메뉴 건너뛰기




Volumn 8, Issue 1, 2015, Pages 11-22

Tools for visualization and analysis of molecular networks, pathways, and -omics data

Author keywords

Biological networks; Genes; Organisms; Protein protein interactions; Proteins; Reactions; Signaling

Indexed keywords


EID: 84940037544     PISSN: None     EISSN: 11786949     Source Type: Journal    
DOI: 10.2147/AABC.S63534     Document Type: Article
Times cited : (50)

References (86)
  • 1
    • 0031300886 scopus 로고    scopus 로고
    • Organizing and computing metabolic pathway data in terms of binary relations
    • Goto S, Bono H, Ogata H, et al. Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput. 1997: 175-186.
    • (1997) Pac Symp Biocomput , pp. 175-186
    • Goto, S.1    Bono, H.2    Ogata, H.3
  • 2
    • 13444259844 scopus 로고    scopus 로고
    • Reactome: a knowledgebase of biological pathways
    • Joshi-Tope G, Gillespie M, Vastrik I, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2005;33(Database issue): D428-D432.
    • (2005) Nucleic Acids Res , vol.33 , Issue.DATABASE ISSUE , pp. D428-D432
    • Joshi-Tope, G.1    Gillespie, M.2    Vastrik, I.3
  • 3
    • 70349581595 scopus 로고    scopus 로고
    • PANTHER pathway: an ontology-based pathway database coupled with data analysis tools
    • Mi H, Thomas P. PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009;563: 123-140.
    • (2009) Methods Mol Biol , vol.563 , pp. 123-140
    • Mi, H.1    Thomas, P.2
  • 4
    • 84891774001 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi R, Altman T, Billington R, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2014;42(Database issue):D459-D471.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D459-D471
    • Caspi, R.1    Altman, T.2    Billington, R.3
  • 7
    • 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(Database issue):D685-D690.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE ISSUE , pp. D685-D690
    • Cerami, E.G.1    Gross, B.E.2    Demir, E.3
  • 8
    • 58149194611 scopus 로고    scopus 로고
    • ConsensusPathDB -a database for integrating human functional interaction networks
    • Kamburov A, Wierling C, Lehrach H, Herwig R. ConsensusPathDB - a database for integrating human functional interaction networks. Nucleic Acids Res. 2009;37(Database issue):D623-D628.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE , pp. D623-D628
    • Kamburov, A.1    Wierling, C.2    Lehrach, H.3    Herwig, R.4
  • 9
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40(Database issue):D109-D114.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE , pp. D109-D114
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 11
    • 27744493624 scopus 로고    scopus 로고
    • KEGG-based pathway visualization tool for complex omics data
    • Arakawa K, Kono N, Yamada Y, Mori H, Tomita M. KEGG-based pathway visualization tool for complex omics data. In Silico Biol. 2005; 5(4):419-423.
    • (2005) In Silico Biol , vol.5 , Issue.4 , pp. 419-423
    • Arakawa, K.1    Kono, N.2    Yamada, Y.3    Mori, H.4    Tomita, M.5
  • 12
    • 34250618297 scopus 로고    scopus 로고
    • MEGU: pathway mapping web-service based on KEGG and SVG
    • Kono N, Arakawa K, Tomita M. MEGU: pathway mapping web-service based on KEGG and SVG. In Silico Biol. 2006;6(6):621-625.
    • (2006) In Silico Biol , vol.6 , Issue.6 , pp. 621-625
    • Kono, N.1    Arakawa, K.2    Tomita, M.3
  • 13
    • 70450179911 scopus 로고    scopus 로고
    • Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API
    • Kono N, Arakawa K, Ogawa R, et al. Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One. 2009;4(11):e7710.
    • (2009) PLoS One , vol.4 , Issue.11
    • Kono, N.1    Arakawa, K.2    Ogawa, R.3
  • 14
    • 84874355250 scopus 로고    scopus 로고
    • Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions
    • Ito T, Tanaka M, Shinkawa H, et al. Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions. Metabolomics. 2013;9(Suppl 1):178-187.
    • (2013) Metabolomics , vol.9 , pp. 178-187
    • Ito, T.1    Tanaka, M.2    Shinkawa, H.3
  • 15
    • 84915813668 scopus 로고    scopus 로고
    • KEGGViewer, a BioJS component to visualize KEGG pathways
    • Villaveces JM, Jimenez RC, Habermann BH. KEGGViewer, a BioJS component to visualize KEGG pathways. F1000Res. 2014;3:43.
