메뉴 건너뛰기




Volumn 4, Issue 6, 2009, Pages

Influence of protein abundance on high-throughput protein-protein interaction detection

Author keywords

[No Author keywords available]

Indexed keywords

ESSENTIAL PROTEIN; FUNGAL PROTEIN; FUNGAL RNA; NONESSENTIAL PROTEIN; UNCLASSIFIED DRUG; ESCHERICHIA COLI PROTEIN; MESSENGER RNA; PROTEIN; PROTEOME;

EID: 67149141471     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005815     Document Type: Article
Times cited : (35)

References (58)
  • 1
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating 'omics' data sets
    • Joyce AR, Palsson BO (2006) The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7: 198-210.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 2
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: Modelling protein interactions
    • Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7: 188-197.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 3
    • 27644576841 scopus 로고    scopus 로고
    • High-throughput two-hybrid analysis. The promise and the peril
    • Fields S (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J 272: 5391-5399.
    • (2005) FEBS J , vol.272 , pp. 5391-5399
    • Fields, S.1
  • 4
    • 0034841844 scopus 로고    scopus 로고
    • The tandem affinity purification (TAP) method: A general procedure of protein complex purification
    • Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24: 218-229.
    • (2001) Methods , vol.24 , pp. 218-229
    • Puig, O.1    Caspary, F.2    Rigaut, G.3    Rutz, B.4    Bouveret, E.5
  • 5
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5
  • 6
    • 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
  • 7
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98: 4569-4574.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5
  • 8
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 9
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.A.4    Judson, R.S.5
  • 10
    • 13444283630 scopus 로고    scopus 로고
    • Interaction network containing conserved and essential protein complexes in Escherichia coli
    • Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
    • (2005) Nature , vol.433 , pp. 531-537
    • Butland, G.1    Peregrin-Alvarez, J.M.2    Li, J.3    Yang, W.4    Yang, X.5
  • 11
    • 33745160404 scopus 로고    scopus 로고
    • Large-scale identification of protein-protein interaction of Escherichia coli K-12
    • Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12 Genome Res 16: 686-691.
    • (2006) Genome Res , vol.16 , pp. 686-691
    • Arifuzzaman, M.1    Maeda, M.2    Itoh, A.3    Nishikata, K.4    Takita, C.5
  • 13
    • 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
  • 14
    • 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
  • 15
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 16
    • 40949088417 scopus 로고    scopus 로고
    • Graph Theory Analysis of Protein-Protein Interactions
    • Jurisica I, Wigle DA, eds, CRC Press
    • Przulj N (2005) Graph Theory Analysis of Protein-Protein Interactions. In: Jurisica I, Wigle DA, eds. Knowledge Discovery in Proteomics: CRC Press.
    • (2005) Knowledge Discovery in Proteomics
    • Przulj, N.1
  • 17
    • 34247623628 scopus 로고    scopus 로고
    • Getting connected: Analysis and principles of biological networks
    • Zhu X, Gerstein M, Snyder M (2007) Getting connected: analysis and principles of biological networks. Genes Dev 21: 1010-1024.
    • (2007) Genes Dev , vol.21 , pp. 1010-1024
    • Zhu, X.1    Gerstein, M.2    Snyder, M.3
  • 18
    • 40949147767 scopus 로고    scopus 로고
    • Evidence of probabilistic behaviour in protein interaction networks
    • Ivanic J, Wallqvist A, Reifman J (2008) Evidence of probabilistic behaviour in protein interaction networks. BMC Syst Biol 2: 11.
    • (2008) BMC Syst Biol , vol.2 , pp. 11
    • Ivanic, J.1    Wallqvist, A.2    Reifman, J.3
  • 19
    • 48249147450 scopus 로고    scopus 로고
    • Ivanic J, Wallqvist A, Reifman J (2008) Probing the extent of randomness in protein interaction networks. PLoS Comput Biol 4: e1000114.
