메뉴 건너뛰기




Volumn 18, Issue 6, 2017, Pages 1057-1070

A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks

Author keywords

Biological network; Network descriptor; Network feature; Web server

Indexed keywords

DRUG;

EID: 85039160255     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbw071     Document Type: Article
Times cited : (44)

References (109)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004;5:101-13
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 2
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: a network-based approach to human disease
    • Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2011;12:56-68
    • (2011) Nat Rev Genet , vol.12 , pp. 56-68
    • Barabasi, A.L.1    Gulbahce, N.2    Loscalzo, J.3
  • 3
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: the next paradigm in drug discovery
    • Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008;4:682-90
    • (2008) Nat Chem Biol , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 4
    • 1842580761 scopus 로고    scopus 로고
    • Functional and topological characterization of protein interaction networks
    • Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics 2004;4:928-42
    • (2004) Proteomics , vol.4 , pp. 928-942
    • Yook, S.H.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 5
    • 80052947609 scopus 로고    scopus 로고
    • Introduction to network analysis in systems biology
    • Ma'ayan A. Introduction to network analysis in systems biology. Sci Signal 2011;4:tr5:22-32
    • (2011) Sci Signal , vol.4 , pp. 22-32
    • Ma'ayan, A.1
  • 7
    • 84875275699 scopus 로고    scopus 로고
    • Human diseases through the lens of network biology
    • Furlong LI. Human diseases through the lens of network biology. Trends Genet 2013;29:150-9
    • (2013) Trends Genet , vol.29 , pp. 150-159
    • Furlong, L.I.1
  • 10
    • 77649182705 scopus 로고    scopus 로고
    • Unveiling the role of network and systems biology in drug discovery
    • Pujol A, Mosca R, Farres J, et al. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 2010;31:115-23
    • (2010) Trends Pharmacol Sci , vol.31 , pp. 115-123
    • Pujol, A.1    Mosca, R.2    Farres, J.3
  • 11
    • 84956680067 scopus 로고    scopus 로고
    • Network-based in silico drug efficacy screening
    • Guney E, Menche J, Vidal M, et al. Network-based in silico drug efficacy screening. Nat Commun 2016;7:10331
    • (2016) Nat Commun , vol.7 , pp. 10331
    • Guney, E.1    Menche, J.2    Vidal, M.3
  • 12
    • 84865730611 scopus 로고
    • A set of measures of centrality based on betweenness
    • Freeman LC. A set of measures of centrality based on betweenness. Sociometry 1977;40:35-41
    • (1977) Sociometry , vol.40 , pp. 35-41
    • Freeman, L.C.1
  • 13
    • 84970096342 scopus 로고
    • Transtivity in structural models of small groups
    • Holland PW, Leinhardt S. Transtivity in structural models of small groups. Small Group Res 1971;2:107-24
    • (1971) Small Group Res , vol.2 , pp. 107-124
    • Holland, P.W.1    Leinhardt, S.2
  • 14
    • 51249195602 scopus 로고
    • Structural parameters of communication networks
    • Shimbel A. Structural parameters of communication networks. Bull Math Biophys 1953;15:501-7
    • (1953) Bull Math Biophys , vol.15 , pp. 501-507
    • Shimbel, A.1
  • 15
    • 84926504765 scopus 로고    scopus 로고
    • Cancer: smoother journeys for molecular data
    • Marx V. Cancer: smoother journeys for molecular data. Nat Methods 2015;12:299-302
    • (2015) Nat Methods , vol.12 , pp. 299-302
    • Marx, V.1
  • 16
    • 33845357608 scopus 로고    scopus 로고
    • An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality
    • Yoon J, Blumer A, Lee K. An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics 2006;22:3106-8
    • (2006) Bioinformatics , vol.22 , pp. 3106-3108
    • Yoon, J.1    Blumer, A.2    Lee, K.3
  • 17
    • 39049153521 scopus 로고    scopus 로고
    • Quantitative systems-level determinants of human genes targeted by successful drugs
    • Yao L, Rzhetsky A. Quantitative systems-level determinants of human genes targeted by successful drugs. Genome Res 2008;18:206-13
