메뉴 건너뛰기




Volumn 13, Issue 2, 2006, Pages 182-199

Pairwise alignment of protein interaction networks

Author keywords

Evolutionary models; Network alignment; Protein protein interactions

Indexed keywords

AMINO ACID; DNA; JANUS KINASE; PROTEIN; REACTIVE OXYGEN METABOLITE; STAT PROTEIN; UBIQUITIN;

EID: 33645985807     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.182     Document Type: Conference Paper
Times cited : (221)

References (51)
  • 2
    • 3042523388 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • Ashtana, S., King, O.D., Gibbons, F.D., and Roth, F.P. 2004. Predicting protein complex membership using probabilistic network reliability. Genome Res. 14, 1170-1175.
    • (2004) Genome Res. , vol.14 , pp. 1170-1175
    • Ashtana, S.1    King, O.D.2    Gibbons, F.D.3    Roth, F.P.4
  • 4
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G.D., and Hogue, C.W.V. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4(2).
    • (2003) BMC Bioinformatics , vol.4 , Issue.2
    • Bader, G.D.1    Hogue, C.W.V.2
  • 5
    • 0142241336 scopus 로고    scopus 로고
    • Greedily building protein networks with confidence
    • Bader, J.S. 2003. Greedily building protein networks with confidence. Bioinformatics 19, 1869-1874.
    • (2003) Bioinformatics , vol.19 , pp. 1869-1874
    • Bader, J.S.1
  • 6
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabási A., and Albert, R. 1999. Emergence of scaling in random networks. Science 286, 509-512.
    • (1999) Science , vol.286 , pp. 509-512
    • Barabási, A.1    Albert, R.2
  • 7
    • 12444301754 scopus 로고    scopus 로고
    • Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications
    • Berg, J., Lässig, M., and Wagner, A. 2004. Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications. BMC Evol. Biol. 5(51).
    • (2004) BMC Evol. Biol. , vol.5 , Issue.51
    • Berg, J.1    Lässig, M.2    Wagner, A.3
  • 8
    • 0242692460 scopus 로고    scopus 로고
    • Duplication models for biological networks
    • Chung, F., Lu, L., Dewey, T.G., and Galas, D.J. 2003. Duplication models for biological networks. J. Comp. Biol. 10(5), 677-687.
    • (2003) J. Comp. Biol. , vol.10 , Issue.5 , pp. 677-687
    • Chung, F.1    Lu, L.2    Dewey, T.G.3    Galas, D.J.4
  • 9
    • 0038652158 scopus 로고    scopus 로고
    • Spectra of random graphs with given expected degrees
    • Chung, F., Lu, L., and Vu, V. 2003. Spectra of random graphs with given expected degrees. PNAS 100(11), 6313-6318.
    • (2003) PNAS , vol.100 , Issue.11 , pp. 6313-6318
    • Chung, F.1    Lu, L.2    Vu, V.3
  • 10
    • 0035675838 scopus 로고    scopus 로고
    • Genetic analysis of calmodulin and its targets in Saccharomyces cerevisiae
    • Cyert, M.S. et al. 2001. Genetic analysis of calmodulin and its targets in Saccharomyces cerevisiae. Ann. Rev. Genet. 35, 647-672.
    • (2001) Ann. Rev. Genet. , vol.35 , pp. 647-672
    • Cyert, M.S.1
  • 11
    • 0033215210 scopus 로고    scopus 로고
    • Pathway alignment: Application to the comparative analysis of glycolytic enzymes
    • Dandekar, T., Schuster, S., Snel, B., Huynen, M., and Bork, P. 1999. Pathway alignment: Application to the comparative analysis of glycolytic enzymes. Biochem. J. 343, 115-124.
    • (1999) Biochem. J. , vol.343 , pp. 115-124
    • Dandekar, T.1    Schuster, S.2    Snel, B.3    Huynen, M.4    Bork, P.5
  • 12
    • 0642285840 scopus 로고    scopus 로고
    • Preferential attachment in the protein network evolution
    • Eisenberg, E., and Levanon, Y. 2003. Preferential attachment in the protein network evolution. Phys. Rev. Let. 91(13), 138701.
    • (2003) Phys. Rev. Let. , vol.91 , Issue.13 , pp. 138701
    • Eisenberg, E.1    Levanon, Y.2
  • 13
    • 0005259971 scopus 로고    scopus 로고
    • The dense k-subgraph problem
    • Feige, U., Peleg, D., and Kortsarz, G. 2001. The dense k-subgraph problem. Algorithmica 29(3), 410-421.
    • (2001) Algorithmica , vol.29 , Issue.3 , pp. 410-421
    • Feige, U.1    Peleg, D.2    Kortsarz, G.3
  • 14
  • 15
    • 0037126632 scopus 로고    scopus 로고
    • Subunit interaction maps for the regulatory particle of the 26S proteasome and the COP9 signalosome
    • Fu, H. et al. 2001. Subunit interaction maps for the regulatory particle of the 26S proteasome and the COP9 signalosome. EMBO J. 20(24), 7096-7107.
    • (2001) EMBO J. , vol.20 , Issue.24 , pp. 7096-7107
    • Fu, H.1
  • 16
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin, A.C. et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868), 141-147.
    • (2002) Nature , vol.415 , Issue.6868 , pp. 141-147
