stearns, T., Botstein, D., Unlinked noncomplementation: Isolation of new conditional lethal mutations in each of the tubulin genes of Saccharomyces cerevisiae. Genetics 1988, 119, 249-260.
    • (1988) Genetics , vol.119 , pp. 249-260
    • Stearns, T.1    Botstein, D.2
  • 62
    • 33645124487 scopus 로고    scopus 로고
    • Derivation of genetic interaction networks from quantitative phenotype data
    • Drees, B. L., Thorsson, V., Carter, G. W., Rives, A. W. et al., Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol. 2005, 6, R38.
    • (2005) Genome Biol. , vol.6
    • Drees, B.L.1    Thorsson, V.2    Carter, G.W.3    Rives, A.W.4
  • 65
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • DOI 10.1038/nbt1096
    • Kelley, R., Ideker, T., Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 2005, 23, 561-566. (Pubitemid 41724894)
    • (2005) Nature Biotechnology , vol.23 , Issue.5 , pp. 561-566
    • Kelley, R.1    Ideker, T.2
  • 66
    • 56849094282 scopus 로고    scopus 로고
    • A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing
    • Wilmes, G. M., Bergkessel, M., Bandyopadhyay, S., Shales, M., A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol. Cell 2008, 32, 735-746.
    • (2008) Mol. Cell , vol.32 , pp. 735-746
    • Wilmes, G.M.1    Bergkessel, M.2    Bandyopadhyay, S.3    Shales, M.4
  • 67
    • 61349119934 scopus 로고    scopus 로고
    • Functional organization of the S. cerevisiae phosphorylation network
    • Fiedler, D., Braberg, H., Mehta, M., Chechik, G. et al., Functional organization of the S. cerevisiae phosphorylation network. Cell 2009, 136, 952-963.
    • (2009) Cell , vol.136 , pp. 952-963
    • Fiedler, D.1    Braberg, H.2    Mehta, M.3    Chechik, G.4
  • 68
    • 55949124306 scopus 로고    scopus 로고
    • Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes
    • Dixon, S. J., Fedyshyn, Y., Koh, J. L., Prasad, T. S. et al., Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc. Natl. Acad. Sci. USA 2008, 105, 16653-16658.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 16653-16658
    • Dixon, S.J.1    Fedyshyn, Y.2    Koh, J.L.3    Prasad, T.S.4
  • 69
    • 54249107599 scopus 로고    scopus 로고
    • Conservation and rewiring of functionalmodules revealed by an epistasis map in fission yeast
    • Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K. et al., Conservation and rewiring of functionalmodules revealed by an epistasis map in fission yeast. Science 2008, 322, 405-410.
    • (2008) Science , vol.322 , pp. 405-410
    • Roguev, A.1    Bandyopadhyay, S.2    Zofall, M.3    Zhang, K.4
  • 70
    • 0029804246 scopus 로고    scopus 로고
    • Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy
    • DOI 10.1038/ng1296-450
    • Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittmann, M., Davis, R. W., Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular barcoding strategy. Nat. Genet. 1996, 14, 450-456. (Pubitemid 26414589)
    • (1996) Nature Genetics , vol.14 , Issue.4 , pp. 450-456
    • Shoemaker, D.D.1    Lashkari, D.A.2    Morris, D.3    Mittmann, M.4    Davis, R.W.5
  • 71
    • 84984933073 scopus 로고    scopus 로고
    • Structure and function of a transcriptional network activated by the MAPK Hog1
    • Capaldi, A. P., Kaplan, T., Liu, Y., Habib, N. et al., Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet. 2008, 40, 1300-1306.