    • (2008) Genome Res , vol.18 , pp. 206-213
    • Yao, L.1    Rzhetsky, A.2
  • 18
    • 25144498379 scopus 로고    scopus 로고
    • A human proteinprotein interaction network: a resource for annotating the proteome
    • Stelzl U, Worm U, Lalowski M, et al. A human proteinprotein interaction network: a resource for annotating the proteome. Cell 2005;122:957-68
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1    Worm, U.2    Lalowski, M.3
  • 19
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • Maslov S, Sneppen K. Specificity and stability in topology of protein networks. Science 2002;296:910-13
    • (2002) Science , vol.296 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2
  • 22
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3
  • 23
    • 84897470845 scopus 로고    scopus 로고
    • NAViGaTOR: large scalable and interactive navigation and analysis of large graphs
    • Djebbari A, Ali M, Otasek D, et al. NAViGaTOR: large scalable and interactive navigation and analysis of large graphs. Internet Math 2011;7:314-47
    • (2011) Internet Math , vol.7 , pp. 314-347
    • Djebbari, A.1    Ali, M.2    Otasek, D.3
  • 25
    • 84925358621 scopus 로고    scopus 로고
    • VANESA-a software application for the visualization and analysis of networks in system biology applications
    • Brinkrolf C, Janowski SJ, Kormeier B, et al. VANESA-a software application for the visualization and analysis of networks in system biology applications. J Integr Bioinform 2014;11:239
    • (2014) J Integr Bioinform , vol.11 , pp. 239
    • Brinkrolf, C.1    Janowski, S.J.2    Kormeier, B.3
  • 26
    • 0002226683 scopus 로고    scopus 로고
    • Pajek-program for large network analysis
    • Batagelj V, Mrvar A. Pajek-program for large network analysis. Connections 1998;21:47-57
    • (1998) Connections , vol.21 , pp. 47-57
    • Batagelj, V.1    Mrvar, A.2
  • 27
    • 27744490562 scopus 로고    scopus 로고
    • SpectralNET-an application for spectral graph analysis and visualization
    • Forman JJ, Clemons PA, Schreiber SL, et al. SpectralNET-an application for spectral graph analysis and visualization. BMC Bioinformatics 2005;6:260
    • (2005) BMC Bioinformatics , vol.6 , pp. 260
    • Forman, J.J.1    Clemons, P.A.2    Schreiber, S.L.3
  • 28
    • 58149271021 scopus 로고    scopus 로고
    • Integrated network analysis platform for protein-protein interactions
    • Wu J, Vallenius T, Ovaska K, et al. Integrated network analysis platform for protein-protein interactions. Nat Methods 2009;6:75-7
    • (2009) Nat Methods , vol.6 , pp. 75-77
    • Wu, J.1    Vallenius, T.2    Ovaska, K.3
  • 29
    • 48449102450 scopus 로고    scopus 로고
    • Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology
    • Lin CY, Chin CH, Wu HH, et al. Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology. Nucleic Acids Res 2008;36:W438-43
    • (2008) Nucleic Acids Res , vol.36 , pp. W438-W443
    • Lin, C.Y.1    Chin, C.H.2    Wu, H.H.3
  • 30
    • 48449099258 scopus 로고    scopus 로고
    • GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
    • Reimand J, Tooming L, Peterson H, et al. GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Res 2008;36: W452-9
    • (2008) Nucleic Acids Res , vol.36 , pp. W452-W459
    • Reimand, J.1    Tooming, L.2    Peterson, H.3
  • 31
    • 33751375646 scopus 로고    scopus 로고
    • The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
    • Yip KY, Yu H, Kim PM, et al. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 2006;22: 2968-70
    • (2006) Bioinformatics , vol.22 , pp. 2968-2970
    • Yip, K.Y.1    Yu, H.2    Kim, P.M.3
  • 32
    • 23144466889 scopus 로고    scopus 로고
    • VisANT: data-integrating visual framework for biological networks and modules
    • Hu Z, Mellor J, Wu J, et al. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res 2005;33:W352-7
    • (2005) Nucleic Acids Res , vol.33 , pp. W352-W357
    • Hu, Z.1    Mellor, J.2    Wu, J.3
  • 34
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst 2006:1695
    • (2006) InterJ Complex Syst , pp. 1695
    • Csardi, G.1    Nepusz, T.2
  • 35
    • 78650544547 scopus 로고    scopus 로고
