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Volumn 8, Issue 1, 2014, Pages

Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery

Author keywords

Core periphery structure; Disease genes; Drug discovery; Essential proteins; Metric spaces; Protein interaction networks; Topological centrality

Indexed keywords

TUMOR SUPPRESSOR PROTEIN;

EID: 84902051575     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-68     Document Type: Article
Times cited : (12)

References (42)
  • 1
    • 84856094560 scopus 로고    scopus 로고
    • Differential network biology
    • Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol 2012, 8(565):565. [http://www.nature.com/doifinder/10.1038/msb.2011.99].
    • (2012) Mol Syst Biol , vol.8 , Issue.565 , pp. 565
    • Ideker, T.1    Krogan, N.J.2
  • 2
    • 79960588850 scopus 로고    scopus 로고
    • Functional integrative levels in the human interactome recapitulate organ organization
    • Souiai O, Becker E, Prieto C, Benkahla A, De Las Rivas J, Brun C. Functional integrative levels in the human interactome recapitulate organ organization. PLoS ONE 2011, 6(7):10. [http://dx.plos.org/10.1371/journal.pone.0022051].
    • (2011) PLoS ONE , vol.6 , Issue.7 , pp. 10
    • Souiai, O.1    Becker, E.2    Prieto, C.3    Benkahla, A.4    De Las Rivas, J.5    Brun, C.6
  • 3
    • 33646112925 scopus 로고    scopus 로고
    • Interactions in protein solutions
    • Sear R. Interactions in protein solutions. Curr Opin Colloid Interface Sci 2006, 11:35-39. [http://linkinghub.elsevier.com/retrieve/pii/S1359029405000610].
    • (2006) Curr Opin Colloid Interface Sci , vol.11 , pp. 35-39
    • Sear, R.1
  • 4
    • 0035970298 scopus 로고    scopus 로고
    • Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
    • Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 2001, 307(3):929-938. [http://www.ncbi.nlm.nih.gov/pubmed/11273711].
    • (2001) J Mol Biol , vol.307 , Issue.3 , pp. 929-938
    • Park, J.1    Lappe, M.2    Teichmann, S.A.3
  • 5
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402(6761 Suppl):C47-52. [http://www.ncbi.nlm.nih.gov/pubmed/10591225].
    • (1999) Nature , vol.402 , Issue.6761 SUPPL
    • Hartwell, L.H.1    Hopfield, J.J.2    Leibler, S.3    Murray, A.W.4
  • 6
    • 0034020583 scopus 로고    scopus 로고
    • Global properties of the metabolic map of Escherichia coli
    • Ouzounis CA, Karp PD. Global properties of the metabolic map of Escherichia coli. Genome Res 2000, 10(4):568-576. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=310896&tool=pmcentrez&rendertype=abstract].
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 568-576
    • Ouzounis, C.A.1    Karp, P.D.2
  • 7
    • 0034175821 scopus 로고    scopus 로고
    • Gene regulation: Towards a circuit engineering discipline
    • McAdams HH, Arkin A. Gene regulation: Towards a circuit engineering discipline. Curr Biol 2000, 10(8):R318-R320. [http://linkinghub.elsevier.com/retrieve/pii/S0960982200004401].
    • (2000) Curr Biol , vol.10 , Issue.8
    • McAdams, H.H.1    Arkin, A.2
  • 8
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403(6767):335-338. [http://dx.doi.org/10.1038/35002125].
    • (2000) Nature , vol.403 , Issue.6767 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 9
    • 0035578429 scopus 로고    scopus 로고
    • Design principles for elementary gene circuits: Elements, methods, and examples
    • Savageau MA. Design principles for elementary gene circuits: Elements, methods, and examples. Chaos Woodbury Ny 2001, 11:142-159. [http://www.ncbi.nlm.nih.gov/pubmed/12779449].
