메뉴 건너뛰기




Volumn 3, Issue 1, 2010, Pages 31-51

Multi-level integrative analysis of protein-protein interaction networks: Connecting completeness, depth and robustness

Author keywords

Depth; Network analysis; Protein protein interactions; Sampling; Stability

Indexed keywords

BIOLOGICAL MARKER; PROTEIN; PROTEIN BIRC 6; RAC1 PROTEIN; UNCLASSIFIED DRUG;

EID: 77955441935     PISSN: 17560756     EISSN: 17560764     Source Type: Journal    
DOI: 10.1504/IJCBDD.2010.034465     Document Type: Article
Times cited : (3)

References (43)
  • 1
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert, R., Jeong, H. and Barabási, A-L. (2000) 'Error and attack tolerance of complex networks', Nature, Vol. 406, pp.378-382.
    • (2000) Nature , vol.406 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabási, A.-L.3
  • 2
    • 1642463859 scopus 로고    scopus 로고
    • Inflammatory mediators in chronic heart failure: An overview
    • Anker, S.D. and von Haehling, S. (2004) 'Inflammatory mediators in chronic heart failure: an overview', Heart, Vol. 90, pp.464-470. (Pubitemid 38406929)
    • (2004) Heart , vol.90 , Issue.4 , pp. 464-470
    • Anker, S.D.1    Von Haehling, S.2
  • 3
    • 33645832196 scopus 로고    scopus 로고
    • PIANA: Protein interactions and network analysis
    • Aragues, R., Jaeggi, D. and Oliva, B. (2006) 'PIANA: protein interactions and network analysis', Bioinformatics, Vol. 22, pp.1015-1017.
    • (2006) Bioinformatics , vol.22 , pp. 1015-1017
    • Aragues, R.1    Jaeggi, D.2    Oliva, B.3
  • 5
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási, A-L. and Oltvai, Z.N. (2004) 'Network biology: understanding the cell's functional organization', Nat. Rev. Gen., Vol. 5, pp.101-113.
    • (2004) Nat. Rev. Gen. , vol.5 , pp. 101-113
    • Barabási, A.-L.1    Oltvai, Z.N.2
  • 6
    • 0036856356 scopus 로고    scopus 로고
    • A duplication growth model of gene expression networks
    • Bhan, A., Galas, D.J. and Dewey, T.G. (2002) 'A duplication growth model of gene expression networks', Bioinformatics, Vol. 18, pp.1486-1493.
    • (2002) Bioinformatics , vol.18 , pp. 1486-1493
    • Bhan, A.1    Galas, D.J.2    Dewey, T.G.3
  • 8
    • 77955460955 scopus 로고    scopus 로고
    • Impact of PPI network depth and node classification on the identification of biologically relevant targets - A case study
    • Cambridge, UK
    • Blayney, J.K., Wang, H., Zheng, H. and Azuaje, F. (2009b) 'Impact of PPI network depth and node classification on the identification of biologically relevant targets - a case study', Proceedings of IET BioSysBio 2009, Cambridge, UK.
    • (2009) Proceedings of IET BioSysBio , vol.2009
    • Blayney, J.K.1    Wang, H.2    Zheng, H.3    Azuaje, F.4
  • 11
    • 44449144053 scopus 로고    scopus 로고
    • Linking gene expression and functional network data in human heart failure
    • DOI 10.1371/journal.pone.0001347
    • Camargo, A. and Azuaje, F. (2007) 'Linking gene expression and functional network data in human heart failure', PLoS One, Vol. 12, doi:10.1371/journal. pone.0001347. (Pubitemid 351756248)
    • (2007) PLoS ONE , vol.2 , Issue.12
    • Camargo, A.1    Azuaje, F.2
  • 12
    • 56149092205 scopus 로고    scopus 로고
    • Identification of dilated cardiomyopathy signature genes through gene expression and network data integration
    • Camargo, A. and Azuaje, F. (2008) 'Identification of dilated cardiomyopathy signature genes through gene expression and network data integration', Genomics, Vol. 92, pp.404-413.
    • (2008) Genomics , vol.92 , pp. 404-413
    • Camargo, A.1    Azuaje, F.2
  • 13
    • 29644446640 scopus 로고    scopus 로고
    • A neighbourhood evolving network model
    • Cao, Y.J., Wang, G.Z., Jiang, Q.Y. and Han, Z.X. (2006) 'A neighbourhood evolving network model', Phys. Lett. A, Vol. 349, pp.462-466.