    • QuACN: an R package for analyzing complex biological networks quantitatively
    • Mueller LA, Kugler KG, Dander A, et al. QuACN: an R package for analyzing complex biological networks quantitatively. Bioinformatics 2011;27:140-1
    • (2011) Bioinformatics , vol.27 , pp. 140-141
    • Mueller, L.A.1    Kugler, K.G.2    Dander, A.3
  • 36
    • 84861779036 scopus 로고    scopus 로고
    • Topological analysis and interactive visualization of biological networks and protein structures
    • Doncheva NT, Assenov Y, Domingues FS, et al. Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc 2012;7:670-85
    • (2012) Nat Protoc , vol.7 , pp. 670-685
    • Doncheva, N.T.1    Assenov, Y.2    Domingues, F.S.3
  • 37
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz E, Somera AL, Mongru DA, et al. Hierarchical organization of modularity in metabolic networks. Science 2002;297:1551-5
    • (2002) Science , vol.297 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3
  • 38
    • 0037197886 scopus 로고    scopus 로고
    • The identification of functional modules from the genomic association of genes
    • Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 2002;99:5890-5
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5890-5895
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 39
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol 2007;3:88
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 40
    • 84862663073 scopus 로고    scopus 로고
    • Predicting candidate genes based on combined network topological features: a case study in coronary artery disease
    • Zhang L, Li X, Tai J, et al. Predicting candidate genes based on combined network topological features: a case study in coronary artery disease. PLoS One 2012;7:e39542
    • (2012) PLoS One , vol.7
    • Zhang, L.1    Li, X.2    Tai, J.3
  • 41
    • 84875963165 scopus 로고    scopus 로고
    • Drug target prediction and repositioning using an integrated network-based approach
    • Emig D, Ivliev A, Pustovalova O, et al. Drug target prediction and repositioning using an integrated network-based approach. PLoS One 2013;8:e60618
    • (2013) PLoS One , vol.8
    • Emig, D.1    Ivliev, A.2    Pustovalova, O.3
  • 42
    • 84862249788 scopus 로고    scopus 로고
    • Prioritizing disease candidate genes by a gene interconnectedness-based approach
    • Hsu CL, Huang YH, Hsu CT, et al. Prioritizing disease candidate genes by a gene interconnectedness-based approach. BMC Genomics 2011;12(Suppl 3):S25
    • (2011) BMC Genomics , vol.12 , pp. S25
    • Hsu, C.L.1    Huang, Y.H.2    Hsu, C.T.3
  • 43
    • 84878889476 scopus 로고    scopus 로고
    • A vertex similaritybased framework to discover and rank orphan diseaserelated genes
    • Zhu C, Kushwaha A, Berman K, et al. A vertex similaritybased framework to discover and rank orphan diseaserelated genes. BMC Syst Biol 2012;6 (Suppl 3):S8
    • (2012) BMC Syst Biol , vol.6 , pp. S8
    • Zhu, C.1    Kushwaha, A.2    Berman, K.3
  • 44
    • 84864070819 scopus 로고    scopus 로고
    • A network-based feature selection approach to identify metabolic signatures in disease
    • Netzer M, Kugler KG, Muller LA, et al. A network-based feature selection approach to identify metabolic signatures in disease. J Theor Biol 2012;310:216-22
    • (2012) J Theor Biol , vol.310 , pp. 216-222
    • Netzer, M.1    Kugler, K.G.2    Muller, L.A.3
  • 45
    • 77953433317 scopus 로고    scopus 로고
    • Centrality analysis methods for biological networks and their application to gene regulatory networks
    • Dirk Koschützki FS. Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul Syst Bio 2008;2:193-201
    • (2008) Gene Regul Syst Bio , vol.2 , pp. 193-201
    • Dirk Koschützki, F.S.1
  • 46
    • 84888014252 scopus 로고    scopus 로고
    • Connecting the dots: applications of network medicine in pharmacology and disease
    • Jacunski A, Tatonetti NP. Connecting the dots: applications of network medicine in pharmacology and disease. Clin Pharmacol Ther 2013;94:659-69
    • (2013) Clin Pharmacol Ther , vol.94 , pp. 659-669
    • Jacunski, A.1    Tatonetti, N.P.2
  • 47