    • (2001) Chaos Woodbury Ny , vol.11 , pp. 142-159
    • Savageau, M.A.1
  • 10
    • 0036901602 scopus 로고    scopus 로고
    • Modeling transcriptional regulatory networks
    • Bolouri H, Davidson EH. Modeling transcriptional regulatory networks. BioEssays 2002, 24(12):1118-1129. [http://www.ncbi.nlm.nih.gov/pubmed/12447977].
    • (2002) BioEssays , vol.24 , Issue.12 , pp. 1118-1129
    • Bolouri, H.1    Davidson, E.H.2
  • 11
    • 0035319006 scopus 로고    scopus 로고
    • Computational studies of gene regulatory networks: in numero molecular biology
    • Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet 2001, 2:268-279.
    • (2001) Nat Rev Genet , vol.2 , pp. 268-279
    • Hasty, J.1    McMillen, D.2    Isaacs, F.3    Collins, J.J.4
  • 12
    • 0037165942 scopus 로고    scopus 로고
    • Combinatorial synthesis of genetic networks
    • Guet CC, Elowitz MB, Hsing W, Leibler S. Combinatorial synthesis of genetic networks. Science 2002, 296(5572):1466-1470. [http://www.ncbi.nlm.nih.gov/pubmed/12029133].
    • (2002) Science , vol.296 , Issue.5572 , pp. 1466-1470
    • Guet, C.C.1    Elowitz, M.B.2    Hsing, W.3    Leibler, S.4
  • 13
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • Newman MEJ. The structure and function of complex networks. SIAM Rev 2003, 45(2):58. [http://arxiv.org/abs/cond-mat/0303516].
    • (2003) SIAM Rev , vol.45 , Issue.2 , pp. 58
    • Newman, M.E.J.1
  • 14
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Nat Acad Sci USA 2003, 100(21):12123-12128. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=218723&tool=pmcentrez&rendertype=abstract].
    • (2003) Proc Nat Acad Sci USA , vol.100 , Issue.21 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 15
    • 84865968015 scopus 로고    scopus 로고
    • Detection of protein complexes using a protein ranking algorithm
    • Zaki N, Berengueres J, Efimov D. Detection of protein complexes using a protein ranking algorithm. Proteins 2012, 80(10):2459-68. [http://www.ncbi.nlm.nih.gov/pubmed/22685080].
    • (2012) Proteins , vol.80 , Issue.10 , pp. 2459-2468
    • Zaki, N.1    Berengueres, J.2    Efimov, D.3
  • 16
    • 84877859040 scopus 로고    scopus 로고
    • Protein complex detection using interaction reliability assessment and weighted clustering coefficient
    • Zaki N, Efimov D, Berengueres J. Protein complex detection using interaction reliability assessment and weighted clustering coefficient. BMC Bioinformatics 2013, 14:163. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3680028&tool=pmcentrez&rendertype=abstract].
    • (2013) BMC Bioinformatics , vol.14 , pp. 163
    • Zaki, N.1    Efimov, D.2    Berengueres, J.3
  • 17
    • 74549134502 scopus 로고    scopus 로고
    • Human cancer protein-protein interaction network: a structural perspective
    • Kar G, Gursoy A, Keskin O. Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol 2009, 5(12):e1000601.
    • (2009) PLoS Comput Biol , vol.5 , Issue.12
    • Kar, G.1    Gursoy, A.2    Keskin, O.3
  • 18
    • 34547672876 scopus 로고    scopus 로고
    • Assessing significance of connectivity and conservation in protein interaction networks
    • Koyutürk M, Szpankowski W, Grama A. Assessing significance of connectivity and conservation in protein interaction networks. J Comput Biol 2007, 14(6):747-764.
    • (2007) J Comput Biol , vol.14 , Issue.6 , pp. 747-764
    • Koyutürk, M.1    Szpankowski, W.2    Grama, A.3
  • 19
    • 33748202182 scopus 로고    scopus 로고
    • Functional clustering of yeast proteins from the protein-protein interaction network
