메뉴 건너뛰기




Volumn 13, Issue 5, 2012, Pages 627-644

Hive plots-rational approach to visualizing networks

Author keywords

Bioinformatics; Computation; Graphs; Networks; Systems biology; Visualization

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DISEASES; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GENETICS; HUMAN;

EID: 84860916660     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr069     Document Type: Article
Times cited : (186)

References (66)
  • 3
    • 79955130092 scopus 로고    scopus 로고
    • Using graph theory to analyze biological networks
    • Pavlopoulos G, Secrier M, Moschopoulos C, et al. Using graph theory to analyze biological networks. BioData Mining 2011;4(1):10.
    • (2011) BioData Mining , vol.4 , Issue.1 , pp. 10
    • Pavlopoulos, G.1    Secrier, M.2    Moschopoulos, C.3
  • 4
    • 45149101194 scopus 로고    scopus 로고
    • Current approaches to gene regulatory network modelling
    • Schlitt T, Brazma A. Current approaches to gene regulatory network modelling. BMC Bioinformatics 2007;8(Suppl 6): S9.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL 6
    • Schlitt, T.1    Brazma, A.2
  • 5
    • 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
  • 6
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: a resource for annotating the proteome
    • Stelzl U, Worm U, Lalowski M, et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005;122(6):957-68.
    • (2005) Cell , vol.122 , Issue.6 , pp. 957-968
    • Stelzl, U.1    Worm, U.2    Lalowski, M.3
  • 7
    • 0345863935 scopus 로고    scopus 로고
    • The kegg resource for deciphering the genome
    • Kanehisa M, Goto S, Kawashima S, et al. The kegg resource for deciphering the genome. Nucleic Acids Res 2004; 32(Database issue):D277-80.
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE ISSUE
    • Kanehisa, M.1    Goto, S.2    Kawashima, S.3
  • 8
    • 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(11):1423-30.
    • (2003) Bioinformatics , vol.19 , Issue.11 , pp. 1423-1430
    • Ma, H.W.1    Zeng, A.P.2
  • 9
    • 58149189856 scopus 로고    scopus 로고
    • Mckusick's online mendelian inheritance in man (omim)
    • Amberger J, Bocchini CA, Scott AF, etal. Mckusick's online mendelian inheritance in man (omim). Nucleic Acids Res 2009;37(Database issue):D793-6.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE
    • Amberger, J.1    Bocchini, C.A.2    Scott, A.-A.3
  • 10
    • 66449136667 scopus 로고    scopus 로고
    • Abyss: A parallel assembler for short read sequence data
    • Simpson JT, Wong K, Jackman SD, et al. Abyss: A parallel assembler for short read sequence data. Genome Res 2009; 19(6):1117-23.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1117-1123
    • Simpson, J.T.1    Wong, K.2    Jackman, S.D.3
  • 11
    • 0035859921 scopus 로고    scopus 로고
    • An eulerian path approach to DNA fragment assembly
    • Pevzner PA, Tang H, Waterman MS. An eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 2001;98(17):9748-53.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.17 , pp. 9748-9753
    • Pevzner, P.A.1    Tang, H.2    Waterman, M.S.3
  • 12
    • 4644275238 scopus 로고    scopus 로고
    • De novo repeat classification and fragment assembly
    • Pevzner PA, Tang H, Tesler G. De novo repeat classification and fragment assembly. Genome Res 2004; 14(9):1786-96.
    • (2004) Genome Res , vol.14 , Issue.9 , pp. 1786-1796
    • Pevzner, P.A.1    Tang, H.2    Tesler, G.3
  • 13
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • Kitano H. Systems biology: a brief overview. Science 2002; 295(5560):1662-4.
    • (2002) Science , vol.295 , Issue.5560 , pp. 1662-1664
    • Kitano, H.1
  • 14
    • 19344372271 scopus 로고    scopus 로고
    • Systems biology: its practice and challenges
    • Aderem A. Systems biology: its practice and challenges. Cell 2005;121(4):511-3.