    • Gavin, A.C.1
  • 17
    • 1842507531 scopus 로고    scopus 로고
    • A statistical framework for combining and interpreting proteomic datasets
    • Gilchrist, M.A., Salter, L.A., and Wagner, A. 2003. A statistical framework for combining and interpreting proteomic datasets. Bioinformatics 20(5), 689-700.
    • (2003) Bioinformatics , vol.20 , Issue.5 , pp. 689-700
    • Gilchrist, M.A.1    Salter, L.A.2    Wagner, A.3
  • 18
    • 0030897031 scopus 로고    scopus 로고
    • Structure of 20S proteasome from yeast at 2.4 Å resolution
    • Groll, M. et al. 1997. Structure of 20S proteasome from yeast at 2.4 Å resolution. Nature 386(6624), 463-471.
    • (1997) Nature , vol.386 , Issue.6624 , pp. 463-471
    • Groll, M.1
  • 20
    • 0012826421 scopus 로고    scopus 로고
    • Approximation algorithms for maximum dispersion
    • Hassin, R., Rubinstein, S., and Tamir, A. 1997. Approximation algorithms for maximum dispersion. Oper. Res. Let. 21, 133-137.
    • (1997) Oper. Res. Let. , vol.21 , pp. 133-137
    • Hassin, R.1    Rubinstein, S.2    Tamir, A.3
  • 21
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisae by mass spectrometry
    • Ho, Y. et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisae by mass spectrometry. Nature 415, 180-183.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1
  • 22
    • 29144474447 scopus 로고    scopus 로고
    • Mining coherent dense subgraphs across massive biological networks for functional discovery
    • Hu, H., Yan, X., Huang, Y., Han, J., and Zhou, X.J. 2005. Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics 21(Suppl. 1), i213-i221.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Hu, H.1    Yan, X.2    Huang, Y.3    Han, J.4    Zhou, X.J.5
  • 23
    • 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., and Sakaki, Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. PNAS 98(8), 4569-4574.
    • (2001) PNAS , vol.98 , Issue.8 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 24
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen, R., Yu, H., Greenbaum, D., et al. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, 449-453.
    • (2003) Science , vol.302 , pp. 449-453
    • Jansen, R.1    Yu, H.2    Greenbaum, D.3
  • 25
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways withing bacteria and yeast as revealed by global protein network alignment
    • Kelley, B.P., Sharan, R., Karp, R.M., Sittler, T., Root, D.E., Stockwell, B.R., and Ideker, T. 2003. Conserved pathways withing bacteria and yeast as revealed by global protein network alignment. PNAS 100(20), 11394-11399.
    • (2003) PNAS , vol.100 , Issue.20 , pp. 11394-11399
    • Kelley, B.P.1    Sharan, R.2    Karp, R.M.3    Sittler, T.4    Root, D.E.5    Stockwell, B.R.6    Ideker, T.7
  • 27
    • 84990479742 scopus 로고
    • An efficient heuristic procedure for partitioning graphs
    • Kernighan, B.W., and Lin, S. 1970. An efficient heuristic procedure for partitioning graphs. The Bell System Tech. J. 49(2), 291-307.
    • (1970) The Bell System Tech. J. , vol.49 , Issue.2 , pp. 291-307
    • Kernighan, B.W.1    Lin, S.2
  • 29
    • 26444593028 scopus 로고    scopus 로고
    • Pairwise local alignment of protein interaction networks guided by models of evolution
    • Koyutürk, M., Grama, A., and Szpankowski, W. 2005. Pairwise local alignment of protein interaction networks guided by models of evolution. RECOMB 2005, Lecture Notes in Bioinformatics, 3500, 48-65.
    • (2005) RECOMB 2005, Lecture Notes in Bioinformatics , vol.3500 , pp. 48-65
    • Koyutürk, M.1    Grama, A.2    Szpankowski, W.3
  • 30
    • 33646016490 scopus 로고    scopus 로고
    • Assessing significance of connectivity and conservation in protein interaction networks
    • Koyutürk, M., Grama, A., and Szpankowski, W. 2006. Assessing significance of connectivity and conservation in protein interaction networks. RECOMB 2006, Lecture Notes in Bioinformatics, 3909, 45-59.
    • (2006) RECOMB 2006, Lecture Notes in Bioinformatics , vol.3909 , pp. 45-59
    • Koyutürk, M.1    Grama, A.2    Szpankowski, W.3
  • 31
    • 3042593155 scopus 로고    scopus 로고
    • Functional evolution of the yeast protein interaction network
    • Kunin, V., Pereira-Leal, J.B., and Ouzounis, C.A. 2004. Functional evolution of the yeast protein interaction network. Mol. Biol. Evol. 21(7), 1171-1176.
    • (2004) Mol. Biol. Evol. , vol.21 , Issue.7 , pp. 1171-1176
    • Kunin, V.1    Pereira-Leal, J.B.2    Ouzounis, C.A.3
  • 32
    • 1942469444 scopus 로고    scopus 로고