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • Joy MP, Brock A, Ingber DE, et al. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005;2005:96-103
    • (2005) J Biomed Biotechnol , vol.2005 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3
  • 48
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
    • Yu H, Kim PM, Sprecher E, et al. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007;3:e59
    • (2007) PLoS Comput Biol , vol.3
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3
  • 49
    • 84888011244 scopus 로고    scopus 로고
    • Network-based approaches in drug discovery and early development
    • Harrold JM, Ramanathan M, Mager DE. Network-based approaches in drug discovery and early development. Clin Pharmacol Ther 2013;94:651-8
    • (2013) Clin Pharmacol Ther , vol.94 , pp. 651-658
    • Harrold, J.M.1    Ramanathan, M.2    Mager, D.E.3
  • 51
    • 84873815205 scopus 로고    scopus 로고
    • Equal opportunity for lowdegree network nodes: a PageRank-based method for protein target identification in metabolic graphs
    • Banky D, Ivan G, Grolmusz V. Equal opportunity for lowdegree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PLoS One 2013;8:e54204
    • (2013) PLoS One , vol.8
    • Banky, D.1    Ivan, G.2    Grolmusz, V.3
  • 52
    • 84863677563 scopus 로고    scopus 로고
    • Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes
    • Winter C, Kristiansen G, Kersting S, et al. Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes. PLoS Comput Biol 2012;8:e1002511
    • (2012) PLoS Comput Biol , vol.8
    • Winter, C.1    Kristiansen, G.2    Kersting, S.3
  • 53
    • 55349094009 scopus 로고    scopus 로고
    • Mining protein networks for synthetic genetic interactions
    • Paladugu SR, Zhao S, Ray A, et al. Mining protein networks for synthetic genetic interactions. BMC Bioinformatics 2008;9:426
    • (2008) BMC Bioinformatics , vol.9 , pp. 426
    • Paladugu, S.R.1    Zhao, S.2    Ray, A.3
  • 54
    • 77955106017 scopus 로고    scopus 로고
    • A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
    • You ZH, Yin Z, Han K, et al. A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. BMC Bioinformatics 2010;11:343
    • (2010) BMC Bioinformatics , vol.11 , pp. 343
    • You, Z.H.1    Yin, Z.2    Han, K.3
  • 55
    • 84855378129 scopus 로고    scopus 로고
    • NEW: network-enabled wisdom in biology, medicine and healthcare
    • Schadt EE, Björkegren JL. NEW: network-enabled wisdom in biology, medicine and healthcare. Sci Transl Med 2012;4:115rv111
    • (2012) Sci Transl Med , vol.4
    • Schadt, E.E.1    Björkegren, J.L.2
  • 56
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005;4:Article17
    • (2005) Stat Appl Genet Mol Biol , vol.4
    • Zhang, B.1    Horvath, S.2
  • 58
    • 84915798929 scopus 로고    scopus 로고
    • Identification of important nodes in directed biological networks: a betwork motif approach
    • Pei Wang JL, Yu X. Identification of important nodes in directed biological networks: a betwork motif approach. PLoS One 2014;9:e106132
    • (2014) PLoS One , vol.9
    • Pei Wang, J.L.1    Yu, X.2
  • 59
    • 34447512704 scopus 로고    scopus 로고
    • Understanding network concepts in modules
    • Dong J, Horvath S. Understanding network concepts in modules. BMC Syst Biol 2007;1:24
    • (2007) BMC Syst Biol , vol.1 , pp. 24
    • Dong, J.1    Horvath, S.2
  • 60
    • 77954385460 scopus 로고    scopus 로고
    • Complex network measures of brain connectivity: uses and interpretations
    • Rubinov M, Sporns O. Complex network measures of brain connectivity: uses and interpretations. Neuroimage 2010;52:1059-69
    • (2010) Neuroimage , vol.52 , pp. 1059-1069
    • Rubinov, M.1    Sporns, O.2
  • 61
    • 79960325408 scopus 로고    scopus 로고
    • Networks for systems biology: conceptual connection of data and function
    • Emmert-Streib F, Dehmer M. Networks for systems biology: conceptual connection of data and function. IET Syst Biol 2011;5:185-207
    • (2011) IET Syst Biol , vol.5 , pp. 185-207
    • Emmert-Streib, F.1    Dehmer, M.2
  • 63
    • 39649124450 scopus 로고    scopus 로고
    • What is a complex graph?