    • Sen TZ, Kloczkowski A, Jernigan RL. Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics 2006, 7:355. [http://www.biomedcentral.com/1471-2105/12/409].
    • (2006) BMC Bioinformatics , vol.7 , pp. 355
    • Sen, T.Z.1    Kloczkowski, A.2    Jernigan, R.L.3
  • 20
    • 48249097433 scopus 로고    scopus 로고
    • The topology of the bacterial co-conserved protein network and its implications for predicting protein function
    • Karimpour-Fard A, Leach SM, Hunter LE, Gill RT. The topology of the bacterial co-conserved protein network and its implications for predicting protein function. BMC Genomics 2008, 9:313. [http://www.ncbi.nlm.nih.gov/pubmed/18590549].
    • (2008) BMC Genomics , vol.9 , pp. 313
    • Karimpour-Fard, A.1    Leach, S.M.2    Hunter, L.E.3    Gill, R.T.4
  • 21
    • 77949728012 scopus 로고    scopus 로고
    • Toponomics: studying protein-protein interactions and protein networks in intact tissue
    • Pierre S, Scholich K. Toponomics: studying protein-protein interactions and protein networks in intact tissue. Mol Biosyst 2010, 6(4):641-647. [http://www.ncbi.nlm.nih.gov/pubmed/20237641].
    • (2010) Mol Biosyst , vol.6 , Issue.4 , pp. 641-647
    • Pierre, S.1    Scholich, K.2
  • 22
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason S, Barabasi A, Oltvai Z. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42. [http://www.ncbi.nlm.nih.gov/pubmed/11333967].
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.2    Barabasi, A.3    Oltvai, Z.4
  • 23
    • 50949092459 scopus 로고    scopus 로고
    • Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
    • Zotenko E, Mestre J, O'Leary D, Przytycka T. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008, 4(8):e1000140.
    • (2008) PLoS Comput Biol , vol.4 , Issue.8
    • Zotenko, E.1    Mestre, J.2    O'Leary, D.3    Przytycka, T.4
  • 24
    • 33745712594 scopus 로고    scopus 로고
    • Why do hubs tend to be essential in protein networks?
    • He X, Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genet 2006, 2(6):e88.
    • (2006) PLoS Genet , vol.2 , Issue.6
    • He, X.1    Zhang, J.2
  • 26
    • 80855134313 scopus 로고    scopus 로고
    • Defining the Role of Essential Genes in Human Disease
    • Dickerson JE, Zhu A, Robertson DL, Hentges KE. Defining the Role of Essential Genes in Human Disease. PLoS ONE 2011, 6(11):e27368. [http://dx.doi.org/10.1371/journal.pone.0027368].
    • (2011) PLoS ONE , vol.6 , Issue.11
    • Dickerson, J.E.1    Zhu, A.2    Robertson, D.L.3    Hentges, K.E.4
  • 28
    • 77952961276 scopus 로고    scopus 로고
    • Network properties of human disease genes with pleiotropic effects
    • Chavali S, Barrenas F, Kanduri K, Benson M. Network properties of human disease genes with pleiotropic effects. BMC Syst Biol 2010, 4:78. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2892460&tool=pmcentrez&rendertype=abstract].
    • (2010) BMC Syst Biol , vol.4 , pp. 78
    • Chavali, S.1    Barrenas, F.2    Kanduri, K.3    Benson, M.4
  • 29
    • 44449119819 scopus 로고    scopus 로고
    • A protein interaction network associated with asthma
    • Hwang S, Son SW, Kim SC, Kim YJ, Jeong H, Lee D. A protein interaction network associated with asthma. J Theor Biol 2008, 252(4):722-731. [http://www.ncbi.nlm.nih.gov/pubmed/18395227].
    • (2008) J Theor Biol , vol.252 , Issue.4 , pp. 722-731
    • Hwang, S.1    Son, S.W.2    Kim, S.C.3    Kim, Y.J.4    Jeong, H.5    Lee, D.6
  • 30
    • 57249114512 scopus 로고    scopus 로고
    • Modularity of cellular networks shows general center-periphery polarization
