메뉴 건너뛰기




Volumn 3, Issue 1, 2007, Pages 65-85

Finding molecular complexes through multiple layer clustering of protein interaction networks

Author keywords

Adjacency matrix; Bioinformatics; Categorical; Clustering; Complex; Graph; Interaction; Matrix; Multiple layer; Neighbourhood similarity; Network; Protein

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; MATHEMATICAL COMPUTING; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION;

EID: 33947519922     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2007.011835     Document Type: Article
Times cited : (4)

References (26)
  • 1
    • 0037050004 scopus 로고    scopus 로고
    • Alfarano, T.B., Dewar, C.D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, I.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, E., Pawson, T., Moran, M.E., Durocher, D., Mann, M., Hogue, C.W., Figeys, D. and Tyers, M. (2003) 'Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry', Nature, 415, No. 6868, pp. 180-183.
    • Alfarano, T.B., Dewar, C.D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, I.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, E., Pawson, T., Moran, M.E., Durocher, D., Mann, M., Hogue, C.W., Figeys, D. and Tyers, M. (2003) 'Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry', Nature, Vol. 415, No. 6868, pp. 180-183.
  • 2
    • 24344452310 scopus 로고    scopus 로고
    • MULIC: Multi-Layer Increasing Coherence Clustering of Categorical Data Sets
    • Department of Computer Science and Engineering, York University, Technical Report CS-2004-07
    • Andreopoulos, B., An, A. and Wang, X. (2004) MULIC: Multi-Layer Increasing Coherence Clustering of Categorical Data Sets, Department of Computer Science and Engineering, York University, Technical Report CS-2004-07.
    • (2004)
    • Andreopoulos, B.1    An, A.2    Wang, X.3
  • 3
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • Amau, V., Mars, S. and Marin, I. (2005) 'Iterative cluster analysis of protein interaction data', Bioinformatics, Vol. 21, No. 3, pp.364-378.
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 364-378
    • Amau, V.1    Mars, S.2    Marin, I.3
  • 4
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi, A.L. and Oltvai, Z.N. (2004) 'Network biology: understanding the cell's functional organization', Nature Reviews Genetics, Vol. 5, pp.101-113.
    • (2004) Nature Reviews Genetics , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 5
    • 2942552459 scopus 로고    scopus 로고
    • An autormated method for finding molecular complexes in large protein interaction networks
    • Bader, G. and Hogue, C. (2003) 'An autormated method for finding molecular complexes in large protein interaction networks', BMC Bioinformatics, Vol. 4, No. 2.
    • (2003) BMC Bioinformatics , vol.4 , Issue.2
    • Bader, G.1    Hogue, C.2
  • 8
    • 0242659154 scopus 로고    scopus 로고
    • Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae
    • Dezso, Z., Oltvai, Z.N. and Barabasi, A-L. (2003) 'Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae', Genome Res., Vol. 13, pp.2450-2454.
    • (2003) Genome Res , vol.13 , pp. 2450-2454
    • Dezso, Z.1    Oltvai, Z.N.2    Barabasi, A.-L.3
  • 9
    • 33947525646 scopus 로고    scopus 로고
    • Multi-protein complex data clustering for detecting protein interactions and functional organizations
    • Baltimore, MD, May 26-29
    • Ding, C., He, X., Meraz, R. and Holbrook, S. (2004) 'Multi-protein complex data clustering for detecting protein interactions and functional organizations', Interface 2004: Computational Biology and Bioinformatics, Baltimore, MD, May 26-29.
    • (2004) Interface 2004: Computational Biology and Bioinformatics
    • Ding, C.1    He, X.2    Meraz, R.3    Holbrook, S.4
  • 10
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • March 1
    • 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, March 1, Vol. 6, No. 1, p.39.
    • (2005) BMC Bioinformatics , vol.6 , Issue.1 , pp. 39
    • Dunn, R.1    Dudbridge, F.2    Sanderson, C.M.3
  • 11
    • 0037050026 scopus 로고    scopus 로고
    • A functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M. and Bauer, A. (2003) 'A functional organization of the yeast proteome by systematic analysis of protein complexes', Nature, Vol. 415, No. 6868, pp.141-147.
    • (2003) Nature , vol.415 , Issue.6868 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5    Bauer, A.6
  • 12
    • 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. and 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. and Rothberg, J.M. (2003) 'A protein interaction map of Drosophila melanogaster', Science, Vol. 302, No. 5651, pp. 1727-1736.
  • 13