    • Kim J, Wilhelm T. What is a complex graph? Physica A 2008;387:2637-52
    • (2008) Physica A , vol.387 , pp. 2637-2652
    • Kim, J.1    Wilhelm, T.2
  • 64
    • 80053904998 scopus 로고    scopus 로고
    • A network-based approach to classify the three domains of life
    • Mueller LA, Kugler KG, Netzer M, et al. A network-based approach to classify the three domains of life. Biol Direct 2011;6:53
    • (2011) Biol Direct , vol.6 , pp. 53
    • Mueller, L.A.1    Kugler, K.G.2    Netzer, M.3
  • 65
    • 77958091914 scopus 로고    scopus 로고
    • A history of graph entropy measures
    • Dehmer M, Mowshowitz A. A history of graph entropy measures. Inf Sci 2011;181:57-78
    • (2011) Inf Sci , vol.181 , pp. 57-78
    • Dehmer, M.1    Mowshowitz, A.2
  • 66
    • 84857678752 scopus 로고    scopus 로고
    • Information indices with high discriminative power for graphs
    • Dehmer M, Grabner M, Varmuza K. Information indices with high discriminative power for graphs. PLoS One 2012;7:e31214
    • (2012) PLoS One , vol.7
    • Dehmer, M.1    Grabner, M.2    Varmuza, K.3
  • 67
    • 84857799805 scopus 로고    scopus 로고
    • Uniquely discriminating molecular structures using novel eigenvalue-based descriptors
    • Dehmer M. Uniquely discriminating molecular structures using novel eigenvalue-based descriptors. MATCH Commun Math Comput Chem 2012;67:147-72
    • (2012) MATCH Commun Math Comput Chem , vol.67 , pp. 147-172
    • Dehmer, M.1
  • 68
    • 79551609075 scopus 로고    scopus 로고
    • When the web meets the cell: using personalized PageRank for analyzing protein interaction networks
    • Ivan G, Grolmusz V. When the web meets the cell: using personalized PageRank for analyzing protein interaction networks. Bioinformatics 2011;27:405-7
    • (2011) Bioinformatics , vol.27 , pp. 405-407
    • Ivan, G.1    Grolmusz, V.2
  • 69
    • 33847254923 scopus 로고    scopus 로고
    • Generalizations of the clustering coefficient to weighted complex networks
    • Saramäki J, Kivelä M, Onnela JP, et al. Generalizations of the clustering coefficient to weighted complex networks. Phys Rev E 2007;75:027105
    • (2007) Phys Rev E , vol.75
    • Saramäki, J.1    Kivelä, M.2    Onnela, J.P.3
  • 70
    • 33747816816 scopus 로고    scopus 로고
    • PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • Li ZR, Lin HH, Han LY, et al. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 2006;34:W32-7
    • (2006) Nucleic Acids Res , vol.34 , pp. W32-W37
    • Li, Z.R.1    Lin, H.H.2    Han, L.Y.3
  • 71
    • 79959928391 scopus 로고    scopus 로고
    • Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • Rao HB, Zhu F, Yang GB, et al. Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 2011;39:W385-90
    • (2011) Nucleic Acids Res , vol.39 , pp. W385-W390
    • Rao, H.B.1    Zhu, F.2    Yang, G.B.3
  • 72
    • 78651332286 scopus 로고    scopus 로고
    • Pathway commons, a web resource for biological pathway data
    • Cerami EG, Gross BE, Demir E, et al. Pathway commons, a web resource for biological pathway data. Nucleic Acids Res 2011;39:D685-90
    • (2011) Nucleic Acids Res , vol.39 , pp. D685-D690
    • Cerami, E.G.1    Gross, B.E.2    Demir, E.3
  • 73
    • 77349091815 scopus 로고    scopus 로고
    • NetPath: a public resource of curated signal transduction pathways
    • Kandasamy K, Mohan SS, Raju R, et al. NetPath: a public resource of curated signal transduction pathways. Genome Biol 2010;11:R3