    • (2014) F1000Res , vol.3 , pp. 43
    • Villaveces, J.M.1    Jimenez, R.C.2    Habermann, B.H.3
  • 16
    • 84876252208 scopus 로고    scopus 로고
    • BioJS: an open source JavaScript framework for biological data visualization
    • Gómez J, García LJ, Salazar GA, et al. BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics. 2013;29(8):1103-1104.
    • (2013) Bioinformatics , vol.29 , Issue.8 , pp. 1103-1104
    • Gómez, J.1    García, L.J.2    Salazar, G.A.3
  • 17
    • 54249091564 scopus 로고    scopus 로고
    • Presenting and exploring biological pathways with PathVisio
    • van Iersel MP, Kelder T, Pico AR, et al. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008;9:399.
    • (2008) BMC Bioinformatics , vol.9 , pp. 399
    • van Iersel, M.P.1    Kelder, T.2    Pico, A.R.3
  • 18
    • 84891320138 scopus 로고    scopus 로고
    • Pathways for ligand activated nuclear receptors to unravel the genomic responses induced by hepatotoxicants
    • Fijten RR, Jennen DG, van Delft JH. Pathways for ligand activated nuclear receptors to unravel the genomic responses induced by hepatotoxicants. Curr Drug Metab. 2013;14(10):1022-1028.
    • (2013) Curr Drug Metab , vol.14 , Issue.10 , pp. 1022-1028
    • Fijten, R.R.1    Jennen, D.G.2    van Delft, J.H.3
  • 19
    • 84880199410 scopus 로고    scopus 로고
    • Pathview: an R/Bioconductor package for pathway-based data integration and visualization
    • Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 2013;29(14):1830-1831.
    • (2013) Bioinformatics , vol.29 , Issue.14 , pp. 1830-1831
    • Luo, W.1    Brouwer, C.2
  • 20
    • 84907363534 scopus 로고    scopus 로고
    • Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer
    • Arthur JC, Gharaibeh RZ, Mühlbauer M, et al. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer. Nat Commun. 2014;5:4724.
    • (2014) Nat Commun , vol.5 , pp. 4724
    • Arthur, J.C.1    Gharaibeh, R.Z.2    Mühlbauer, M.3
  • 21
    • 84902595133 scopus 로고    scopus 로고
    • Intracellular bacteria interfere with dendritic cell functions: role of the type I interferon pathway
    • Gorvel L, Textoris J, Banchereau R, et al. Intracellular bacteria interfere with dendritic cell functions: role of the type I interferon pathway. PLoS One. 2014;9(6):e99420.
    • (2014) PLoS One , vol.9 , Issue.6
    • Gorvel, L.1    Textoris, J.2    Banchereau, R.3
  • 22
    • 39949084468 scopus 로고    scopus 로고
    • iPath: interactive exploration of biochemical pathways and networks
    • Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci. 2008; 33(3):101-103.
    • (2008) Trends Biochem Sci , vol.33 , Issue.3 , pp. 101-103
    • Letunic, I.1    Yamada, T.2    Kanehisa, M.3    Bork, P.4
  • 24
    • 84870398009 scopus 로고    scopus 로고
    • Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach
    • Navid A, Almaas E. Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach. BMC Syst Biol. 2012;6(1):150.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 150
    • Navid, A.1    Almaas, E.2
  • 25
    • 84870322666 scopus 로고    scopus 로고
    • Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease
    • Erickson AR, Cantarel BL, Lamendella R, et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One. 2012;7(11):e49138.
    • (2012) PLoS One , vol.7 , Issue.11
    • Erickson, A.R.1    Cantarel, B.L.2    Lamendella, R.3
  • 26
    • 84919683973 scopus 로고    scopus 로고
    • The evolution of fungal metabolic pathways
    • Wisecaver JH, Slot JC, Rokas A. The evolution of fungal metabolic pathways. PLoS Genet. 2014;10(12):e1004816.
    • (2014) PLoS Genet , vol.10 , Issue.12
    • Wisecaver, J.H.1    Slot, J.C.2    Rokas, A.3
  • 29
    • 84869210275 scopus 로고    scopus 로고
    • Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis
    • Guzman F, Almerão MP, Körbes AP, Loss-Morais G, Margis R. Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis. PLoS One. 2012;7(11): e49811.
    • (2012) PLoS One , vol.7 , Issue.11
    • Guzman, F.1    Almerão, M.P.2    Körbes, A.P.3    Loss-Morais, G.4    Margis, R.5
  • 30
    • 84864660437 scopus 로고    scopus 로고
    • Transcriptome profiling of the cancer, adjacent non-tumor and distant normal tissues from a colorectal cancer patient by deep sequencing
