메뉴 건너뛰기




Volumn 12, Issue 1, 2015, Pages 179-192

Identification of protein complexes using weighted PageRank-nibble algorithm and core-attachment structure

Author keywords

PageRank Nibble algorithm; protein complex; Protein interaction network; random walk

Indexed keywords

ALGORITHMS; COMPLEX NETWORKS; MOBILE SECURITY; PROTEINS; RANDOM PROCESSES;

EID: 84923167599     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2014.2343954     Document Type: Article
Times cited : (61)

References (36)
  • 1
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin, "A generic protein purification method for protein complex characterization and proteome exploration," Nature Biotechnol., vol. 17, no. 10, pp. 1030-1032, 1999.
    • (1999) Nature Biotechnol , vol.17 , Issue.10 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6
  • 2
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki, "A comprehensive two-hybrid analysis to explore the yeast protein interactome," Proc. Nat. Acad. Sci., vol. 98, no. 8, pp. 4569-4574, 2001.
    • (2001) Proc. Nat. Acad. Sci , 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
  • 3
    • 84896760571 scopus 로고    scopus 로고
    • Dynamic protein interaction network construction and applications
    • J. Wang, X. Peng, W. Peng, and F.-X. Wu, "Dynamic protein interaction network construction and applications," Proteomics, vol. 14, no. 4/5, pp. 338-352, 2014.
    • (2014) Proteomics , vol.14 , Issue.4-5 , pp. 338-352
    • Wang, J.1    Peng, X.2    Peng, W.3    Wu, F.-X.4
  • 6
    • 0037062448 scopus 로고    scopus 로고
    • Community structure in social and biological networks
    • M. Girvan and M. Newman, "Community structure in social and biological networks," Proc. Nat. Acad. Sci., vol. 99, no. 12, pp. 7821-7826, 2002.
    • (2002) Proc. Nat. Acad. Sci , vol.99 , Issue.12 , pp. 7821-7826
    • Girvan, M.1    Newman, M.2
  • 8
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • A. Enright, S. Van Dongen, and C. Ouzounis, "An efficient algorithm for large-scale detection of protein families," Nucleic Acids Res., vol. 30, no. 7, pp. 1575-1584, 2002.
    • (2002) Nucleic Acids Res , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.1    Van Dongen, S.2    Ouzounis, C.3
  • 9
    • 76749150479 scopus 로고    scopus 로고
    • Computational approaches for detecting protein complexes from protein interaction networks: A survey
    • X. Li, M. Wu, C. Kwoh, and S. Ng, "Computational approaches for detecting protein complexes from protein interaction networks: A survey," BMC Genomics, vol. 11, no. 1, p. S3, 2010.
    • (2010) BMC Genomics , vol.11 , Issue.1 , pp. S3
    • Li, X.1    Wu, M.2    Kwoh, C.3    Ng, S.4
  • 10
    • 77957734120 scopus 로고    scopus 로고
    • MCL-CAW: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure
    • S. Srihari, K. Ning, and H. Leong, "MCL-CAW: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure," BMC Bioinformat., vol. 11, no. 1, p. 504, 2010.
    • (2010) BMC Bioinformat , vol.11 , Issue.1 , pp. 504
    • Srihari, S.1    Ning, K.2    Leong, H.3
  • 11
    • 67650735594 scopus 로고    scopus 로고
    • Complex discovery from weighted PPI networks
    • G. Liu, L. Wong, and H. Chua, "Complex discovery from weighted PPI networks," Bioinformatics, vol. 25, no. 15, pp. 1891-1897, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1891-1897
    • Liu, G.1    Wong, L.2    Chua, H.3
  • 12
    • 33645830948 scopus 로고    scopus 로고
    • Cfinder: Locating cliques and overlapping modules in biological networks
    • B. Adamcsek, G. Palla, I. Farkas, I. Derenyi, and T. Vicsek, "Cfinder: Locating cliques and overlapping modules in biological networks," Bioinformatics, vol. 22, no. 8, pp. 1021-1023, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.3    Derenyi, I.4    Vicsek, T.5
  • 13
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • G. Palla, I. Dernyi, I. Farkas, and T. Vicsek, "Uncovering the overlapping community structure of complex networks in nature and society," Nature, vol. 435, no. 7043, pp. 814-818, 2005.
    • (2005) Nature , vol.435 , Issue.7043 , pp. 814-818
    • Palla, G.1    Dernyi, I.2    Farkas, I.3    Vicsek, T.4
  • 14
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • G. Bader and C. Hogue, "An automated method for finding molecular complexes in large protein interaction networks," BMC Bioinformat., vol. 4, no. 1, p. 2, 2003.