    • (2005) Cell , vol.121 , Issue.4 , pp. 511-513
    • Aderem, A.1
  • 15
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • Kitano H. Computational systems biology. Nature 2002; 420(6912):206-10.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 206-210
    • Kitano, H.1
  • 16
    • 1942470073 scopus 로고    scopus 로고
    • Metabolomics by numbers: acquiring and understanding global metabolite data
    • Goodacre R, Vaidyanathan S, Dunn WB, et al. Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 2004;22(5):245-52.
    • (2004) Trends Biotechnol , vol.22 , Issue.5 , pp. 245-252
    • Goodacre, R.1    Vaidyanathan, S.2    Dunn, W.B.3
  • 17
    • 78649682830 scopus 로고    scopus 로고
    • A comparative study of cancer proteins in the human protein-protein interaction network
    • Sun J, Zhao Z. A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics 2010;11(Suppl 3):S5.
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL 3
    • Sun, J.1    Zhao, Z.2
  • 18
    • 33947619951 scopus 로고    scopus 로고
    • Graph theory and networks in biology
    • Mason O, Verwoerd M. Graph theory and networks in biology. IETSyst Biol 2007;1(2):89-119.
    • (2007) IETSyst Biol , vol.1 , Issue.2 , pp. 89-119
    • Mason, O.1    Verwoerd, M.2
  • 19
    • 33748798478 scopus 로고    scopus 로고
    • Graph-based methods for analysing networks in cell biology
    • Aittokallio T, Schwikowski B. Graph-based methods for analysing networks in cell biology. Brief Bioinform 2006; 7(3):243-55.
    • (2006) Brief Bioinform , vol.7 , Issue.3 , pp. 243-255
    • Aittokallio, T.1    Schwikowski, B.2
  • 20
    • 77649252269 scopus 로고    scopus 로고
    • Visualization of omics data for systems biology
    • Gehlenborg N, O'Donoghue SI, Baliga NS, et al. Visualization of omics data for systems biology. Nat Methods 2010;7(Suppl 3):S56-68.
    • (2010) Nat Methods , vol.7 , Issue.SUPPL 3
    • Gehlenborg, N.1    O'Donoghue, S.I.2    Baliga, N.S.3
  • 21
    • 35748962289 scopus 로고    scopus 로고
    • Tools for visually exploring biological networks
    • Suderman M, Hallett M. Tools for visually exploring biological networks. Bioinformatics 2007;23(20):2651-9.
    • (2007) Bioinformatics , vol.23 , Issue.20 , pp. 2651-2659
    • Suderman, M.1    Hallett, M.2
  • 22
    • 33747832812 scopus 로고    scopus 로고
    • Biologicalnetworks: visualization and analysis tool for systems biology
    • Baitaluk M, Sedova M, Ray A, et al. Biologicalnetworks: visualization and analysis tool for systems biology. Nucleic Acids Res 2006;34(Web Server issue):W466-71.
    • (2006) Nucleic Acids Res , vol.34 , Issue.WEB SERVER ISSUE
    • Baitaluk, M.1    Sedova, M.2    Ray, A.3
  • 23
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2 8: New features for data integration and network visualization
    • Smoot ME, Ono K, Ruscheinski J, et al. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 2011;27(3):431-2.
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3
  • 24
    • 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(11): 2498-504.
    • (2003) Genome Res , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3
  • 26
    • 33845678910 scopus 로고    scopus 로고
    • Matrixexplorer: a dual-representation system to explore social networks
    • Henry N, Fekete JD. Matrixexplorer: a dual-representation system to explore social networks. IEEE TransVisu Comput Graph 2006;12(5):677-84.
    • (2006) IEEE TransVisu Comput Graph , vol.12 , Issue.5 , pp. 677-684
    • Henry, N.1    Fekete, J.D.2
  • 28
    • 58149193234 scopus 로고    scopus 로고
    • String 8 - a global view on proteins and their functional interactions in 630 organisms
    • Jensen LJ, Kuhn M, Stark M, et al. String 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009;37(Suppl 1): D412-6.
    • (2009) Nucleic Acids Res , vol.37 , Issue.SUPPL 1
    • Jensen, L.J.1    Kuhn, M.2    Stark, M.3
  • 32
    • 0019530043 scopus 로고
    • Methods for visual understandings of hierarchical system structures
    • Sugiyama K, Tagawa S, Toda M. Methods for visual understandings of hierarchical system structures. IEEETrans SystMan Cybernetics 1981;smc-11(2):109-25.
