메뉴 건너뛰기




Volumn 29, Issue 3, 2013, Pages 355-364

A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84873298120     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts688     Document Type: Article
Times cited : (178)

References (49)
  • 1
    • 3042523388 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • DOI 10.1101/gr.2203804
    • Asthana, S. et al. (2004) Predicting protein complex membership using probabilistic network reliability. Genome Res., 14, 1170-1175. (Pubitemid 38811553)
    • (2004) Genome Research , vol.14 , Issue.6 , pp. 1170-1175
    • Asthana, S.1    King, O.D.2    Gibbons, F.D.3    Roth, F.P.4
  • 2
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • Bader, G. and Hogue, C. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol., 20, 991-997.
    • (2002) Nat. Biotechnol , vol.20 , pp. 991-997
    • Bader, G.1    Hogue, C.2
  • 3
    • 33751255087 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein-protein interaction networks
    • Brohee, S. and van Helden, J. (2006) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics, 7, 488.
    • (2006) BMC Bioinformatics , vol.7 , pp. 488
    • Brohee, S.1    Van Helden, J.2
  • 4
    • 77955287981 scopus 로고    scopus 로고
    • Microarray meta-analysis database (m2db): A uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
    • Cheng, W.-C. et al. (2010) Microarray meta-analysis database (m2db): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics, 11, 421.
    • (2010) BMC Bioinformatics , vol.11 , pp. 421
    • Cheng, W.-C.1
  • 5
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • DOI 10.1093/bioinformatics/btl145
    • Chua, H.N. et al. (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 22, 1623-1630. (Pubitemid 43985296)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.-K.2    Wong, L.3
  • 6
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • Chuang, H.Y. et al. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol., 3, 140-140.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 140-140
    • Chuang, H.Y.1
  • 7
    • 6044249965 scopus 로고    scopus 로고
    • Saccharomyces genome database: Underlying principles and organisation
    • Dwight, S. et al. (2004) Saccharomyces genome database: underlying principles and organisation. Brief. Bioinform., 5, 9-22.
    • (2004) Brief. Bioinform , vol.5 , pp. 9-22
    • Dwight, S.1
  • 8
    • 79955787030 scopus 로고    scopus 로고
    • Global geometric affinity for revealing high fidelity protein interaction network
    • Fang, Y. et al. (2011) Global geometric affinity for revealing high fidelity protein interaction network. PLoS ONE, 6, e19349.
    • (2011) PLoS ONE , vol.6
    • Fang, Y.1
  • 9
    • 33847766633 scopus 로고    scopus 로고
    • Random-walk computation of similarities between nodes of a graph with application to collaborative recommendation
    • DOI 10.1109/TKDE.2007.46
    • Fouss, F. et al. (2007) Random-walk computation of similarities between nodes of a graph with application to collaborative recommendation. IEEE Trans. Knowl. Data Eng., 19, 355-369. (Pubitemid 46374533)
    • (2007) IEEE Transactions on Knowledge and Data Engineering , vol.19 , Issue.3 , pp. 355-369
    • Fouss, F.1    Pirotte, A.2    Renders, J.-M.3    Saerens, M.4
  • 10
    • 84945923591 scopus 로고
    • A method for comparing two hierarchical clusterings
    • Fowlkes, E. and Mallows, C. (1983) A method for comparing two hierarchical clusterings. J. Am. Stat. Assoc., 78, 553-569.
    • (1983) J. Am. Stat. Assoc , vol.78 , pp. 553-569
    • Fowlkes, E.1    Mallows, C.2
  • 11
    • 70349212097 scopus 로고    scopus 로고
    • Bootstrapping the interactome: Unsupervised identification of protein complexes in yeast
    • Friedel, C. et al. (2009) Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J. Comput. Biol., 16, 1-17.
    • (2009) J. Comput. Biol , vol.16 , pp. 1-17
    • Friedel, C.1
  • 12
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch, A. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
    • (2000) Mol. Biol. Cell , vol.11 , pp. 4241-4257
    • Gasch, A.1
  • 13
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin, A. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.1
  • 14
    • 0038607954 scopus 로고    scopus 로고
    • Mnd2 and Swm1 are core subunits of the Saccharomyces cerevisiae anaphase-promoting complex
    • DOI 10.1074/jbc.M213109200
    • Hall, M.C. et al. (2003) Mnd2 and swm1 are core subunits of the saccharomyces cerevisiae anaphase-promoting complex. J. Biol. Chem., 278, 16698-16705. (Pubitemid 36799534)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.19 , pp. 16698-16705
    • Hall, M.C.1    Torres, M.P.2    Schroeder, G.K.3    Borchers, C.H.4
  • 15
    • 74249100674 scopus 로고    scopus 로고
    • Genome-wide association data reveal a global map of genetic interactions among protein complexes
    • Hannum, G. et al. (2009) Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet., 5, e1000782.