    • (2003) BMC Bioinformat , vol.4 , Issue.1 , pp. 2
    • Bader, G.1    Hogue, C.2
  • 15
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • M. Altaf-Ul-Amin, Y. Shinbo, K. Mihara, K. Kurokawa, and S. Kanaya, "Development and implementation of an algorithm for detection of protein complexes in large interaction networks," BMC Bioinformat., vol. 7, no. 1, p. 207, 2006.
    • (2006) BMC Bioinformat , vol.7 , Issue.1 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 16
    • 54349096842 scopus 로고    scopus 로고
    • Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    • M. Li, J. Chen, J. Wang, B. Hu, and G. Chen, "Modifying the DPClus algorithm for identifying protein complexes based on new topological structures," BMC Bioinformat., vol. 9, no. 1, p. 398, 2008.
    • (2008) BMC Bioinformat , vol.9 , Issue.1 , pp. 398
    • Li, M.1    Chen, J.2    Wang, J.3    Hu, B.4    Chen, G.5
  • 17
    • 79952841798 scopus 로고    scopus 로고
    • A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks
    • J. Wang, M. Li, J. Chen, and Y. Pan, "A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks," IEEE/ACM Trans. Comput. Biol. Bioinformat., vol. 8, no. 3, pp. 607-620, 2011.
    • (2011) IEEE/ACM Trans. Comput. Biol. Bioinformat , vol.8 , Issue.3 , pp. 607-620
    • Wang, J.1    Li, M.2    Chen, J.3    Pan, Y.4
  • 18
    • 77951967208 scopus 로고    scopus 로고
    • SPICi: A fast clustering algorithm for large biological networks
    • P. Jiang and M. Singh, "SPICi: A fast clustering algorithm for large biological networks," Bioinformatics, vol. 26, no. 8, pp. 1105-1111, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 1105-1111
    • Jiang, P.1    Singh, M.2
  • 19
    • 84860361165 scopus 로고    scopus 로고
    • Detecting overlapping protein complexes in protein-protein interaction networks
    • T. Nepusz, H. Yu, and A. Paccanaro, "Detecting overlapping protein complexes in protein-protein interaction networks," Nature Methods, vol. 9, no. 5, pp. 471-472, 2012.
    • (2012) Nature Methods , vol.9 , Issue.5 , pp. 471-472
    • Nepusz, T.1    Yu, H.2    Paccanaro, A.3
  • 21
    • 59649099220 scopus 로고    scopus 로고
    • Predicting protein complexes from PPI data: A core-attachment approach
    • H. Leung, Q. Xiang, S. Yiu, and F. Chin, "Predicting protein complexes from PPI data: A core-attachment approach," J. Comput. Biol., vol. 16, no. 2, pp. 133-144, 2009.
    • (2009) J. Comput. Biol , vol.16 , Issue.2 , pp. 133-144
    • Leung, H.1    Xiang, Q.2    Yiu, S.3    Chin, F.4
  • 22
    • 67649518162 scopus 로고    scopus 로고
    • A core-attachment based method to detect protein complexes in PPI networks
    • M. Wu, X. Li, C. Kwoh, and S. Ng, "A core-attachment based method to detect protein complexes in PPI networks," BMC Bioinformat., vol. 10, no. 1, p. 169, 2009.
    • (2009) BMC Bioinformat , vol.10 , Issue.1 , pp. 169
    • Wu, M.1    Li, X.2    Kwoh, C.3    Ng, S.4
  • 24
    • 84861503105 scopus 로고    scopus 로고
    • Using PageRank to locally partition a graph
    • R. Andersen, F. Chung, and K. Lang, "Using PageRank to locally partition a graph," Internet Math., vol. 4, no. 1, pp. 35-64, 2007.
    • (2007) Internet Math , vol.4 , Issue.1 , pp. 35-64
    • Andersen, R.1    Chung, F.2    Lang, K.3
  • 25
    • 84924178998 scopus 로고    scopus 로고
    • Community structure in large networks: Natural cluster sizes and the absence of large well-defined clusters
    • J. Leskovec, K. Lang, A. Dasgupta, and M. Mahoney, "Community structure in large networks: Natural cluster sizes and the absence of large well-defined clusters," Internet Math., vol. 6, no. 1, pp. 29-123, 2009.
    • (2009) Internet Math , vol.6 , Issue.1 , pp. 29-123
    • Leskovec, J.1    Lang, K.2    Dasgupta, A.3    Mahoney, M.4
  • 26
    • 70449359805 scopus 로고    scopus 로고
    • Finding local communities in protein networks
    • K. Voevodski, S. Teng, and Y. Xia, "Finding local communities in protein networks," BMC Bioinformat., vol. 10, no. 1, p. 297, 2009.
    • (2009) BMC Bioinformat , vol.10 , Issue.1 , pp. 297
    • Voevodski, K.1    Teng, S.2    Xia, Y.3
  • 27
    • 84861515900 scopus 로고    scopus 로고
    • Algorithms to detect multiprotein modularity conserved during evolution
    • L. Hodgkinson, and R. Karp, "Algorithms to detect multiprotein modularity conserved during evolution," IEEE/ACM Trans. Comput. Biol. Bioinformat., vol. 9, no. 4, pp. 1046-1058, 2012.