    • (1981) IEEETrans SystMan Cybernetics , vol.SMC-11 , Issue.2 , pp. 109-125
    • Sugiyama, K.1    Tagawa, S.2    Toda, M.3
  • 33
    • 33845625463 scopus 로고    scopus 로고
    • An efficient implementation of sugiyama's algorithm for layered graph drawing
    • Eiglsperger M, Siebenhaller M, Kaufmann M. An efficient implementation of sugiyama's algorithm for layered graph drawing. JGraph AlgorithmsAppl 2005;9(3):305-25.
    • (2005) JGraph AlgorithmsAppl , vol.9 , Issue.3 , pp. 305-325
    • Eiglsperger, M.1    Siebenhaller, M.2    Kaufmann, M.3
  • 34
    • 79951472501 scopus 로고    scopus 로고
    • Metaknowledge
    • Evans JA, Foster JG. Metaknowledge. Science 2011; 331(6018):721-5.
    • (2011) Science , vol.331 , Issue.6018 , pp. 721-725
    • Evans, J.A.1    Foster, J.G.2
  • 35
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual JF, Venkatesan K, Hao T, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005;437(7062):1173-8.
    • (2005) Nature , vol.437 , Issue.7062 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3
  • 36
    • 78651299341 scopus 로고    scopus 로고
    • Regulondb version 7 0: Transcriptional regulation of escherichia coli k-12 integrated within genetic sensory response units (gensor units)
    • Gama-Castro S, Salgado H, Peralta-Gil M, et al. Regulondb version 7.0: Transcriptional regulation of escherichia coli k-12 integrated within genetic sensory response units (gensor units). Nucleic Acids Res 2011;39:D98-105.
    • (2011) Nucleic Acids Res , vol.39
    • Gama-Castro, S.1    Salgado, H.2    Peralta-Gil, M.3
  • 37
    • 0031811851 scopus 로고    scopus 로고
    • Regulondb: a database on transcriptional regulation in escherichia coli
    • Huerta AM, Salgado H, Thieffry D, et al. Regulondb: a database on transcriptional regulation in escherichia coli. Nucleic Acids Res 1998;26(1):55-9.
    • (1998) Nucleic Acids Res , vol.26 , Issue.1 , pp. 55-59
    • Huerta, A.M.1    Salgado, H.2    Thieffry, D.3
  • 39
    • 79952202448 scopus 로고    scopus 로고
    • Cytoscape: software for visualization and analysis of biological networks
    • Kohl M, Wiese S, Warscheid B. Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 2011;696:291-303.
    • (2011) Methods Mol Biol , vol.696 , pp. 291-303
    • Kohl, M.1    Wiese, S.2    Warscheid, B.3
  • 40
    • 0030401382 scopus 로고    scopus 로고
    • Aesthetics-based graph layout for human consumption
    • Coleman MK, Parker DS. Aesthetics-based graph layout for human consumption. Softw Pract Exp 1996;26(12): 1415-38.
    • (1996) Softw Pract Exp , vol.26 , Issue.12 , pp. 1415-1438
    • Coleman, M.K.1    Parker, D.S.2
  • 41
    • 84950434348 scopus 로고
    • Hyperdimensional data analysis using parallel coordinates
    • Wegman EJ. Hyperdimensional data analysis using parallel coordinates. JAm StatAssoc 1990;85(411):664-75.
    • (1990) JAm StatAssoc , vol.85 , Issue.411 , pp. 664-675
    • Wegman, E.J.1
  • 42
    • 50649112392 scopus 로고    scopus 로고
    • Genome sequence of the beta-rhizobium cupriavidus taiwanensis and comparative genomics of rhizobia
    • Amadou C, Pascal G, Mangenot S, et al. Genome sequence of the beta-rhizobium cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res 2008;18(9): 1472-83.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1472-1483
    • Amadou, C.1    Pascal, G.2    Mangenot, S.3
  • 43
    • 13544250517 scopus 로고    scopus 로고
    • Complete genome sequence of the hyperthermophilic archaeon thermococcus kodakaraensis kod1 and comparison with pyrococcus genomes
    • Fukui T, Atomi H, Kanai T, et al. Complete genome sequence of the hyperthermophilic archaeon thermococcus kodakaraensis kod1 and comparison with pyrococcus genomes. Genome Res 2005;15(3):352-63.