    • 0000411214 scopus 로고
    • Tabu search, part I
    • Glover, E. (1989) 'Tabu search, part I', ORSA Journal on Computing, Vol. 1, No. 3, pp.190-206.
    • (1989) ORSA Journal on Computing , vol.1 , Issue.3 , pp. 190-206
    • Glover, E.1
  • 14
    • 0034515528 scopus 로고    scopus 로고
    • A clustering algorithm based on graph connectivity
    • Hartuv, E. and Shamir, R. (2000) 'A clustering algorithm based on graph connectivity', Information Processing Letters, Vol. 76, Nos. 4-6, pp. 175-181.
    • (2000) Information Processing Letters , vol.76 , Issue.4-6 , pp. 175-181
    • Hartuv, E.1    Shamir, R.2
  • 15
    • 27144536001 scopus 로고    scopus 로고
    • Extensions to the k-means algorithm for clustering large data sets with categorical values
    • Huang, Z. (1998) 'Extensions to the k-means algorithm for clustering large data sets with categorical values', Data Mining and Knowledge Discovery, Vol. 2, No. 3, pp.283-304.
    • (1998) Data Mining and Knowledge Discovery , vol.2 , Issue.3 , pp. 283-304
    • Huang, Z.1
  • 16
    • 85142147616 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • King, A.D., Prulj, N. and Jurisica, I. (2004) 'Protein complex prediction via cost-based clustering', Bioinformatics, Vol. 20, No. 3, pp.340-348.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 340-348
    • King, A.D.1    Prulj, N.2    Jurisica, I.3
  • 17
    • 9144264169 scopus 로고    scopus 로고
    • Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D.J., 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., 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., Cusick, M.E., Roth, F.P., Hill, D.E. and Vidal, M. (2004) 'A map of the interactome network of the metazoan C. elegans', Science, 303, No. 5657. pp.540-543.
    • Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D.J., 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., 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., Cusick, M.E., Roth, F.P., Hill, D.E. and Vidal, M. (2004) 'A map of the interactome network of the metazoan C. elegans', Science, Vol. 303, No. 5657. pp.540-543.
  • 18
    • 4644302726 scopus 로고    scopus 로고
    • Genomic approach to identification of mutations affecting caspofungin susceptibility in Saccharomyces cerevisiae
    • Markovich, S. (2004) 'Genomic approach to identification of mutations affecting caspofungin susceptibility in Saccharomyces cerevisiae', Antimicrob Agents Chemother, Vol. 48, No. 10, pp.3871-3876.
    • (2004) Antimicrob Agents Chemother , vol.48 , Issue.10 , pp. 3871-3876
    • Markovich, S.1
  • 20
    • 37649028224 scopus 로고    scopus 로고
    • Finding and evaluating community structure in networks
    • Newman, M.E.J, and Girvan, M. (2004) 'Finding and evaluating community structure in networks', Physical Review E, Vol. 69, No. 2, p.026113.
    • (2004) Physical Review E , vol.69 , Issue.2 , pp. 026113
    • Newman, M.E.J.1    Girvan, M.2
  • 21
    • 0346433839 scopus 로고    scopus 로고
    • The yeast protein kinase C cell integrity pathway mediates tolerance to the antifungal drug caspofungin through activation of Slt2p mitogen-activated proteinkinase signaling
    • Reinoso-Martin, C., Schuller, C., Schuetzer-Muehlbauer, M. and Kuchler, K. (2003) 'The yeast protein kinase C cell integrity pathway mediates tolerance to the antifungal drug caspofungin through activation of Slt2p mitogen-activated proteinkinase signaling', Eukaryot Cell, Vol. 2, No. 6, pp.1200-1210, http://www.pdg.cnb.uam.es/UniPub/iHOP/gs/31559.html.
    • (2003) Eukaryot Cell , vol.2 , Issue.6 , pp. 1200-1210
    • Reinoso-Martin, C.1    Schuller, C.2    Schuetzer-Muehlbauer, M.3    Kuchler, K.4
  • 22
    • 0002607026 scopus 로고
    • Bayesian classification (AutoClass): Theory and results
    • AAAI Press, Menlo Park, CA, pp
    • Stutz, J. and Cheeseman, P. (1995) 'Bayesian classification (AutoClass): theory and results', Advances in Knowledge Discovery and Data Mining, AAAI Press, Menlo Park, CA, pp. 153-180.
    • (1995) Advances in Knowledge Discovery and Data Mining , pp. 153-180
    • Stutz, J.1    Cheeseman, P.2
  • 24
    • 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, S.G., Fields, S. and Bork, P. (2002) 'Comparative assessment of large-scale data sets of protein-protein interactions', Nature, Vol. 417, No. 6887, pp.399-403.
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 25
    • 0003736078 scopus 로고    scopus 로고
    • 2nd ed, Prentice-Hall, Upper Saddle River, NJ
    • West, D.B. (2001) Introduction to Graph Theory, 2nd ed., Prentice-Hall, Upper Saddle River, NJ.
    • (2001) Introduction to Graph Theory
    • West, D.B.1
  • 26


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.