    • Ivanic J, Wallqvist A, Reifman J (2008) Probing the extent of randomness in protein interaction networks. PLoS Comput Biol 4: e1000114.
  • 20
    • 33746631391 scopus 로고    scopus 로고
    • Evolutionary and physiological importance of hub proteins
    • Batada NN, Hurst LD, Tyers M (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2: e88.
    • (2006) PLoS Comput Biol , vol.2
    • Batada, N.N.1    Hurst, L.D.2    Tyers, M.3
  • 23
    • 50949092459 scopus 로고    scopus 로고
    • Zotenko E, Mestre J, O'Leary DP, Przytycka TM (2008) Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 4: e1000140.
    • Zotenko E, Mestre J, O'Leary DP, Przytycka TM (2008) Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 4: e1000140.
  • 25
    • 16844363315 scopus 로고    scopus 로고
    • Modularity and evolutionary constraint on proteins
    • Fraser HB (2005) Modularity and evolutionary constraint on proteins. Nat Genet 37: 351-352.
    • (2005) Nat Genet , vol.37 , pp. 351-352
    • Fraser, H.B.1
  • 26
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22: 803-806.
    • (2005) Mol Biol Evol , vol.22 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 27
    • 33748464764 scopus 로고    scopus 로고
    • Combining functional and topological properties to identify core modules in protein interaction networks
    • Lubovac Z, Gamalielsson J, Olsson B (2006) Combining functional and topological properties to identify core modules in protein interaction networks. Proteins 64: 948-959.
    • (2006) Proteins , vol.64 , pp. 948-959
    • Lubovac, Z.1    Gamalielsson, J.2    Olsson, B.3
  • 28
    • 33748202182 scopus 로고    scopus 로고
    • Functional clustering of yeast proteins from the protein-protein interaction network
    • Sen TZ, Kloczkowski A, Jernigan RL (2006) Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics 7: 355.
    • (2006) BMC Bioinformatics , vol.7 , pp. 355
    • Sen, T.Z.1    Kloczkowski, A.2    Jernigan, R.L.3
  • 29
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100: 12123-12128.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 30
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl 1): S233-240.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 31
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • Przulj N, Wigle DA, Jurisica I (2004) Functional topology in a network of protein interactions. Bioinformatics 20: 340-348.
    • (2004) Bioinformatics , vol.20 , pp. 340-348
    • Przulj, N.1    Wigle, D.A.2    Jurisica, I.3
  • 33
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • Ulitsky I, Shamir R (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 1: 8.
    • (2007) BMC Syst Biol , vol.1 , pp. 8
    • Ulitsky, I.1    Shamir, R.2
  • 34
    • 18944391092 scopus 로고    scopus 로고
    • Biological networks and analysis of experimental data in drug discovery
    • Nikolsky Y, Nikolskaya T, Bugrim A (2005) Biological networks and analysis of experimental data in drug discovery. Drug Discov Today 10: 653-662.
    • (2005) Drug Discov Today , vol.10 , pp. 653-662
    • Nikolsky, Y.1    Nikolskaya, T.2    Bugrim, A.3
  • 35
    • 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, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5
  • 36
    • 0035212065 scopus 로고    scopus 로고
    • Is there a bias in proteome research?
    • Mrowka R, Patzak A, Herzel H (2001) Is there a bias in proteome research? Genome Res 11: 1971-1973.
    • (2001) Genome Res , vol.11 , pp. 1971-1973
    • Mrowka, R.1    Patzak, A.2    Herzel, H.3
  • 37
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • Sprinzak E, Sattath S, Margalit H (2003) How reliable are experimental protein-protein interaction data? J Mol Biol 327: 919-923.
    • (2003) J Mol Biol , vol.327 , pp. 919-923
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 39
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yildirim, M.A.3    Lemmens, I.4    Venkatesan, K.5
  • 40
    • 55849109221 scopus 로고    scopus 로고
