메뉴 건너뛰기




Volumn 3, Issue 1, 2009, Pages 68-84

A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks

Author keywords

Bioinformatics; Data mining; Functional modules; LGT; Line graph transformation; Network clustering; PPI; Protein complexes; Protein protein interaction network

Indexed keywords


EID: 63049124067     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2009.023885     Document Type: Article
Times cited : (11)

References (30)
  • 1
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • Bader, G.D. and Hogue, C.W. (2002) 'Analyzing yeast protein-protein interaction data obtained from different sources', Nat. Biotechnol. Vol. 20, pp.991-997.
    • (2002) Nat. Biotechnol , vol.20 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 2
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G.D. and Hogue, C.W. (2003) 'An automated method for finding molecular complexes in large protein interaction networks', BMC Bioinformatics, Vol. 4, p.2.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 3
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization'
    • Barabasi, A. and Oltvai, Z. (2004) 'Network biology: Understanding the cell's functional organization', Nature Rev. Gen., Vol. 5, pp.101-113.
    • (2004) Nature Rev. Gen , vol.5 , pp. 101-113
    • Barabasi, A.1    Oltvai, Z.2
  • 4
    • 1442329655 scopus 로고    scopus 로고
    • Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
    • Brun, C., Chevenet, F., Martin, D., Wojcik, J., Guenoche, A. and Jacq, B. (2003) 'Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network', Genome Biol., Vol. 5, p.R6.
    • (2003) Genome Biol , vol.5
    • Brun, C.1    Chevenet, F.2    Martin, D.3    Wojcik, J.4    Guenoche, A.5    Jacq, B.6
  • 6
    • 34548511546 scopus 로고    scopus 로고
    • Semantic integration to identify overlapping functional modules in protein interaction networks
    • Cho, Y., Hwang, W., Ramanathan, M. and Zhang, A. (2007) 'Semantic integration to identify overlapping functional modules in protein interaction networks', BMC Bioinformatics, Vol. 8, p.265.
    • (2007) BMC Bioinformatics , vol.8 , pp. 265
    • Cho, Y.1    Hwang, W.2    Ramanathan, M.3    Zhang, A.4
  • 7
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • Dunn, R., Dudbridge, F. and Sanderson, C.M. (2005) 'The use of edge-betweenness clustering to investigate biological function in protein interaction networks', BMC Bioinformatics, Vol. 6, p.39.
    • (2005) BMC Bioinformatics , vol.6 , pp. 39
    • Dunn, R.1    Dudbridge, F.2    Sanderson, C.M.3
  • 8
    • 0034786143 scopus 로고    scopus 로고
    • BioLayout - an automatic graph layout algorithm for similarity visualization
    • Enright, A.J. and Ouzounis, C.A. (2001) 'BioLayout - an automatic graph layout algorithm for similarity visualization', Bioinformatics, Vol. 17, No. 9, pp.853-854.
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 853-854
    • Enright, A.J.1    Ouzounis, C.A.2
  • 10
    • 0345600247 scopus 로고    scopus 로고
    • Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C.A., Finley Jr., R.L., White, K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J., Rothberg, J.M. (2003) 'A protein interaction map of drosophila melanogaster', Science, 302, No. 5651, pp.1727-1736.
    • Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C.A., Finley Jr., R.L., White, K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J., Rothberg, J.M. (2003) 'A protein interaction map of drosophila melanogaster', Science, Vol. 302, No. 5651, pp.1727-1736.
  • 12
    • 4644306020 scopus 로고    scopus 로고
    • Analyzing protein function on a genomic scale: The importance of gold-standard positives and negatives for network prediction
    • Jansen, R. and Gerstein, M. (2004) 'Analyzing protein function on a genomic scale: The importance of gold-standard positives and negatives for network prediction', Current Opinion in Microbiology, Vol. 7, pp.535-545.
    • (2004) Current Opinion in Microbiology , vol.7 , pp. 535-545
    • Jansen, R.1    Gerstein, M.2
  • 13
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • King, A.D., Przulj, N. and Jurisica, I. (2004) 'Protein complex prediction via cost-based clustering', Bioinformatics, Vol. 20, No. 17, pp.3013-3020.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 14
    • 9144264169 scopus 로고    scopus 로고
    • Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M. (2004) 'A map of the interactome network of the metazoan C. elegans', Science 303, pp.540-543.
    • Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M. (2004) 'A map of the interactome network of the metazoan C. elegans', Science Vol. 303, pp.540-543.
  • 15
    • 4444281384 scopus 로고    scopus 로고
    • The interactome as a tree - an attempt to visualize the protein-protein interaction network in yeast
