메뉴 건너뛰기




Volumn 7, Issue 1, 2009, Pages 1-17

Co-expression among constituents of a motif in the protein-protein interaction network

Author keywords

Co expression; Interaction motif; Microarray; Orthologs; Protein interaction network; Robustness

Indexed keywords

PROTEIN;

EID: 65549090475     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720009003959     Document Type: Article
Times cited : (10)

References (49)
  • 1
    • 0033764169 scopus 로고    scopus 로고
    • The small world of metabolism
    • Fell DA,Wagner A, The small world of metabolism, Nat Biotechnol 18(11):1121-1122, 2000.
    • (2000) Nat Biotechnol , vol.18 , Issue.11 , pp. 1121-1122
    • Fell, D.A.1    Wagner, A.2
  • 2
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • Guelzim N, Bottani S, Bourgine P et al., Topological and causal structure of the yeast transcriptional regulatory network, Nat Genet 31(1):60-63, 2002.
    • (2002) Nat Genet , vol.31 , Issue.1 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3
  • 3
    • 0032077377 scopus 로고    scopus 로고
    • From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli
    • Thieffry D, Huerta AM, Perez-Rueda E et al., From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli, Bioessays 20(5):433-440, 1998.
    • (1998) Bioessays , vol.20 , Issue.5 , pp. 433-440
    • Thieffry, D.1    Huerta, A.M.2    Perez-Rueda, E.3
  • 4
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN, Network biology: Understanding the cell's functional organization, Nat Rev Genet 5(2):101-113, 2004.
    • (2004) Nat Rev Genet , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 5
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields S, Song O, A novel genetic system to detect protein-protein interactions, Nature 340(6230):245-246, 1989.
    • (1989) Nature , vol.340 , Issue.6230 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 6
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito T, Chiba T, Ozawa R et al., A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proc Natl Acad Sci USA 98(8):4569-4574, 2001.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.8 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3
  • 7
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P, Giot L, Cagney G et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature 403(6770):623-627, 2000.
    • (2000) Nature , vol.403 , Issue.6770 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3
  • 8
    • 4444282070 scopus 로고    scopus 로고
    • Studying the interactome with the yeast two-hybrid system and mass spectrometry
    • Causier B, Studying the interactome with the yeast two-hybrid system and mass spectrometry, Mass Spectrom Rev 23(5):350-367, 2004.
    • (2004) Mass Spectrom Rev , vol.23 , Issue.5 , pp. 350-367
    • Causier, B.1
  • 9
    • 0035369531 scopus 로고    scopus 로고
    • Protein-protein interaction maps: A lead towards cellular functions
    • Legrain P, Wojcik J, Gauthier JM, Protein-protein interaction maps: A lead towards cellular functions, Trends Genet 17 (6):346-352, 2001.
    • (2001) Trends Genet , vol.17 , Issue.6 , pp. 346-352
    • Legrain, P.1    Wojcik, J.2    Gauthier, J.M.3
  • 10
    • 0036921994 scopus 로고    scopus 로고
    • Phage display: Practicalities and prospects
    • Willats WG, Phage display: Practicalities and prospects, Plant Mol Biol 50(6):837-854, 2002.
    • (2002) Plant Mol Biol , vol.50 , Issue.6 , pp. 837-854
    • Willats, W.G.1
  • 11
    • 0034841844 scopus 로고    scopus 로고
    • A general procedure of protein complex purification
    • The tandem affinity purification (TAP) method
    • Puig O, Caspary F, Rigaut G et al., The tandem affinity purification (TAP) method: A general procedure of protein complex purification, Methods 24(3):218-229, 2001.
    • (2001) Methods , vol.24 , Issue.3 , pp. 218-229
    • Puig, O.1    Caspary, F.2    Rigaut, G.3
  • 12
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • Rigaut G, Shevchenko A, Rutz B et al., A generic protein purification method for protein complex characterization and proteome exploration, Nat Biotechnol 17(10):1030-1032, 1999.
    • (1999) Nat Biotechnol , vol.17 , Issue.10 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3
  • 13
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M, Mass spectrometry-based proteomics, Nature 422(6928):198-207, 2003.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 14
    • 0037294003 scopus 로고    scopus 로고
    • Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes
    • Bauer A, Kuster B, Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes, Eur J Biochem 270(4):570-578, 2003.
    • (2003) Eur J Biochem , vol.270 , Issue.4 , pp. 570-578
    • Bauer, A.1    Kuster, B.2
  • 15
    • 1842580761 scopus 로고    scopus 로고
    • Functional and topological characterization of protein interaction networks
    • Yook SH, Oltvai ZN, Barabasi AL, Functional and topological characterization of protein interaction networks, Proteomics 4 (4):928-942, 2004.
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 928-942
    • Yook, S.H.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 16
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason SP, Barabasi AL et al., Lethality and centrality in protein networks, Nature 411(6833):41-42, 2001.