    • (2009) PLoS Genet , vol.5
    • Hannum, G.1
  • 17
    • 66249129037 scopus 로고    scopus 로고
    • A dynamic network approach for the study of human phenotypes
    • Hidalgo, C. et al. (2009) A dynamic network approach for the study of human phenotypes. PLoS Comput. Biol., 5, e1000353.
    • (2009) PLoS Comput. Biol , vol.5
    • Hidalgo, C.1
  • 18
    • 36949000237 scopus 로고    scopus 로고
    • Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
    • Huang, H. et al. (2007) Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput. Biol., 3, e214.
    • (2007) PLoS Comput. Biol , vol.3
    • Huang, H.1
  • 19
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • DOI 10.1101/gr.071852.107
    • Ideker, T. and Sharan, R. (2008) Protein networks in disease. Genome Res., 18, 644-652. (Pubitemid 351482789)
    • (2008) Genome Research , vol.18 , Issue.4 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 20
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • DOI 10.1038/35075138
    • Jeong, H. et al. (2001) Lethality and centrality in protein networks. Nature, 411, 41-42. (Pubitemid 32428180)
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.-L.3    Oltvai, Z.N.4
  • 21
    • 58149193222 scopus 로고    scopus 로고
    • Human protein reference database-2009 update
    • Keshava Prasad, T.S. et al. (2009) Human protein reference database-2009 update. Nucleic Acids Res., 37, D767-D772.
    • (2009) Nucleic Acids Res , vol.37
    • Keshava Prasad, T.S.1
  • 22
    • 79953645463 scopus 로고    scopus 로고
    • Identifying causal genes and dysregulated pathways in complex diseases
    • Kim, Y. et al. (2011) Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput. Biol., 7, e1001095.
    • (2011) PLoS Comput. Biol , vol.7
    • Kim, Y.1
  • 23
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • DOI 10.1093/bioinformatics/bth351
    • King, A. et al. (2004) Protein complex prediction via cost-based clustering. Bioinformatics, 20, 3013-3020. (Pubitemid 39619193)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 24
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast saccharomyces cerevisiae
    • Krogan, N. et al. (2006) Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature, 440, 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.1
  • 25
    • 70049106408 scopus 로고    scopus 로고
    • Geometric de-noising of protein-protein interaction networks
    • Kuchaiev, O. et al. (2009) Geometric de-noising of protein-protein interaction networks. PLoS Comput. Biol., 5, e1000454.
    • (2009) PLoS Comput. Biol , vol.5
    • Kuchaiev, O.1
  • 26
    • 56649094590 scopus 로고    scopus 로고
    • Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species
    • Lee, K. et al. (2008) Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res., 36, e136.
    • (2008) Nucleic Acids Res , vol.36
    • Lee, K.1
  • 27
    • 33846705486 scopus 로고    scopus 로고
    • Network neighborhood analysis with the multi-node topological overlap measure
    • DOI 10.1093/bioinformatics/btl581
    • Li, A. and Horvath, S. (2007) Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics, 23, 222-231. (Pubitemid 46189613)
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 222-231
    • Li, A.1    Horvath, S.2
  • 29
    • 78751613300 scopus 로고    scopus 로고
    • Link prediction in complex networks: A survey
    • Lü, L. and Zhou, T. (2011) Link prediction in complex networks: a survey. Physica A, 390, 1150-1170.
    • (2011) Physica A , vol.390 , pp. 1150-1170
    • Lü, L.1    Zhou, T.2
  • 31
    • 33644875537 scopus 로고    scopus 로고
    • MIPS: Analysis and annotation of proteins from whole genomes in 2005
    • Mewes, H. et al. (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res., 34, D169-D172.
    • (2006) Nucleic Acids Res , vol.34
    • Mewes, H.1
  • 32
    • 78651455332 scopus 로고    scopus 로고
    • Protein-protein interactions: Making sense of networks via graph-theoretic modeling
    • Przulj, N. (2011) Protein-protein interactions: making sense of networks via graph-theoretic modeling. Bioessays, 33, 115-123.