    • Lu, H., Zhu, X., Liu, H., Skogerbo, G., Zhang, J., Zhang, Y., Cai, L., Zhao, Y., Sun, S., Xu, J., Bu, D. and Chen, R. (2004) 'The interactome as a tree - an attempt to visualize the protein-protein interaction network in yeast', Nucleic Acids Res., Vol. 32, No. 16, pp.4804-4811.
    • (2004) Nucleic Acids Res , vol.32 , Issue.16 , pp. 4804-4811
    • Lu, H.1    Zhu, X.2    Liu, H.3    Skogerbo, G.4    Zhang, J.5    Zhang, Y.6    Cai, L.7    Zhao, Y.8    Sun, S.9    Xu, J.10    Bu, D.11    Chen, R.12
  • 17
    • 13244251110 scopus 로고    scopus 로고
    • Clustering under the line graph transformation: Application to reaction network
    • Nacher, J.C., Ueda, N., Yamada, T., Kanehisa, M. and Akutsu, T. (2004) 'Clustering under the line graph transformation: Application to reaction network', BMC Bioinformatics, Vol. 5, p.207.
    • (2004) BMC Bioinformatics , vol.5 , pp. 207
    • Nacher, J.C.1    Ueda, N.2    Yamada, T.3    Kanehisa, M.4    Akutsu, T.5
  • 18
    • 12344318211 scopus 로고    scopus 로고
    • Two complementary representations of scale-free networks
    • Nacher, J.C., Yamada, T., Goto, S., Kanehisa, M. and Akutsu, T. (2005) 'Two complementary representations of scale-free networks', Physica A Vol. 349, pp.349-363.
    • (2005) Physica A , vol.349 , pp. 349-363
    • Nacher, J.C.1    Yamada, T.2    Goto, S.3    Kanehisa, M.4    Akutsu, T.5
  • 19
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • Palla, G., Derényi, I., Farkas, I. and Vicsek, T. (2005) 'Uncovering the overlapping community structure of complex networks in nature and society', Nature, Vol. 435, pp.814-818.
    • (2005) Nature , vol.435 , pp. 814-818
    • Palla, G.1    Derényi, I.2    Farkas, I.3    Vicsek, T.4
  • 20
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal, J.B., Enright, A.J. and Ouzounis, C.A. (2004) 'Detection of functional modules from protein interaction networks', Proteins Vol. 54, pp.49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3
  • 21
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N. and Barabasi, A.L. (2002) 'Hierarchical organization of modularity in metabolic networks', Science, Vol. 297, pp.1551-1555.
    • (2002) Science , vol.297 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 22
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • Rives, A.W. and Galitski, T. (2003) 'Modular organization of cellular networks', Proc. Natl. Acad. Sci., USA, Vol. 100, pp.1128-1133.
    • (2003) Proc. Natl. Acad. Sci., USA , vol.100 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 24
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • Segal, E., Wang, H. and Koller, D. (2003) 'Discovering molecular pathways from protein interaction and gene expression data', Bioinformatics, Vol. 19, pp.i264-i272.
    • (2003) Bioinformatics , vol.19
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 25
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan, R., Ulitsky, I. and Shamir, R. (2007) 'Network-based prediction of protein function', Mol. Syst. Biol., Vol. 3, p.88.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 26
    • 13444263410 scopus 로고    scopus 로고
    • Self-similarity of complex networks
    • Song, C., Havlin, S. and Makse, H.A. (2005) 'Self-similarity of complex networks', Nature, Vol. 433, pp.392-395.
    • (2005) Nature , vol.433 , pp. 392-395
    • Song, C.1    Havlin, S.2    Makse, H.A.3
  • 27
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin, V. and Mirny, L.A. (2003) 'Protein complexes and functional modules in molecular networks', Proc. Natl. Acad. Sci., USA, Vol. 100, No. 21, pp.12123-12126.
    • (2003) Proc. Natl. Acad. Sci., USA , vol.100 , Issue.21 , pp. 12123-12126
    • Spirin, V.1    Mirny, L.A.2
  • 28
    • 34548407017 scopus 로고    scopus 로고
    • Discovering functions and revealing mechanisms at molecular level from biological networks
    • Zhang, S., Jin, G., Zhang, X.S. and Chen, L. (2007a) 'Discovering functions and revealing mechanisms at molecular level from biological networks', Proteomics, Vol. 7, No. 16, pp.2856-2869.
    • (2007) Proteomics , vol.7 , Issue.16 , pp. 2856-2869
    • Zhang, S.1    Jin, G.2    Zhang, X.S.3    Chen, L.4
  • 29
    • 34249915290 scopus 로고    scopus 로고
    • Graph kernels, hierarchical clustering, network community structure: Experiment and comparative analysis
    • Zhang, S., Ning, X.M. and Zhang, X.S. (2007c) 'Graph kernels, hierarchical clustering, network community structure: Experiment and comparative analysis', Eur. Phys. J. B., Vol. 57, pp.67-74.
    • (2007) Eur. Phys. J. B , vol.57 , pp. 67-74
    • Zhang, S.1    Ning, X.M.2    Zhang, X.S.3
  • 30
    • 35248856486 scopus 로고    scopus 로고
    • Uncovering fuzzy community structure in complex networks
    • Zhang, S., Wang, R.S. and Zhang, X.S. (2007b) 'Uncovering fuzzy community structure in complex networks', Phys. Rev. E., Vol. 76, p.046103.
    • (2007) Phys. Rev. E , vol.76 , pp. 046103
    • Zhang, S.1    Wang, R.S.2    Zhang, X.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.