    • Network motifs in integrated cellular networks of transcription- regulation and protein-protein interaction
    • Lotem, E.Y., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R.Y., Alon, U., and Margalit, H. 2004. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. PNAS 101(16), 5934-5939.
    • (2004) PNAS , vol.101 , Issue.16 , pp. 5934-5939
    • Lotem, E.Y.1    Sattath, S.2    Kashtan, N.3    Itzkovitz, S.4    Milo, R.5    Pinter, R.Y.6    Alon, U.7    Margalit, H.8
  • 33
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-Satorras, R., Smith, E., and Sole, R.V. 2003. Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222, 199-210.
    • (2003) J. Theor. Biol. , vol.222 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, E.2    Sole, R.V.3
  • 35
    • 0242300098 scopus 로고    scopus 로고
    • Evolution of the yeast protein interaction network
    • Qin, H., Lu, H.H.S., Wu, W.B., and Li, W. 2003. Evolution of the yeast protein interaction network. PNAS 100(22), 12820-12824.
    • (2003) PNAS , vol.100 , Issue.22 , pp. 12820-12824
    • Qin, H.1    Lu, H.H.S.2    Wu, W.B.3    Li, W.4
  • 36
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm, M., Storm, C.E.V., and Sonnhammer, E.L.L. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052.
    • (2001) J. Mol. Biol. , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.V.2    Sonnhammer, E.L.L.3
  • 37
    • 24144486554 scopus 로고    scopus 로고
    • Local modeling of global interactome networks
    • Scholtens, D., Vidal, M., and Gentleman, R. 2005. Local modeling of global interactome networks. Bioinformatics 21(17), 3548-3557.
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3548-3557
    • Scholtens, D.1    Vidal, M.2    Gentleman, R.3
  • 40
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F., and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195-197.
    • (1981) J. Mol. Biol. , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 41
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucl. Acids Res. 28, 33-36.
    • (2000) Nucl. Acids Res. , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 42
    • 0027968068 scopus 로고
    • CLUSTAL-W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL-W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 43
    • 23744481400 scopus 로고    scopus 로고
    • What do we learn from high-throughput protein interaction data?
    • Titz, B., Schlesner, M., and Uetz, P. 2004. What do we learn from high-throughput protein interaction data? Exp. Rev. Prot. 1(1), 111-121.
    • (2004) Exp. Rev. Prot. , vol.1 , Issue.1 , pp. 111-121
    • Titz, B.1    Schlesner, M.2    Uetz, P.3
  • 45
    • 0345305369 scopus 로고    scopus 로고
    • Functional modules by relating protein interaction networks and gene expression
    • Tornow, S., and Mewes, H.W. 2003. Functional modules by relating protein interaction networks and gene expression. Nucl. Acids Res. 31(21), 6283-6289.
    • (2003) Nucl. Acids Res. , vol.31 , Issue.21 , pp. 6283-6289
    • Tornow, S.1    Mewes, H.W.2
  • 47
    • 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(7), 1283-1292.
    • (2001) Mol. Biol. Evol. , vol.18 , Issue.7 , pp. 1283-1292
    • Wagner, A.1
  • 48
    • 0037423828 scopus 로고    scopus 로고
    • How the global structure of protein interaction networks evolves
    • Wagner, A. 2003. How the global structure of protein interaction networks evolves. Proc. R. Soc. Lond. Biol. Sci. 270(1514), 457-466.
    • (2003) Proc. R. Soc. Lond. Biol. Sci. , vol.270 , Issue.1514 , pp. 457-466
    • Wagner, A.1
  • 49
    • 3543099834 scopus 로고    scopus 로고
    • Evolution and topology in the yeast protein interaction network
    • Wuchty, S. 2004. Evolution and topology in the yeast protein interaction network. Genome Res. 14, 1310-1314.
    • (2004) Genome Res. , vol.14 , pp. 1310-1314
    • Wuchty, S.1
  • 50
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituents in the yeast protein interaction network
    • Wuchty, S., Oltvai, Z.N., and Barabási, A.L. 2003. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nature Genet. 35(2), 176-179.
    • (2003) Nature Genet. , vol.35 , Issue.2 , pp. 176-179
    • Wuchty, S.1    Oltvai, Z.N.2    Barabási, A.L.3
  • 51
    • 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, X.J., Higney, P., Kim, S., and Eisenberg, D. 2002. DIP: The Database of Interacting Proteins. A research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30, 303-305.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.5    Eisenberg, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.