    • Quantitative assessment of the structural bias in protein-protein interaction assays
    • Bjorklund AK, Light S, Hedin L, Elofsson A (2008) Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics 8: 4657-4667.
    • (2008) Proteomics , vol.8 , pp. 4657-4667
    • Bjorklund, A.K.1    Light, S.2    Hedin, L.3    Elofsson, A.4
  • 41
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5
  • 43
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    • Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840-846.
    • (2006) Nature , vol.441 , pp. 840-846
    • Newman, J.R.1    Ghaemmaghami, S.2    Ihmels, J.3    Breslow, D.K.4    Noble, M.5
  • 46
    • 12144290243 scopus 로고    scopus 로고
    • Structure-based assembly of protein complexes in yeast
    • Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, et al. (2004) Structure-based assembly of protein complexes in yeast. Science 303: 2026-2029.
    • (2004) Science , vol.303 , pp. 2026-2029
    • Aloy, P.1    Bottcher, B.2    Ceulemans, H.3    Leutwein, C.4    Mellwig, C.5
  • 48
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 49
    • 13244289800 scopus 로고    scopus 로고
    • Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function
    • Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187: 1135-1160.
    • (2005) J Bacteriol , vol.187 , pp. 1135-1160
    • Kang, Y.1    Weber, K.D.2    Qiu, Y.3    Kiley, P.J.4    Blattner, F.R.5
  • 50
    • 17644381300 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12: Effects of oxygen availability and ArcA
    • Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, et al. (2005) Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem 280: 15084-15096.
    • (2005) J Biol Chem , vol.280 , pp. 15084-15096
    • Salmon, K.A.1    Hung, S.P.2    Steffen, N.R.3    Krupp, R.4    Baldi, P.5
  • 52
    • 10544256600 scopus 로고    scopus 로고
    • Expression monitoring by hybridization to high-density oligonucleotide arrays
    • Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680.
    • (1996) Nat Biotechnol , vol.14 , pp. 1675-1680
    • Lockhart, D.J.1    Dong, H.2    Byrne, M.C.3    Follettie, M.T.4    Gallo, M.V.5
  • 53
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 54
    • 35648957173 scopus 로고    scopus 로고
    • Heme levels switch the function of Hap1 of Saccharomyces cerevisiae between transcriptional activator and transcriptional repressor
    • Hickman MJ, Winston F (2007) Heme levels switch the function of Hap1 of Saccharomyces cerevisiae between transcriptional activator and transcriptional repressor. Mol Cell Biol 27: 7414-7424.
    • (2007) Mol Cell Biol , vol.27 , pp. 7414-7424
    • Hickman, M.J.1    Winston, F.2
  • 55
    • 0042357079 scopus 로고    scopus 로고
    • Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells
    • Bro C, Regenberg B, Lagniel G, Labarre J, Montero-Lomeli M, et al. (2003) Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. J Biol Chem 278: 32141-32149.
    • (2003) J Biol Chem , vol.278 , pp. 32141-32149
    • Bro, C.1    Regenberg, B.2    Lagniel, G.3    Labarre, J.4    Montero-Lomeli, M.5
  • 56
    • 0142059575 scopus 로고    scopus 로고
    • DNA damage and stress transcripts in Saccharomyces cerevisiae mutant sgs1
    • Fry RC, Sambandan TG, Rha C (2003) DNA damage and stress transcripts in Saccharomyces cerevisiae mutant sgs1. Mech Ageing Dev 124: 839-846.
    • (2003) Mech Ageing Dev , vol.124 , pp. 839-846
    • Fry, R.C.1    Sambandan, T.G.2    Rha, C.3
  • 57
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18: 1283-1292.
    • (2001) Mol Biol Evol , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 58
    • 49449110197 scopus 로고    scopus 로고
    • Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size
    • Zhang J, Maslov S, Shakhnovich EI (2008) Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 4: 210.
    • (2008) Mol Syst Biol , vol.4 , pp. 210
    • Zhang, J.1    Maslov, S.2    Shakhnovich, E.I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.