    • (2008) Nat. Genet. , vol.40 , pp. 1300-1306
    • Capaldi, A.P.1    Kaplan, T.2    Liu, Y.3    Habib, N.4
  • 72
    • 2942618604 scopus 로고    scopus 로고
    • Quantitative genome-wide analysis of yeast deletion strain sensitivities to oxidative and chemical stress
    • DOI 10.1002/cfg.391
    • Tucker, C. L., Fields, S., Quantitative genome-wide analysis of yeast deletion strain sensitivities to oxidative and chemical stress. Comp. Funct. Genomics 2004, 5, 216-224. (Pubitemid 38744660)
    • (2004) Comparative and Functional Genomics , vol.5 , Issue.3 , pp. 216-224
    • Tucker, C.L.1    Fields, S.2
  • 77
    • 33847064282 scopus 로고    scopus 로고
    • Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    • Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J. et al., Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 2005, 5, 11.
    • (2005) J. Biol. , vol.5 , pp. 11
    • Reguly, T.1    Breitkreutz, A.2    Boucher, L.3    Breitkreutz, B.J.4
  • 78
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast inter-actome network
    • Yu, H., Braun, P., Yildirim, M. A., Lemmens, I. et al., High-quality binary protein interaction map of the yeast inter-actome network. Science 2008, 322, 104-110.
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yildirim, M.A.3    Lemmens, I.4
  • 79
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • Deane, C. M., Salwinski, L., Xenarios, I., Eisenberg, D., Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell. Proteomics 2002, 1, 349-356.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 80
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • Bader, G. D., Hogue, C. W., Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 2002, 20, 991-997.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 81
    • 34548024598 scopus 로고    scopus 로고
    • Integrating physical and genetic maps: From genomes to interaction networks
    • DOI 10.1038/nrg2144, PII NRG2144
    • Beyer, A., Bandyopadhyay, S., Ideker, T., Integrating physical and genetic maps: from genomes to interaction networks. Nat. Rev. Genet. 2007, 8, 699-710. (Pubitemid 47281988)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.9 , pp. 699-710
    • Beyer, A.1    Bandyopadhyay, S.2    Ideker, T.3
  • 82
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan, R., Ulitsky, I., Shamir, R., Network-based prediction of protein function. Mol. Syst. Biol. 2007, 3, 88.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 83
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski, B., Uetz, P., Fields, S., A network of protein-protein interactions in yeast. Nat. Biotechnol. 2000, 18, 1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 84
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • DOI 10.1038/nbt825
    • Vazquez, A., Flammini, A., Maritan, A., Vespignani, A., Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 2003, 21, 697-700. (Pubitemid 36638099)
    • (2003) Nature Biotechnology , vol.21 , Issue.6 , pp. 697-700
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 85
    • 0742304254 scopus 로고    scopus 로고
    • Prediction of Protein Function Using Protein-Protein Interaction Data
    • DOI 10.1089/106652703322756168
    • Deng, M., Zhang, K., Mehta, S., Chen, T. et al., Prediction of protein function using protein-protein interaction data. J. Comput. Biol. 2003, 10, 947-960. (Pubitemid 38156407)
    • (2003) Journal of Computational Biology , vol.10 , Issue.6 , pp. 947-960
    • Deng, M.1    Zhang, K.2    Mehta, S.3    Chen, T.4    Sun, F.5
  • 87
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G. D., Hogue, C. W., An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4, 2.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 88
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • DOI 10.1186/1471-2105-7-207
    • Altaf-Ul-Amin, M., Shinbo, Y., Mihara, K., Kurokawa, K., Kanaya, S., Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 2006, 7, 207. (Pubitemid 43833590)
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-Ul-Amin, Md.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 89
    • 23844447959 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • DOI 10.1089/cmb.2005.12.835
    • Sharan, R., Ideker, T., Kelley, B., Shamir, R., Karp, R. M., Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J. Comput. Biol. 2005, 12, 835-846. (Pubitemid 41170485)
    • (2005) Journal of Computational Biology , vol.12 , Issue.6 , pp. 835-846
    • Sharan, R.1    Ideker, T.2    Kelley, B.3    Shamir, R.4    Karp, R.M.5
  • 90
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • DOI 10.1093/bioinformatics/bti021
    • Arnau, V., Mars, S., Marín, I., Iterative cluster analysis of protein interaction data. Bioinformatics 2005, 21, 364-378. (Pubitemid 40246608)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Marin, I.3
  • 91
    • 48249087654 scopus 로고    scopus 로고
    • Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
    • Greene, D., Cagney, G., Krogan, N., Cunningham, P., Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. Bioinformatics 2008, 24, 1722-1728.