    • (2005) Genome Res , vol.15 , Issue.3 , pp. 352-363
    • Fukui, T.1    Atomi, H.2    Kanai, T.3
  • 44
    • 53549102749 scopus 로고    scopus 로고
    • Comparative genome analysis of salmonella enteritidis pt4 and salmonella gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
    • Thomson NR, Clayton DJ, Windhorst D, et al. Comparative genome analysis of salmonella enteritidis pt4 and salmonella gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res 2008;18(10):1624-37.
    • (2008) Genome Res , vol.18 , Issue.10 , pp. 1624-1637
    • Thomson, N.R.1    Clayton, D.J.2    Windhorst, D.3
  • 46
    • 37749022621 scopus 로고    scopus 로고
    • Designing semantic substrates for visual network exploration
    • Aris A, Shneiderman B. Designing semantic substrates for visual network exploration. Information Visualization 2007; 6(4):281-300.
    • (2007) Information Visualization , vol.6 , Issue.4 , pp. 281-300
    • Aris, A.1    Shneiderman, B.2
  • 48
    • 76249092018 scopus 로고    scopus 로고
    • Coordinate assignment for cyclic level graphs
    • Ngo H, (ed). Berlin/Heidelberg: Springer
    • Bachmaier C, Brandenburg F, Brunner W, et al. Coordinate assignment for cyclic level graphs. In: Ngo H, (ed). Computing and Combinatorics, Vol. 5609. Berlin/Heidelberg: Springer, 2009, 66-75.
    • (2009) Computing and Combinatorics , vol.5609 , pp. 66-75
    • Bachmaier, C.1    Brandenburg, F.2    Brunner, W.3
  • 49
    • 84873219978 scopus 로고    scopus 로고
    • Yfiles (11 August date last accessed)
    • Yfiles. http://www.yworks.com/en/products_yfiles_about.html (11 August 2011, date last accessed).
    • (2011)
  • 50
    • 71549169542 scopus 로고    scopus 로고
    • A generic algorithm for layout of biological networks
    • Schreiber F, Dwyer T, Marriott K, et al. A generic algorithm for layout of biological networks. BMC Bioinformatics 2009; 10:375.
    • (2009) BMC Bioinformatics , vol.10 , pp. 375
    • Schreiber, F.1    Dwyer, T.2    Marriott, K.3
  • 51
    • 16244407402 scopus 로고    scopus 로고
    • Pathway-oriented profiling of lipid mediators in macrophages
    • Kita Y, Takahashi T, Uozumi N, et al. Pathway-oriented profiling of lipid mediators in macrophages. BiochemBiophys Res Commun 2005;330(3):898-906.
    • (2005) BiochemBiophys Res Commun , vol.330 , Issue.3 , pp. 898-906
    • Kita, Y.1    Takahashi, T.2    Uozumi, N.3
  • 52
    • 77951967380 scopus 로고    scopus 로고
    • Inferring dynamic gene networks under varying conditions for transcriptomic network comparison
    • Shimamura T, Imoto S, Yamaguchi R, et al. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics 2010;26(8): 1064-72.
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 1064-1072
    • Shimamura, T.1    Imoto, S.2    Yamaguchi, R.3
  • 53
    • 77956810194 scopus 로고    scopus 로고
    • Fast diploidization in close mesopolyploid relatives of arabidopsis
    • Mandakova T, Joly S, Krzywinski M, et al. Fast diploidization in close mesopolyploid relatives of arabidopsis. Plant Cell 2010;22(7):2277-90.
    • (2010) Plant Cell , vol.22 , Issue.7 , pp. 2277-2290
    • Mandakova, T.1    Joly, S.2    Krzywinski, M.3
  • 54
    • 84856534859 scopus 로고    scopus 로고
    • Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
    • doi/10.1101/gr.126516.111, Advance Access publication 18 October 2011
    • Castellarin M, Warren RL, Freeman JD, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2011. doi/10.1101/gr.126516.111, Advance Access publication 18 October 2011.