    • (2010) Genome Biol , vol.11 , pp. R3
    • Kandasamy, K.1    Mohan, S.S.2    Raju, R.3
  • 75
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998;393:440-2
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 76
    • 13944252976 scopus 로고    scopus 로고
    • A measure of betweenness centrality based on random walks
    • Newman MEJ. A measure of betweenness centrality based on random walks. Soc Networks 2003;27:39-54
    • (2003) Soc Networks , vol.27 , pp. 39-54
    • Newman, M.E.J.1
  • 77
    • 34147120474 scopus 로고
    • A note on two problems in connexion with graphs
    • Dijkstra EW. A note on two problems in connexion with graphs. Numer Math 1959;1:269-71
    • (1959) Numer Math , vol.1 , pp. 269-271
    • Dijkstra, E.W.1
  • 78
    • 0035648637 scopus 로고    scopus 로고
    • A faster algorithm for betweenness centrality
    • Brandes U. A faster algorithm for betweenness centrality. J Math Sociol 2001;25:163-77
    • (2001) J Math Sociol , vol.25 , pp. 163-177
    • Brandes, U.1
  • 79
    • 33244458912 scopus 로고    scopus 로고
    • Laplacian energy of a graph
    • Gutman I, Zhou B. Laplacian energy of a graph. Linear Algebra Appl 2006;414:29-37
    • (2006) Linear Algebra Appl , vol.414 , pp. 29-37
    • Gutman, I.1    Zhou, B.2
  • 81
    • 0042093610 scopus 로고    scopus 로고
    • The connectivity structure, giant strong component and centrality of metabolic networks
    • Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003;19:1423-30
    • (2003) Bioinformatics , vol.19 , pp. 1423-1430
    • Ma, H.W.1    Zeng, A.P.2
  • 82
    • 84877983676 scopus 로고    scopus 로고
    • Node-weighted interacting network measures improve the representation of real-world complex systems
    • Wiedermann M, Donges JF, Heitzig J, et al. Node-weighted interacting network measures improve the representation of real-world complex systems. EPL 2013;102:28007
    • (2013) EPL , vol.102 , pp. 28007
    • Wiedermann, M.1    Donges, J.F.2    Heitzig, J.3
  • 83
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • UniProt C. UniProt: a hub for protein information. Nucleic Acids Res 2015;43:D204-12
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
    • UniProt, C.1
  • 84
    • 84946735654 scopus 로고    scopus 로고
    • Gene Ontology Consortium: going forward
    • Gene Ontology C. Gene Ontology Consortium: going forward. Nucleic Acids Res 2015;43:D1049-56
    • (2015) Nucleic Acids Res , vol.43 , pp. D1049-D1056
    • Gene Ontology, C.1
  • 85
    • 64049086247 scopus 로고    scopus 로고
    • Topological and organizational properties of the products of house-keeping and tissuespecific genes in protein-protein interaction networks
    • Lin WH, Liu WC, Hwang MJ. Topological and organizational properties of the products of house-keeping and tissuespecific genes in protein-protein interaction networks. BMC Syst Biol 2009;3:32
    • (2009) BMC Syst Biol , vol.3 , pp. 32
    • Lin, W.H.1    Liu, W.C.2    Hwang, M.J.3
  • 86
    • 85039150228 scopus 로고    scopus 로고
    • Computational methods to identify metabolic sub-networks based on metabolomic profiles
    • Frainay C, Jourdan F. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Brief Bioinform 2016;pii: bbv115
    • (2016) Brief Bioinform
    • Frainay, C.1    Jourdan, F.2
  • 87
    • 84879911126 scopus 로고    scopus 로고