    • (2008) Bioinformatics , vol.24 , pp. 1722-1728
    • Greene, D.1    Cagney, G.2    Krogan, N.3    Cunningham, P.4
  • 93
    • 3042523388 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • DOI 10.1101/gr.2203804
    • Asthana, S., King, O. D., Gibbons, F. D., Roth, F. P., Predicting protein complex membership using probabilistic network reliability. Genome Res. 2004, 14, 1170-1175. (Pubitemid 38811553)
    • (2004) Genome Research , vol.14 , Issue.6 , pp. 1170-1175
    • Asthana, S.1    King, O.D.2    Gibbons, F.D.3    Roth, F.P.4
  • 94
    • 0142241336 scopus 로고    scopus 로고
    • Greedily building protein networks with confidence
    • Bader, J. S., Greedily building protein networks with confidence. Bioinformatics 2003, 19, 1869-1874.
    • (2003) Bioinformatics , vol.19 , pp. 1869-1874
    • Bader, J.S.1
  • 95
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., Mason, S. P., Barabasi, A. L., Oltvai, Z. N., Lethality and centrality in protein networks. Nature 2001, 411, 4142.
    • (2001) Nature , vol.411 , pp. 4142
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 96
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts, D. J., Strogatz, S. H., Collective dynamics of 'small-world' networks. Nature 1998, 393, 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 97
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • DOI 10.1038/ng881
    • Shen-Orr, S. S., Milo, R., Mangan, S., Alon, U., Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 2002, 31, 64-68. (Pubitemid 34887640)
    • (2002) Nature Genetics , vol.31 , Issue.1 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 98
    • 33847051248 scopus 로고    scopus 로고
    • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
    • Zhang, L. V., King, O. D., Wong, S. L., Goldberg, D. S. et al., Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J. Biol. 2005, 4, 6.
    • (2005) J. Biol. , vol.4 , pp. 6
    • Zhang, L.V.1    King, O.D.2    Wong, S.L.3    Goldberg, D.S.4
  • 100
    • 33748798478 scopus 로고    scopus 로고
    • Graph-based methods for analysing networks in cell biology
    • DOI 10.1093/bib/bbl022
    • Aittokallio, T., Schwikowski, B., Graph-based methods for analysing networks in cell biology. Brief Bioinform. 2006, 7, 243-255. (Pubitemid 44404874)
    • (2006) Briefings in Bioinformatics , vol.7 , Issue.3 , pp. 243-255
    • Aittokallio, T.1    Schwikowski, B.2
  • 101
    • 3042523388 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • DOI 10.1101/gr.2203804
    • Asthana, S., King, O. D., Gibbons, F. D., Roth, F. P., Predicting protein complex membership using probabilistic network reliability. Genome Res. 2004, 14, 1170-1175. (Pubitemid 38811553)
    • (2004) Genome Research , vol.14 , Issue.6 , pp. 1170-1175
    • Asthana, S.1    King, O.D.2    Gibbons, F.D.3    Roth, F.P.4
  • 102
    • 0142148210 scopus 로고    scopus 로고
    • A comprehensive set of protein complexes in yeast: Mining large scale protein-protein interaction screens
    • DOI 10.1093/bioinformatics/btg344
    • Krause, R., von Mering, C., Bork, P., A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Bioinformatics 2003 19, 1901-1908. (Pubitemid 37322333)
    • (2003) Bioinformatics , vol.19 , Issue.15 , pp. 1901-1908
    • Krause, R.1    Von Mering, C.2    Bork, P.3
  • 104
    • 34547787599 scopus 로고    scopus 로고
    • A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
    • DOI 10.1186/1471-2105-8-236
    • Hart, G. T., Lee, I., Marcotte, E. R., A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 2007, 8, 236. (Pubitemid 47225392)
    • (2007) BMC Bioinformatics , vol.8 , pp. 236
    • Hart, G.T.1    Lee, I.2    Marcotte, E.R.3
  • 106
    • 33645983211 scopus 로고    scopus 로고
    • Efficient algorithms for detecting signaling pathways in protein interaction networks
    • Scott, J., Ideker, T., Karp, R. M., Sharan, R. J., Efficient algorithms for detecting signaling pathways in protein interaction networks. Comput. Biol. 2006, 13, 133-144.