    • (2006) Phys. Lett. A , vol.349 , pp. 462-466
    • Cao, Y.J.1    Wang, G.Z.2    Jiang, Q.Y.3    Han, Z.X.4
  • 14
    • 0242692460 scopus 로고    scopus 로고
    • Duplication models for biological networks
    • Chung, F., Lu, L., Dewey, G. and Galas, D.J. (2003) 'Duplication models for biological networks', J. Comput. Biol., Vol. 10, pp.677-687.
    • (2003) J. Comput. Biol. , vol.10 , pp. 677-687
    • Chung, F.1    Lu, L.2    Dewey, G.3    Galas, D.J.4
  • 15
    • 65549138481 scopus 로고    scopus 로고
    • Identifying disease-specific genes based on their topological significance in protein networks
    • doi: 10.1186/1752-0509-3-36
    • Dezso, Z., Nikolsky, Y., Nikolskaya, T., Miller, J., Cherba, D., Webb, C. and Bugrim, A. (2009) 'Identifying disease-specific genes based on their topological significance in protein networks', BMC Syst. Biol., Vol. 3, doi: 10.1186/1752-0509-3-36.
    • (2009) BMC Syst. Biol. , vol.3
    • Dezso, Z.1    Nikolsky, Y.2    Nikolskaya, T.3    Miller, J.4    Cherba, D.5    Webb, C.6    Bugrim, A.7
  • 16
    • 34848826034 scopus 로고    scopus 로고
    • Influence of degree correlations on network structure and stability in protein-protein interaction networks
    • DOI 10.1186/1471-2105-8-297
    • Friedel, C. and Zimmer, R. (2007) 'Influence of degree correlations on network structure and stability in protein-protein interaction networks', BMC Bioinformatics, Vol. 8, doi:10.1186/1471-2105-8-297. (Pubitemid 47497178)
    • (2007) BMC Bioinformatics , vol.8 , pp. 297
    • Friedel, C.C.1    Zimmer, R.2
  • 17
    • 33745088071 scopus 로고    scopus 로고
    • Toward the complete interactome
    • Friedel, C.C. and Zimmer, R. (2006) 'Toward the complete interactome', Nat. Biotech., Vol. 24, pp.614-615.
    • (2006) Nat. Biotech. , vol.24 , pp. 614-615
    • Friedel, C.C.1    Zimmer, R.2
  • 20
    • 24944442468 scopus 로고    scopus 로고
    • Effect of sampling on topology predictions of protein-protein interaction networks
    • Han, J-D.J., Dupuy, D., Bertin, N., Cusick, M.E. and Vidal, M. (2005) 'Effect of sampling on topology predictions of protein-protein interaction networks', Nat. Biotech., Vol. 23, pp.839-844.
    • (2005) Nat. Biotech. , vol.23 , pp. 839-844
    • Han, J.-D.J.1    Dupuy, D.2    Bertin, N.3    Cusick, M.E.4    Vidal, M.5
  • 21
    • 34547558890 scopus 로고    scopus 로고
    • Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution
    • DOI 10.1371/journal.pcbi.0030118
    • Hormozdiari, F., Berenbrink, P., Pržulj, N. and Sahinalp, S.C. (2007) 'Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution', PLoS Comput. Biol., Vol. 3, e118, doi/10.1371/journal.pcbi.0030118. (Pubitemid 47196177)
    • (2007) PLoS Computational Biology , vol.3 , Issue.7 , pp. 1373-1384
    • Hormozdiari, F.1    Berenbrink, P.2    Przulj, N.3    Sahinalp, S.C.4
  • 22
  • 23
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • Joy, M.P., Brock, A., Ingber, D.E. and Huang, S. (2005) 'High-betweenness proteins in the yeast protein interaction network', J. Biomed. Biotech., Vol. 2, pp.96-103.
    • (2005) J. Biomed. Biotech. , vol.2 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 26
    • 32144441867 scopus 로고    scopus 로고
    • Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustness
    • DOI 10.1002/pmic.200500228
    • Li, D., Li, J., Ouyang, S., Wang. J., Wu, S., Wan, P., Zhu, Y., Xu, X. and He, F. (2006) 'Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness', Proteomics, Vol. 6, pp.456-461. (Pubitemid 43208025)
    • (2006) Proteomics , vol.6 , Issue.2 , pp. 456-461
    • Li, D.1    Li, J.2    Ouyang, S.3    Wang, J.4    Wu, S.5    Wan, P.6    Zhu, Y.7    Xu, X.8    He, F.9
  • 28
    • 64049086247 scopus 로고    scopus 로고
    • Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks
    • doi: 10.1186/1752-0509-3-32
    • Lin, W-H., Liu, W.C. and Hwang, M-J. (2009) 'Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks', BMC Syst. Biol., Vol. 3, doi: 10.1186/1752-0509-3-32.
    • (2009) BMC Syst. Biol. , vol.3
    • Lin, W.-H.1    Liu, W.C.2    Hwang, M.-J.3
  • 29
    • 34247217200 scopus 로고    scopus 로고
    • Hubs in biological interaction networks exhibit low changes in expression in experimental asthma
    • DOI 10.1038/msb4100138, PII MSB4100138
    • Lu, X., Jain, V.V., Finn, P.W. and Perkins, D.L. (2007) 'Hubs in biological interaction networks exhibit low changes in expression in experimental data', Mol. Syst. Biol., Vol. 3, doi:10.1038/msb4100138. (Pubitemid 46625184)
    • (2007) Molecular Systems Biology , vol.3 , pp. 98
    • Lu, X.1    Jain, V.V.2    Finn, P.W.3    Perkins, D.L.4
  • 31
    • 65149092690 scopus 로고    scopus 로고
    • Evolution of cooperation on scale-free networks subject to error and attack
    • doi: 10.1088/1367-2630/11/3/033027
    • Perc, M. (2009) 'Evolution of cooperation on scale-free networks subject to error and attack', New Journal of Physics, Vol. 11, doi: 10.1088/1367-2630/ 11/3/033027.
    • (2009) New Journal of Physics , vol.11
    • Perc, M.1
  • 33
    • 84930064585 scopus 로고    scopus 로고
    • Hierarchical organization in complex networks
    • doi:10.1103/PhysRevE.67.026112
    • Ravasz, E. and Barabási, A-L. (2003) 'Hierarchical organization in complex networks', Phys. Rev. E, Vol. 67, doi:10.1103/PhysRevE.67.026112.
    • (2003) Phys. Rev. E , vol.67
    • Ravasz, E.1    Barabási, A.-L.2
  • 34
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N. and Barabási, 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    Barabási, A.L.5
  • 38
    • 15444372528 scopus 로고    scopus 로고
    • Subnets of scale-free networks are not scale-free: Sampling properties of networks
    • Stumpf, M.P.H., Wiuf, C. and May, R.M. (2005) 'Subnets of scale-free networks are not scale-free: Sampling properties of networks', PNAS, Vol. 102, pp.4221-4224.
    • (2005) PNAS , vol.102 , pp. 4221-4224
    • Stumpf, M.P.H.1    Wiuf, C.2    May, R.M.3
  • 39
    • 38549097071 scopus 로고    scopus 로고
    • The uniprot consortium: The universal protein resource (UniProt)
    • UniProt
    • UniProt (2008) 'The uniprot consortium: the universal protein resource (UniProt)', Nucleic Acids Res., Vol. 36, pp.D190-D195.
    • (2008) Nucleic Acids Res. , vol.36
  • 41
    • 39049153521 scopus 로고    scopus 로고
    • Quantitative systems-level determinants of human genes targeted by successful drugs
    • Yao, L. and Rzhestsky, A. (2008) 'Quantitative systems-level determinants of human genes targeted by successful drugs', Gen. Res., Vol. 18, pp.206-213.
    • (2008) Gen. Res. , vol.18 , pp. 206-213
    • Yao, L.1    Rzhestsky, A.2
  • 42
    • 34247549810 scopus 로고    scopus 로고
    • Statistical properties of sampled networks by random walks
    • Yoon, S., Lee, S., Yook, S.H. and Kim, Y. (2007) 'Statistical properties of sampled networks by random walks', Phys. Rev. E, Vol. 75, p.046114.
    • (2007) Phys. Rev. E , vol.75 , pp. 046114
    • Yoon, S.1    Lee, S.2    Yook, S.H.3    Kim, Y.4
  • 43
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
    • DOI 10.1371/journal.pcbi.0030059
    • Yu, H., Kim, P.M., Sprecher, E., Trifonov, V. and Gerstein, M. (2007) 'The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics', PLoS Comput. Biol., Vol. 3, doi:10.1371/journal.pcbi.0030059. (Pubitemid 46683453)
    • (2007) PLoS Computational Biology , vol.3 , Issue.4 , pp. 713-720
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3    Trifonov, V.4    Gerstein, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.