    • Vinogradov AE. Modularity of cellular networks shows general center-periphery polarization. Bioinformatics 2008, 24(24):2814-2817. [http://www.ncbi.nlm.nih.gov/pubmed/18953046].
    • (2008) Bioinformatics , vol.24 , Issue.24 , pp. 2814-2817
    • Vinogradov, A.E.1
  • 31
    • 67650270380 scopus 로고    scopus 로고
    • Identifying drug-target proteins based on network features
    • Zhu M, Gao L, Li X, Liu Z. Identifying drug-target proteins based on network features. Sci China Series C Life Sci Chin Acad Sci 2009, 52(4):398-404. [http://www.ncbi.nlm.nih.gov/pubmed/19381466].
    • (2009) Sci China Series C Life Sci Chin Acad Sci , vol.52 , Issue.4 , pp. 398-404
    • Zhu, M.1    Gao, L.2    Li, X.3    Liu, Z.4
  • 32
    • 84892473115 scopus 로고    scopus 로고
    • Protein interaction networks as metric spaces: a novel perspective on distribution of hubs
    • Fadhal E, Gamieldien J, Mwambene EC. Protein interaction networks as metric spaces: a novel perspective on distribution of hubs. BMC Syst Biol 2014, 8:6.
    • (2014) BMC Syst Biol , vol.8 , pp. 6
    • Fadhal, E.1    Gamieldien, J.2    Mwambene, E.C.3
  • 33
    • 77952310528 scopus 로고    scopus 로고
    • A human functional protein interaction network and its application to cancer data analysis
    • Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010, 11(5):R53.
    • (2010) Genome Biol , vol.11 , Issue.5
    • Wu, G.1    Feng, X.2    Stein, L.3
  • 34
    • 84863547465 scopus 로고    scopus 로고
    • The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer
    • Li L, Tibiche C, Fu C, Kaneko T, Moran MF, Schiller MR, Li SS, Wang E. The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res 2012, 22(7):1222-1230.
    • (2012) Genome Res , vol.22 , Issue.7 , pp. 1222-1230
    • Li, L.1    Tibiche, C.2    Fu, C.3    Kaneko, T.4    Moran, M.F.5    Schiller, M.R.6    Li, S.S.7    Wang, E.8
  • 37
    • 9244222261 scopus 로고    scopus 로고
    • Targeted cancer therapy
    • Sawyers C. Targeted cancer therapy. Nature 2004, 432(7015):294-7. [http://www.ncbi.nlm.nih.gov/pubmed/15549090].
    • (2004) Nature , vol.432 , Issue.7015 , pp. 294-297
    • Sawyers, C.1
  • 38
    • 84984763775 scopus 로고    scopus 로고
    • Signal transduction as a drug-discovery platform Mapping the key signaling molecules in biochemical pathways will be central
    • Pharmaceuticals A, Pharmaceuticals K. Signal transduction as a drug-discovery platform Mapping the key signaling molecules in biochemical pathways will be central. Nature Biotechnol 2000, VOL 18(3):37-39.
    • (2000) Nature Biotechnol , vol.18 , Issue.3 , pp. 37-39
    • Pharmaceuticals, A.1    Pharmaceuticals, K.2
  • 41
    • 84859267371 scopus 로고    scopus 로고
    • Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery
    • D1128-36
    • Zhu F, Shi Z, Qin C, Tao L, Liu X, Xu F, Zhang L, Song Y, Liu X, Zhang J, Han B, Zhang P, Chen Y. Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res 2012, 40(Database issue):D1128-36. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3245130&tool=pmcentrez&rendertype=abstract].
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Zhu, F.1    Shi, Z.2    Qin, C.3    Tao, L.4    Liu, X.5    Xu, F.6    Zhang, L.7    Song, Y.8    Liu, X.9    Zhang, J.10    Han, B.11    Zhang, P.12    Chen, Y.13
  • 42
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38(suppl 1):D355-D360.
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL. 1
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5


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