    • Simple topological properties predict functional misannotations in a metabolic network
    • Liberal R, Pinney JW. Simple topological properties predict functional misannotations in a metabolic network. Bioinformatics 2013;29:i154-61
    • (2013) Bioinformatics , vol.29 , pp. i154-i161
    • Liberal, R.1    Pinney, J.W.2
  • 88
    • 70350482286 scopus 로고    scopus 로고
    • Evolution of biomolecular networks: lessons from metabolic and protein interactions
    • Yamada T, Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 2009;10:791-803
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 791-803
    • Yamada, T.1    Bork, P.2
  • 89
    • 55749096609 scopus 로고    scopus 로고
    • Phylogenetic distances are encoded in networks of interacting pathways
    • Mazurie A, Bonchev D, Schwikowski B, et al. Phylogenetic distances are encoded in networks of interacting pathways. Bioinformatics 2008;24:2579-85
    • (2008) Bioinformatics , vol.24 , pp. 2579-2585
    • Mazurie, A.1    Bonchev, D.2    Schwikowski, B.3
  • 90
    • 0035931072 scopus 로고    scopus 로고
    • A compendium of gene expression in normal human tissues
    • Hsiao LL, Dangond F, Yoshida T, et al. A compendium of gene expression in normal human tissues. Physiol Genomics 2001;7:97-104
    • (2001) Physiol Genomics , vol.7 , pp. 97-104
    • Hsiao, L.L.1    Dangond, F.2    Yoshida, T.3
  • 91
    • 10744224197 scopus 로고    scopus 로고
    • Development of human protein reference database as an initial platform for approaching systems biology in humans
    • Peri S, Navarro JD, Amanchy R, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003;13:2363-71
    • (2003) Genome Res , vol.13 , pp. 2363-2371
    • Peri, S.1    Navarro, J.D.2    Amanchy, R.3
  • 92
    • 33645211903 scopus 로고    scopus 로고
    • The effect of oxygen on biochemical networks and the evolution of complex life
    • Raymond J, Segre D. The effect of oxygen on biochemical networks and the evolution of complex life. Science 2006;311:1764-7
    • (2006) Science , vol.311 , pp. 1764-1767
    • Raymond, J.1    Segre, D.2
  • 93
    • 0015980083 scopus 로고
    • On earlier states of the biochemical system
    • Ycas M. On earlier states of the biochemical system. J Theor Biol 1974;44:145-60
    • (1974) J Theor Biol , vol.44 , pp. 145-160
    • Ycas, M.1
  • 94
    • 39749195677 scopus 로고    scopus 로고
    • Impacts of yeast metabolic network structure on enzyme evolution
    • Lu C, Zhang Z, Leach L, et al. Impacts of yeast metabolic network structure on enzyme evolution. Genome Biol 2007;8:407
    • (2007) Genome Biol , vol.8 , pp. 407
    • Lu, C.1    Zhang, Z.2    Leach, L.3
  • 95
    • 34447502516 scopus 로고    scopus 로고
    • A network perspective on the evolution of metabolism by gene duplication
    • Diaz-Mejia JJ, Perez-Rueda E, Segovia L. A network perspective on the evolution of metabolism by gene duplication. Genome Biol 2007;8:R26
    • (2007) Genome Biol , vol.8 , pp. R26
    • Diaz-Mejia, J.J.1    Perez-Rueda, E.2    Segovia, L.3
  • 96
    • 33646754515 scopus 로고    scopus 로고
    • Therapeutic targets: progress of their exploration and investigation of their characteristics
    • Zheng CJ, Han LY, Yap CW, et al. Therapeutic targets: progress of their exploration and investigation of their characteristics. Pharmacol Rev 2006;58:259-79
    • (2006) Pharmacol Rev , vol.58 , pp. 259-279
    • Zheng, C.J.1    Han, L.Y.2    Yap, C.W.3