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3
  • 17
    • 3042848952 scopus 로고    scopus 로고
    • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    • Han JD, Bertin N, Hao T et al., Evidence for dynamically organized modularity in the yeast protein-protein interaction network, Nature 430(6995):88-93, 2004.
    • (2004) Nature , vol.430 , Issue.6995 , pp. 88-93
    • Han, J.D.1    Bertin, N.2    Hao, T.3
  • 18
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz E, Somera AL, Mongru DA et al., Hierarchical organization of modularity in metabolic networks, Science 297 (5586):1551-1555, 2002.
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3
  • 19
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • Maslov S, Sneppen K, Specificity and stability in topology of protein networks, Science 296(5569):910-913, 2002.
    • (2002) Science , vol.296 , Issue.5569 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2
  • 20
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • Hartwell LH, Hopfield JJ, Leibler S et al., From molecular to modular cell biology, Nature 402 (6761 Suppl):C47-52, 1999.
    • (1999) Nature , vol.402 , Issue.6761 SUPPL.
    • Hartwell, L.H.1    Hopfield, J.J.2    Leibler, S.3
  • 21
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny LA, Protein complexes and functional modules in molecular networks, Proc Natl Acad Sci USA 100 (21):12123-12128, 2003.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.21 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 22
    • 2942695714 scopus 로고    scopus 로고
    • Coevolution of gene expression among interacting proteins
    • Fraser HB, Hirsh AE, Wall DP et al., Coevolution of gene expression among interacting proteins, Proc Natl Acad Sci USA 101 (24):9033-9038, 2004.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.24 , pp. 9033-9038
    • Fraser, H.B.1    Hirsh, A.E.2    Wall, D.P.3
  • 23
    • 2942624159 scopus 로고    scopus 로고
    • Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets
    • Bloom JD, Adami C, Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets, BMC Evol Biol 3:21, 2003.
    • (2003) BMC Evol Biol , vol.3 , pp. 21
    • Bloom, J.D.1    Adami, C.2
  • 24
    • 0842291785 scopus 로고    scopus 로고
    • No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly
    • Jordan IK, Wolf YI, Koonin EV, No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly, BMC Evol Biol 3:1, 2003.
    • (2003) BMC Evol Biol , vol.3 , pp. 1
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 25
    • 33748202182 scopus 로고    scopus 로고
    • Functional clustering of yeast proteins from the protein-protein interaction network
    • Sen TZ, Kloczkowski A, Jernigan RL, Functional clustering of yeast proteins from the protein-protein interaction network, BMC Bioinformatics 7:355, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 355
    • Sen, T.Z.1    Kloczkowski, A.2    Jernigan, R.L.3
  • 26
    • 33644931696 scopus 로고    scopus 로고
    • Stable evolutionary signal in a yeast protein interaction network
    • Wuchty S, Barabasi AL, Ferdig MT, Stable evolutionary signal in a yeast protein interaction network, BMC Evol Biol 6:8, 2006.
    • (2006) BMC Evol Biol , vol.6 , pp. 8
    • Wuchty, S.1    Barabasi, A.L.2    Ferdig, M.T.3
  • 28
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios I, Salwinski L, Duan XJ et al., DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions, Nucleic Acids Res 30(1):303-305, 2002.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3
  • 29
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • Milo R, Shen-Orr S, Itzkovitz S et al., Network motifs: Simple building blocks of complex networks, Science 298 (5594):824-827, 2002.
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3
  • 30
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr SS, Milo R, Mangan S et al., Network motifs in the transcriptional regulation network of Escherichia coli, Nat Genet 31(1):64-68, 2002.
    • (2002) Nat Genet , vol.31 , Issue.1 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3
  • 31
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituents in the yeast protein interaction network
    • Wuchty S, Oltvai ZN, Barabasi AL, Evolutionary conservation of motif constituents in the yeast protein interaction network, Nat Genet 35(2):176-179, 2003.
    • (2003) Nat Genet , vol.35 , Issue.2 , pp. 176-179
    • Wuchty, S.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 32
    • 3543099834 scopus 로고    scopus 로고
    • Evolution and topology in the yeast protein interaction network
    • Wuchty S, Evolution and topology in the yeast protein interaction network, Genome Res 14(7):1310-1314, 2004.
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1310-1314
    • Wuchty, S.1
  • 33
    • 25444531429 scopus 로고    scopus 로고
    • Computational verification of protein-protein interactions by orthologous co-expression
    • Tirosh I, Barkai N, Computational verification of protein-protein interactions by orthologous co-expression, BMC Bioinformatics 6 40, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. 40
    • Tirosh, I.1    Barkai, N.2
  • 34
    • 14744270216 scopus 로고    scopus 로고