    • (2011) Genome Res
    • Castellarin, M.1    Warren, R.L.2    Freeman, J.D.3
  • 55
    • 69649109364 scopus 로고    scopus 로고
    • Circos: an information aesthetic for comparative genomics
    • Krzywinski M, Schein J, Birol I, etal. Circos: an information aesthetic for comparative genomics. GenomeRes 2009;19(9): 1639-45.
    • (2009) GenomeRes , vol.19 , Issue.9 , pp. 1639-1645
    • Krzywinski, M.1    Schein, J.2    Birol, I.3
  • 56
    • 1842559907 scopus 로고    scopus 로고
    • Enhancing scatterplots with smoothed densities
    • Eilers PH, Goeman JJ. Enhancing scatterplots with smoothed densities. Bioinformatics 2004;20(5):623-8.
    • (2004) Bioinformatics , vol.20 , Issue.5 , pp. 623-628
    • Eilers, P.H.1    Goeman, J.J.2
  • 57
    • 0035648637 scopus 로고    scopus 로고
    • A faster algorithm for betweenness centrality
    • Brandes U. A faster algorithm for betweenness centrality. JMath Sociol 2001;25:163-77.
    • (2001) JMath Sociol , vol.25 , pp. 163-177
    • Brandes, U.1
  • 58
    • 70349914258 scopus 로고    scopus 로고
    • Pagerank for ranking authors in co-citation networks
    • Ding Y, Yan E, Frazho A, etal. Pagerank for ranking authors in co-citation networks. JAmSoc Inf SciTechnol 2009;60(11): 2229-43.
    • (2009) JAmSoc Inf SciTechnol , vol.60 , Issue.11 , pp. 2229-2243
    • Ding, Y.1    Yan, E.2    Frazho, A.3
  • 59
    • 34447512704 scopus 로고    scopus 로고
    • Understanding network concepts in modules
    • Dong J, Horvath S. Understanding network concepts in modules. BMCSyst Biol 2007;1:24.
    • (2007) BMCSyst Biol , vol.1 , pp. 24
    • Dong, J.1    Horvath, S.2
  • 60
    • 33846705486 scopus 로고    scopus 로고
    • Network neighborhood analysis with the multi-node topological overlap measure
    • Li A, Horvath S. Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics 2007;23(2):222-31.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 222-231
    • Li, A.1    Horvath, S.2
  • 62
    • 34249736324 scopus 로고    scopus 로고
    • Biological impacts and context of network theory
    • Almaas E. Biological impacts and context of network theory. J ExpBiol 2007;210(Pt 9):1548-58.
    • (2007) J ExpBiol , vol.210 , Issue.PT 9 , pp. 1548-1558
    • Almaas, E.1
  • 63
    • 77952691738 scopus 로고    scopus 로고
    • Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
    • Yan KK, Fang G, Bhardwaj N, et al. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc Natl Acad SciUSA 2010;107(20):9186-91.
    • (2010) Proc Natl Acad SciUSA , vol.107 , Issue.20 , pp. 9186-9191
    • Yan, K.K.1    Fang, G.2    Bhardwaj, N.3
  • 64
    • 33745012299 scopus 로고    scopus 로고
    • Modularity and community structure in networks
    • Newman ME. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006;103(23): 8577-82.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.23 , pp. 8577-8582
    • Newman, M.E.1
  • 65
    • 77957873035 scopus 로고    scopus 로고
    • Characterizing the community structure of complex networks
    • Lancichinetti A, Kivela M, Saramaki J, et al. Characterizing the community structure of complex networks. PloS One 2010;5(8):e11976.
    • (2010) PloS One , vol.5 , Issue.8
    • Lancichinetti, A.1    Kivela, M.2    Saramaki, J.3
  • 66
    • 27844434308 scopus 로고    scopus 로고
    • Approximating clustering coefficient and transitivity
    • Schank T, Wagner D. Approximating clustering coefficient and transitivity. JGraphAlgorAppl 2005;9.
    • (2005) JGraphAlgorAppl , pp. 9
    • Schank, T.1    Wagner, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.