  • 97
  • 98
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteomescale map of the human protein-protein interaction network
    • Rual JF, Venkatesan K, Hao T, et al. Towards a proteomescale map of the human protein-protein interaction network. Nature 2005;437:1173-8
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3
  • 99
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • Hanley J, McNeil B. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982;143:29-36
    • (1982) Radiology , vol.143 , pp. 29-36
    • Hanley, J.1    McNeil, B.2
  • 100
    • 84922591049 scopus 로고    scopus 로고
    • Efficient behavior of small-world networks
    • Latora V, Marchiori M. Efficient behavior of small-world networks. Phys Rev Lett 2001;87:198701
    • (2001) Phys Rev Lett , vol.87
    • Latora, V.1    Marchiori, M.2
  • 101
    • 0013987194 scopus 로고
    • The centrality index of a graph
    • Sabidussi G. The centrality index of a graph. Psychometrika 1966;31:581-603
    • (1966) Psychometrika , vol.31 , pp. 581-603
    • Sabidussi, G.1
  • 102
    • 85055760867 scopus 로고
    • Clustering and hierarchy in interpersonal relations: testing two graph theoretical models on 742 sociomatrices
    • Davis JA. Clustering and hierarchy in interpersonal relations: testing two graph theoretical models on 742 sociomatrices. Am Sociol Rev 1970;35:843-51
    • (1970) Am Sociol Rev , vol.35 , pp. 843-851
    • Davis, J.A.1
  • 103
    • 84865705620 scopus 로고    scopus 로고
    • Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors
    • Zhang J, Jia J, Zhu F, et al. Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors. Mol Biosyst 2012;8:2645-56
    • (2012) Mol Biosyst , vol.8 , pp. 2645-2656
    • Zhang, J.1    Jia, J.2    Zhu, F.3
  • 104
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: back to metabolism in KEGG
    • Kanehisa M, Goto S, Sato Y, et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014;42:D199-205
    • (2014) Nucleic Acids Res , vol.42 , pp. D199-D205
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3
  • 106
    • 58149200933 scopus 로고    scopus 로고
    • Update of KDBI: kinetic data of bio-molecular interaction database
    • Kumar P, Han BC, Shi Z, et al. Update of KDBI: kinetic data of bio-molecular interaction database. Nucleic Acids Res 2009;37:D636-41
    • (2009) Nucleic Acids Res , vol.37 , pp. D636-D641
    • Kumar, P.1    Han, B.C.2    Shi, Z.3
  • 107
    • 84941051170 scopus 로고    scopus 로고
    • STRING v10: protein-protein interaction networks, integrated over the tree of life
    • Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015;43:D447-52
    • (2015) Nucleic Acids Res , vol.43 , pp. D447-D452
    • Szklarczyk, D.1    Franceschini, A.2    Wyder, S.3
  • 108
    • 84891799734 scopus 로고    scopus 로고
    • The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
    • Orchard S, Ammari M, Aranda B, et al. The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 2014;42: D358-63
    • (2014) Nucleic Acids Res , vol.42 , pp. D358-D363
    • Orchard, S.1    Ammari, M.2    Aranda, B.3
  • 109
    • 3042786293 scopus 로고    scopus 로고
    • A gene network for navigating the literature
    • Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004;36:664
    • (2004) Nat Genet , vol.36 , pp. 664
    • Hoffmann, R.1    Valencia, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.