    • (2006) Comput. Biol. , vol.13 , pp. 133-144
    • Scott, J.1    Ideker, T.2    Karp, R.M.3    Sharan, R.J.4
  • 108
    • 33746898247 scopus 로고    scopus 로고
    • Gene function prediction from congruent synthetic lethal interactions in yeast
    • Ye, P., Peyser, B. D., Pan, X., Boeke, J. D. et al., Gene function prediction from congruent synthetic lethal interactions in yeast. Mol. Syst. Biol. 2005, 1, 2005.0026.
    • (2005) Mol. Syst. Biol. , vol.1
    • Ye, P.1    Peyser, B.D.2    Pan, X.3    Boeke, J.D.4
  • 109
    • 47349120555 scopus 로고    scopus 로고
    • From E-MAPs to module maps: Dissecting quantitative genetic interactions using physical interactions
    • DOI 10.1038/msb.2008.42, PII MSB200842
    • Ulitsky, I., Shlomi, T., Kupiec, M., Shamir, R., From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol. Syst. Biol. 2008, 4, 209. (Pubitemid 352001267)
    • (2008) Molecular Systems Biology , vol.4 , pp. 209
    • Ulitsky, I.1    Shlomi, T.2    Kupiec, M.3    Shamir, R.4
  • 110
    • 43249117094 scopus 로고    scopus 로고
    • Functional maps of protein complexes from quantitative genetic interaction data
    • DOI 10.1371/journal.pcbi.1000065
    • Bandyopadhyay, S., Kelley, R., Krogan, N. J., Ideker, T., Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput. Biol. 2008, 4, e1000065. (Pubitemid 351656716)
    • (2008) PLoS Computational Biology , vol.4 , Issue.4
    • Bandyopadhyay, S.1    Kelley, R.2    Krogan, N.J.3    Ideker, T.4
  • 111
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • DOI 10.1126/science.1105103
    • de Lichtenberg, U., Jensen, L. J., Brunak, S., Bork, P., Dynamic complex formation during the yeast cell cycle. Science 2005, 307, 724-727. (Pubitemid 40194642)
    • (2005) Science , vol.307 , Issue.5710 , pp. 724-727
    • De Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 114
    • 0034633626 scopus 로고    scopus 로고
    • Lineage-specific loss and divergence2000, of functionally linked genes in eukaryotes
    • Aravind, L., Watanabe, H., Lipman, D. J., Koonin, E. V., Lineage-specific loss and divergence2000, of functionally linked genes in eukaryotes. Proc. Natl. Acad. Sci. USA 97, 11319-11324.
    • Proc. Natl. Acad. Sci. USA , vol.97 , pp. 11319-11324
    • Aravind, L.1    Watanabe, H.2    Lipman, D.J.3    Koonin, E.V.4
  • 115
    • 34249740079 scopus 로고    scopus 로고
    • RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions
    • Lehner, B., Tischler, J., Fraser, A. G., RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat. Protocols 2006, 1, 1617-1620.
    • (2006) Nat. Protocols , vol.1 , pp. 1617-1620
    • Lehner, B.1    Tischler, J.2    Fraser, A.G.3
  • 116
    • 41349102391 scopus 로고    scopus 로고
    • Evolutionary plasticity of genetic interaction networks
    • Tischler, J., Lehner, B., Fraser, A. G., Evolutionary plasticity of genetic interaction networks. Nat. Genet. 2008, 40, 390-391.
    • (2008) Nat. Genet. , vol.40 , pp. 390-391
    • Tischler, J.1    Lehner, B.2    Fraser, A.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.