    • (2011) Bioessays , vol.33 , pp. 115-123
    • Przulj, N.1
  • 34
    • 33750719615 scopus 로고    scopus 로고
    • Identification and evaluation of weak community structures in networks
    • Proceedings of the 21st National Conference on Artificial Intelligence and the 18th Innovative Applications of Artificial Intelligence Conference, AAAI-06/IAAI-06
    • Ruan, J. and Zhang, W. (2006) Identification and evaluation of weak community structures in networks. In Proceedings National Conference on Artificial Intelligence (AAAI-06). Boston, MA, AAAI press, pp. 470-475. (Pubitemid 44705328)
    • (2006) Proceedings of the National Conference on Artificial Intelligence , vol.1 , pp. 470-475
    • Ruan, J.1    Zhang, W.2
  • 35
    • 38349191347 scopus 로고    scopus 로고
    • Identifying network community structures with a high resolution
    • Ruan, J. and Zhang, W. (2008) Identifying network community structures with a high resolution. Phys. Rev. E, 77, 016104.
    • (2008) Phys. Rev. e , vol.77 , pp. 016104
    • Ruan, J.1    Zhang, W.2
  • 36
    • 77951202722 scopus 로고    scopus 로고
    • A fully automated method for discovering community structures in high dimensional data
    • Miami, FL, IEEE
    • Ruan, J. (2009) A fully automated method for discovering community structures in high dimensional data. In Proceedings of IEEE International Conference on Data Mining (ICDM-09). Miami, FL, IEEE.
    • (2009) Proceedings of IEEE International Conference on Data Mining (ICDM-09)
    • Ruan, J.1
  • 37
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan, R. et al. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 88
    • Sharan, R.1
  • 38
    • 78651328883 scopus 로고    scopus 로고
    • The BioGRID interaction database: 2011 update
    • Stark, C. et al. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res., 39, D698-D704.
    • (2011) Nucleic Acids Res , vol.39
    • Stark, C.1
  • 40
    • 34748827346 scopus 로고    scopus 로고
    • Fast random walk with restart and its applications
    • ICDM '06. Washington DC IEEE Computer Society
    • Tong, H. et al. (2006) Fast random walk with restart and its applications. In Proceedings of the Sixth International Conference on Data Mining, 2006, ICDM '06. Washington, DC, IEEE Computer Society, pp. 613-622.
    • (2006) Proceedings of the Sixth International Conference on Data Mining 2006 , pp. 613-622
    • Tong, H.1
  • 41
    • 65449141657 scopus 로고    scopus 로고
    • Identifying functional modules using expression profiles and confidence-scored protein interactions
    • Ulitsky, I. and Shamir, R. (2009) Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics, 25, 1158-1164.
    • (2009) Bioinformatics , vol.25 , pp. 1158-1164
    • Ulitsky, I.1    Shamir, R.2
  • 42
    • 65849100458 scopus 로고    scopus 로고
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    • Vlasblom, J. and Wodak, S. (2009) Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics, 10, 99.
    • (2009) BMC Bioinformatics , vol.10 , pp. 99
    • Vlasblom, J.1    Wodak, S.2
  • 43
    • 40449109730 scopus 로고    scopus 로고
    • Consistent dissection of the protein interaction network by combining global and local metrics
    • Wang, C. et al. (2007a) Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biol., 8, R271.
    • (2007) Genome Biol , vol.8
    • Wang, C.1
  • 44
    • 34447294237 scopus 로고    scopus 로고
    • A new method to measure the semantic similarity of GO terms
    • DOI 10.1093/bioinformatics/btm087
    • Wang, J. et al. (2007b) A new method to measure the semantic similarity of go terms. Bioinformatics, 23, 1274-1281. (Pubitemid 47050544)
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1274-1281
    • Wang, J.Z.1    Du, Z.2    Payattakool, R.3    Yu, P.S.4    Chen, C.-F.5
  • 45
    • 78649679994 scopus 로고    scopus 로고
    • Recent advances in clustering methods for protein interaction networks
    • Wang, J. et al. (2010) Recent advances in clustering methods for protein interaction networks. BMC Genomics, 11 (Suppl. 3), S10.
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 3
    • Wang, J.1
  • 46
    • 77950444122 scopus 로고    scopus 로고
    • Building and analyzing protein interactome networks by cross-species comparisons
    • Wiles, A. et al. (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst. Biol., 4, 36.
    • (2010) BMC Syst. Biol , vol.4 , pp. 36
    • Wiles, A.1
  • 47
    • 77951942707 scopus 로고    scopus 로고
    • Gosemsim: An R package for measuring semantic similarity among go terms and gene products
    • Yu, G. et al. (2010) Gosemsim: an R package for measuring semantic similarity among go terms and gene products. Bioinformatics, 26, 976-978.
    • (2010) Bioinformatics , vol.26 , pp. 976-978
    • Yu, G.1
  • 48
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
    • Yu, H. et al. (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput. Biol., 3, e59.
    • (2007) PLoS Comput. Biol , vol.3
    • Yu, H.1
  • 49
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu, H. et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science, 322, 1158684-1158110.
    • (2008) Science , vol.322 , pp. 1158684-1158110
    • Yu, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.