    • (2012) IEEE/ACM Trans. Comput. Biol. Bioinformat , vol.9 , Issue.4 , pp. 1046-1058
    • Hodgkinson, L.1    Karp, R.2
  • 28
    • 84861492539 scopus 로고    scopus 로고
    • Identification of essential proteins based on edge clustering coefficient
    • J. Wang, M. Li, H. Wang, and Y. Pan, "Identification of essential proteins based on edge clustering coefficient," IEEE/ACM Trans. Comput. Biol. Bioinformat., vol. 9, no. 4, pp. 1070-1080, 2012.
    • (2012) IEEE/ACM Trans. Comput. Biol. Bioinformat , vol.9 , Issue.4 , pp. 1070-1080
    • Wang, J.1    Li, M.2    Wang, H.3    Pan, Y.4
  • 29
    • 84900017400 scopus 로고    scopus 로고
    • Predicting essential proteins based on weighted degree centrality
    • X. Tang, J. Wang, J. Zhong, and Y. Pan, "Predicting essential proteins based on weighted degree centrality," IEEE/ACM Trans. Comput. Biol. Bioinformat., vol. 11, no. 2, pp. 407-418, 2014.
    • (2014) IEEE/ACM Trans. Comput. Biol. Bioinformat , vol.11 , Issue.2 , pp. 407-418
    • Tang, X.1    Wang, J.2    Zhong, J.3    Pan, Y.4
  • 30
    • 84901397951 scopus 로고    scopus 로고
    • Effective identification of essential proteins based on priori knowledge, network topology and gene expressions
    • M. Li, R. Zheng, H. Zhang, J. Wang, and Y. Pan, "Effective identification of essential proteins based on priori knowledge, network topology and gene expressions," Methods, vol. 67, pp. 325-333, 2014.
    • (2014) Methods , vol.67 , pp. 325-333
    • Li, M.1    Zheng, R.2    Zhang, H.3    Wang, J.4    Pan, Y.5
  • 31
    • 70349754527 scopus 로고    scopus 로고
    • RRW: Repeated random walks on genome-scale protein networks for local cluster discovery
    • K. Macropol, T. Can, and A. Singh, "RRW: Repeated random walks on genome-scale protein networks for local cluster discovery," BMC Bioinformat., vol. 10, no. 1, p. 283, 2009.
    • (2009) BMC Bioinformat , vol.10 , Issue.1 , pp. 283
    • Macropol, K.1    Can, T.2    Singh, A.3
  • 32
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions
    • I. Xenarios, L. Salwinski, X. Duan, P. Higney, S. Kim, and D. Eisenberg, "DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions," Nucleic Acids Res., vol. 30, no. 1, pp. 303-305, 2002.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.3    Higney, P.4    Kim, S.5    Eisenberg, D.6
  • 33
    • 79959695371 scopus 로고    scopus 로고
    • A local average connectivity-based method for identifying essential proteins from the network level
    • M. Li, J. Wang, X. Chen, H. Wang, and Y. Pan, "A local average connectivity-based method for identifying essential proteins from the network level," Comput. Biol. Chem., vol. 35, no. 3, pp. 143-150, 2011.
    • (2011) Comput. Biol. Chem , vol.35 , Issue.3 , pp. 143-150
    • Li, M.1    Wang, J.2    Chen, X.3    Wang, H.4    Pan, Y.5
  • 34
    • 63349085550 scopus 로고    scopus 로고
    • Up-to-date catalogues of yeast protein complexes
    • S. Pu, J. Wong, B. Turner, E. Cho, and S. Wodak, "Up-to-date catalogues of yeast protein complexes," Nucleic Acids Res., vol. 37, no. 3, pp. 825-831, 2009.
    • (2009) Nucleic Acids Res , vol.37 , Issue.3 , pp. 825-831
    • Pu, S.1    Wong, J.2    Turner, B.3    Cho, E.4    Wodak, S.5
  • 35
    • 12344269924 scopus 로고    scopus 로고
    • Go::TermFinder-Open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes
    • E. Boyle, S. Weng, J. Gollub, H. Jin, D. Botstein, J. Cherry, and G. Sherlock, "Go::TermFinder-Open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes," Bioinformatics, vol. 20, no. 18, pp. 3710-3715, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.6    Sherlock, G.7
  • 36
    • 0032504104 scopus 로고    scopus 로고
    • A subset of TAF(II)s are integral components of the saga complex required for nucleosome acetylation and transcriptional stimulation
    • P. A. Grant, D. Schieltz, M. G. Pray-Grant, D. J. Steger, J. C. Reese, J. R. Yates III, and J. L. Workman, "A subset of TAF(II)s are integral components of the saga complex required for nucleosome acetylation and transcriptional stimulation." Cell, vol. 94, no. 1, pp. 45-53, 1998.
    • (1998) Cell , vol.94 , Issue.1 , pp. 45-53
    • Grant, P.A.1    Schieltz, D.2    Pray-Grant, M.G.3    Steger, D.J.4    Reese, J.C.5    Yates, J.R.6    Workman, J.L.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.