    • A first-draft human protein-interaction map
    • Lehner B, Fraser AG, A first-draft human protein-interaction map, Genome Biol 5(9):R63, 2004.
    • (2004) Genome Biol , vol.5 , Issue.9
    • Lehner, B.1    Fraser, A.G.2
  • 35
    • 2442477788 scopus 로고    scopus 로고
    • Genomic analysis of essentiality within protein networks
    • Yu H, Greenbaum D, Xin Lu H et al., Genomic analysis of essentiality within protein networks, Trends Genet 20 (6):227-231, 2004.
    • (2004) Trends Genet , vol.20 , Issue.6 , pp. 227-231
    • Yu, H.1    Greenbaum, D.2    Xin Lu, H.3
  • 36
    • 17944372930 scopus 로고    scopus 로고
    • Serial regulation of transcriptional regulators in the yeast cell cycle
    • Simon I, Barnett J, Hannett N et al., Serial regulation of transcriptional regulators in the yeast cell cycle, Cell 106 (6):697-708, 2001.
    • (2001) Cell , vol.106 , Issue.6 , pp. 697-708
    • Simon, I.1    Barnett, J.2    Hannett, N.3
  • 37
    • 28444448000 scopus 로고    scopus 로고
    • Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
    • Wachi S, Yoneda K, Wu R, Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues, Bioinformatics (Oxford, England) 21(23):4205-4208, 2005.
    • (2005) Bioinformatics (Oxford, England) , vol.21 , Issue.23 , pp. 4205-4208
    • Wachi, S.1    Yoneda, K.2    Wu, R.3
  • 38
    • 0035445792 scopus 로고    scopus 로고
    • A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae
    • Grigoriev A, A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae, Nucleic Acids Res 29 (17):3513-3519, 2001.
    • (2001) Nucleic Acids Res , vol.29 , Issue.17 , pp. 3513-3519
    • Grigoriev, A.1
  • 39
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with protein-protein interactions
    • Jansen R, Greenbaum D, Gerstein M, Relating whole-genome expression data with protein-protein interactions, Genome Res 12(1):37-46, 2002.
    • (2002) Genome Res , vol.12 , Issue.1 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 40
    • 20744456475 scopus 로고    scopus 로고
    • Correlation between gene expression profiles and protein-protein interactions within and across genomes
    • Bhardwaj N, Lu H, Correlation between gene expression profiles and protein-protein interactions within and across genomes, Bioinformatics 21(11):2730-2738, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2730-2738
    • Bhardwaj, N.1    Lu, H.2
  • 41
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC et al., Protein interaction maps for complete genomes based on gene fusion events, Nature 402(6757):86-90, 1999.
    • (1999) Nature , vol.402 , Issue.6757 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3
  • 42
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and inparalogs from pairwise species comparisons
    • Remm M, Storm CE, Sonnhammer EL, Automatic clustering of orthologs and inparalogs from pairwise species comparisons, J Mol Biol 314 (5):1041-1052, 2001.
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 43
    • 0037249405 scopus 로고    scopus 로고
    • The Stanford Microarray Database: Data access and quality assessment tools
    • Gollub J, Ball CA, Binkley G et al., The Stanford Microarray Database: Data access and quality assessment tools, Nucleic Acids Res 31(1):94-96, 2003.
    • (2003) Nucleic Acids Res , vol.31 , Issue.1 , pp. 94-96
    • Gollub, J.1    Ball, C.A.2    Binkley, G.3
  • 44
    • 2642517306 scopus 로고    scopus 로고
    • Application of z-score transformation to Affymetrix data
    • Cheadle C, Cho-Chung YS, Becker KG et al., Application of z-score transformation to Affymetrix data, Appl Bioinformatics 2 (4):209-217, 2003.
    • (2003) Appl Bioinformatics , vol.2 , Issue.4 , pp. 209-217
    • Cheadle, C.1    Cho-Chung, Y.S.2    Becker, K.G.3
  • 46
    • 33748253652 scopus 로고    scopus 로고
    • Predicting essential genes in fungal genomes
    • Seringhaus M, Paccanaro A, Borneman A et al., Predicting essential genes in fungal genomes, Genome Res 16(9):1126-1135, 2006.
    • (2006) Genome Res , vol.16 , Issue.9 , pp. 1126-1135
    • Seringhaus, M.1    Paccanaro, A.2    Borneman, A.3
  • 47
    • 0037173615 scopus 로고    scopus 로고
    • Functional profiling of the Saccharomyces cerevisiae genome
    • Giaever G, Chu AM, Ni L et al., Functional profiling of the Saccharomyces cerevisiae genome, Nature 418 (6896):387-391, 2002.
    • (2002) Nature , vol.418 , Issue.6896 , pp. 387-391
    • Giaever, G.1    Chu, A.M.2    Ni, L.3
  • 48
    • 0038135024 scopus 로고    scopus 로고
    • Computational analyses of high-throughput protein-protein interaction data
    • Chen Y, Xu D, Computational analyses of high-throughput protein-protein interaction data, Curr Protein Pept Sci 4(3):159-181, 2003.
    • (2003) Curr Protein Pept Sci , vol.4 , Issue.3 , pp. 159-181
    • Chen, Y.1    Xu, D.2
  • 49
    • 1542271409 scopus 로고    scopus 로고
    • Predicting protein function from protein/protein interaction data: A probabilistic approach
    • Letovsky S, Kasif S, Predicting protein function from protein/protein interaction data: A probabilistic approach, Bioinformatics 19 (Suppl 1):i197-204, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Letovsky, S.1    Kasif, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.