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Volumn 11, Issue SUPPL. 4, 2010, Pages

Exploring hierarchical and overlapping modular structure in the yeast protein interaction network

Author keywords

[No Author keywords available]

Indexed keywords

A DENSITY BASED HIERARCHICAL AND OVERLAPPING CLUSTERING; ALGORITHM; ARTICLE; COMPUTER GRAPHICS; INTERMETHOD COMPARISON; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; STATISTICAL ANALYSIS; YEAST; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; SACCHAROMYCES CEREVISIAE;

EID: 78649782914     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S4-S17     Document Type: Article
Times cited : (16)

References (26)
  • 1
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • 10.1038/nature04670, 16554755
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440:637-643. 10.1038/nature04670, 16554755.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 2
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • 10.1038/415180a, 11805837
    • Ho Y, Gruhler A, Heilbut A, Bader G, Moore L, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415:180-183. 10.1038/415180a, 11805837.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.4    Moore, L.5
  • 3
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • 31875, 11283351, 10.1073/pnas.061034498
    • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001, 98:4569-74. 31875, 11283351, 10.1073/pnas.061034498.
    • (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    Sakaki, Y.6
  • 4
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • 10.1038/nrg1272, 14735121
    • Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113. 10.1038/nrg1272, 14735121.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 5
    • 23744481400 scopus 로고    scopus 로고
    • What do we learn from high-throughput protein interaction data?
    • 10.1586/14789450.1.1.111, 15966804
    • Titz B, Schlesner M, Uetz P. What do we learn from high-throughput protein interaction data?. Expert Rev Proteomics 2004, 1:111-121. 10.1586/14789450.1.1.111, 15966804.
    • (2004) Expert Rev Proteomics , vol.1 , pp. 111-121
    • Titz, B.1    Schlesner, M.2    Uetz, P.3
  • 6
    • 77952251569 scopus 로고    scopus 로고
    • Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins
    • 10.1186/1471-2105-11-S3-S3, 20438650
    • Cho YR, Zhang A. Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. BMC Bioinformatics 2010, 11(Suppl 3):S3. 10.1186/1471-2105-11-S3-S3, 20438650.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL 3
    • Cho, Y.R.1    Zhang, A.2
  • 7
    • 75149164017 scopus 로고    scopus 로고
    • A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
    • 10.1186/1471-2105-11-S1-S25, 20122197
    • Chin CH, Chen SH, Ho CW, Ko MT, Lin CY. A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. BMC Bioinformatics 2010, 11(Suppl 1):S25. 10.1186/1471-2105-11-S1-S25, 20122197.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL 1
    • Chin, C.H.1    Chen, S.H.2    Ho, C.W.3    Ko, M.T.4    Lin, C.Y.5
  • 8
  • 10
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • 218723, 14517352, 10.1073/pnas.2032324100
    • Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003, 100:12123-12128. 218723, 14517352, 10.1073/pnas.2032324100.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 11
    • 2942552459 scopus 로고    scopus 로고
    • An automatedmethod for findingmolecular complexes in large protein interaction networks
    • 149346, 12525261, 10.1186/1471-2105-4-2
    • Bader GD, Hogue CW. An automatedmethod for findingmolecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 149346, 12525261, 10.1186/1471-2105-4-2.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 12
    • 33645830948 scopus 로고    scopus 로고
    • CFinder: locating cliques and overlapping modules in biological networks
    • 10.1093/bioinformatics/btl039, 16473872
    • Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22:1021-1023. 10.1093/bioinformatics/btl039, 16473872.
    • (2006) Bioinformatics , vol.22 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.J.3    Derényi, I.4    Vicsek, T.5
  • 13
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • 1473204, 16613608, 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. 1473204, 16613608, 10.1186/1471-2105-7-207.
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 14
    • 54349096842 scopus 로고    scopus 로고
    • Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    • 2570695, 18816408, 10.1186/1471-2105-9-398
    • Li M, Chen J, Wang J, Hu B, Chen G. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 2008, 9:398. 2570695, 18816408, 10.1186/1471-2105-9-398.
    • (2008) BMC Bioinformatics , vol.9 , pp. 398
    • Li, M.1    Chen, J.2    Wang, J.3    Hu, B.4    Chen, G.5
  • 15
    • 0034515057 scopus 로고    scopus 로고
    • The genetics of peroxisome biogenesis
    • 10.1146/annurev.genet.34.1.623, 11092841
    • Sacksteder KA, Gould SJ. The genetics of peroxisome biogenesis. Annu Rev Genet 2000, 34:623-652. 10.1146/annurev.genet.34.1.623, 11092841.
    • (2000) Annu Rev Genet , vol.34 , pp. 623-652
    • Sacksteder, K.A.1    Gould, S.J.2
  • 16
    • 0035184338 scopus 로고    scopus 로고
    • Peroxisome biogenesis
    • 10.1146/annurev.cellbio.17.1.701, 11687502
    • Purdue PE, Lazarow PB. Peroxisome biogenesis. Annu Rev Cell Dev Biol 2001, 17:701-752. 10.1146/annurev.cellbio.17.1.701, 11687502.
    • (2001) Annu Rev Cell Dev Biol , vol.17 , pp. 701-752
    • Purdue, P.E.1    Lazarow, P.B.2
  • 17
    • 0037192780 scopus 로고    scopus 로고
    • COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression
    • 10.1074/jbc.C200023200, 11805083
    • Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A. COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression. J Biol Chem 2002, 277:10753-10755. 10.1074/jbc.C200023200, 11805083.
    • (2002) J Biol Chem , vol.277 , pp. 10753-10755
    • Krogan, N.J.1    Dover, J.2    Khorrami, S.3    Greenblatt, J.F.4    Schneider, J.5    Johnston, M.6    Shilatifard, A.7
  • 18
    • 0036682601 scopus 로고    scopus 로고
    • Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination
    • 126137, 12145212, 10.1093/emboj/cdf390
    • Dichtl B, Blank D, Sadowski M, Hübner W, Weiser S, Keller W. Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination. EMBO J 2002, 21:4125-4135. 126137, 12145212, 10.1093/emboj/cdf390.
    • (2002) EMBO J , vol.21 , pp. 4125-4135
    • Dichtl, B.1    Blank, D.2    Sadowski, M.3    Hübner, W.4    Weiser, S.5    Keller, W.6
  • 19
    • 1642309579 scopus 로고    scopus 로고
    • The essential WD repeat protein Swd2 has dual functions in RNA polymerase II transcription termination and lysine 4 methylation of histone H3
    • 371121, 15024081, 10.1128/MCB.24.7.2932-2943.2004
    • Cheng H, He X, Moore C. The essential WD repeat protein Swd2 has dual functions in RNA polymerase II transcription termination and lysine 4 methylation of histone H3. Mol Cell Biol 2004, 24:2932-2943. 371121, 15024081, 10.1128/MCB.24.7.2932-2943.2004.
    • (2004) Mol Cell Biol , vol.24 , pp. 2932-2943
    • Cheng, H.1    He, X.2    Moore, C.3
  • 20
    • 54349106706 scopus 로고    scopus 로고
    • A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge
    • 2570367, 18801191, 10.1186/1471-2105-9-382
    • Cho YR, Shi L, Ramanathan M, Zhang A. A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. BMC Bioinformatics 2008, 9:382. 2570367, 18801191, 10.1186/1471-2105-9-382.
    • (2008) BMC Bioinformatics , vol.9 , pp. 382
    • Cho, Y.R.1    Shi, L.2    Ramanathan, M.3    Zhang, A.4
  • 21
    • 55449131589 scopus 로고    scopus 로고
    • Probabilistic protein function prediction from heterogeneous genome-wide data
    • 1828618, 17396164, 10.1371/journal.pone.0000337
    • Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE 2007, 2:e337. 1828618, 17396164, 10.1371/journal.pone.0000337.
    • (2007) PLoS ONE , vol.2
    • Nariai, N.1    Kolaczyk, E.D.2    Kasif, S.3
  • 23
    • 43149087837 scopus 로고    scopus 로고
    • Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast
    • Jin G, Zhang S, Zhang XS, Chen L. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS One 2007, 2:el207.
    • (2007) PLoS One , vol.2
    • Jin, G.1    Zhang, S.2    Zhang, X.S.3    Chen, L.4
  • 25
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • 10.1038/35075138, 11333967
    • Jeong H, Mason SP, Barabási 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    Barabási, A.L.3    Oltvai, Z.N.4
  • 26
    • 33745712594 scopus 로고    scopus 로고
    • Why do hubs tend to be essential in protein networks?
    • 1473040, 16751849, 10.1371/journal.pgen.0020088
    • He X, Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genet 2006, 2:e88. 1473040, 16751849, 10.1371/journal.pgen.0020088.
    • (2006) PLoS Genet , vol.2
    • He, X.1    Zhang, J.2


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