    • Wu Y, Wang X, Wu F, et al. Transcriptome profiling of the cancer, adjacent non-tumor and distant normal tissues from a colorectal cancer patient by deep sequencing. PloS One. 2012;7(8):e41001.
    • (2012) PloS One , vol.7 , Issue.8
    • Wu, Y.1    Wang, X.2    Wu, F.3
  • 31
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • Accessed March 31, 2015
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28(9):977-982. Accessed March 31, 2015.
    • (2010) Nat Biotechnol , vol.28 , Issue.9 , pp. 977-982
    • Henry, C.S.1    DeJongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5    Stevens, R.L.6
  • 32
    • 84940078164 scopus 로고    scopus 로고
    • The openCOBRA Project [homepage on the Internet], Accessed
    • The openCOBRA Project [homepage on the Internet]. Available from: http://opencobra.sourceforge.net/openCOBRA/Welcome.html. Accessed.
  • 33
    • 84859057484 scopus 로고    scopus 로고
    • CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
    • DeJongh M, Bockstege B, Frybarger P, Hazekamp N, Kammeraad J, McGeehan T. CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED. Bioinformatics. 2012;28(6):891-892.
    • (2012) Bioinformatics , vol.28 , Issue.6 , pp. 891-892
    • DeJongh, M.1    Bockstege, B.2    Frybarger, P.3    Hazekamp, N.4    Kammeraad, J.5    McGeehan, T.6
  • 34
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
    • Schellenberger J, Que R, Fleming RM, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011;6(9):1290-1307.
    • (2011) Nat Protoc , vol.6 , Issue.9 , pp. 1290-1307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.3
  • 35
    • 84881152495 scopus 로고    scopus 로고
    • COBRApy: constraints-based reconstruction and analysis for python
    • Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. COBRApy: constraints-based reconstruction and analysis for python. BMC Syst Biol. 2013;7(1):74.
    • (2013) BMC Syst Biol , vol.7 , Issue.1 , pp. 74
    • Ebrahim, A.1    Lerman, J.A.2    Palsson, B.O.3    Hyduke, D.R.4
  • 36
    • 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):2498-2504.
    • (2003) Genome Res , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3
  • 38
    • 84861779036 scopus 로고    scopus 로고
    • Topological analysis and interactive visualization of biological networks and protein structures
    • Doncheva NT, Assenov Y, Domingues FS, Albrecht M. Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc. 2012;7(4):670-685.
    • (2012) Nat Protoc , vol.7 , Issue.4 , pp. 670-685
    • Doncheva, N.T.1    Assenov, Y.2    Domingues, F.S.3    Albrecht, M.4
  • 39
    • 0035648637 scopus 로고    scopus 로고
    • A faster algorithm for betweenness centrality
    • Brandes U. A faster algorithm for betweenness centrality. J Math Sociol. 2001;25(2):163-177.
    • (2001) J Math Sociol , vol.25 , Issue.2 , pp. 163-177
    • Brandes, U.1
  • 40
    • 51249195602 scopus 로고
    • Structural parameters of communication networks
    • Shimbel A. Structural parameters of communication networks. Bull Math Biol. 1953;15(4):501-507.
    • (1953) Bull Math Biol , vol.15 , Issue.4 , pp. 501-507
    • Shimbel, A.1
  • 41
    • 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. 2005;27(1):39-54.
    • (2005) Soc Networks , vol.27 , Issue.1 , pp. 39-54
    • Newman, M.E.J.1
  • 42
    • 84869054051 scopus 로고    scopus 로고
    • A travel guide to Cytoscape plugins
    • Saito R, Smoot ME, Ono K, et al. A travel guide to Cytoscape plugins. Nat Methods. 2012;9(11):1069-1076.
    • (2012) Nat Methods , vol.9 , Issue.11 , pp. 1069-1076
    • Saito, R.1    Smoot, M.E.2    Ono, K.3
  • 43
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005;21(16):3448-3449.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 44
    • 84915746374 scopus 로고    scopus 로고
    • WikiPathways App for Cytoscape: making biological pathways amenable to network analysis and visualization
    • Kutmon M, Lotia S, Evelo CT, Pico AR. WikiPathways App for Cytoscape: making biological pathways amenable to network analysis and visualization. F1000Res. 2014;3:152.
    • (2014) F1000Res , vol.3 , pp. 152
    • Kutmon, M.1    Lotia, S.2    Evelo, C.T.3    Pico, A.R.4
  • 45
    • 84923261228 scopus 로고    scopus 로고
    • CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows
    • Nersisyan L, Samsonyan R, Arakelyan A. CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows. F1000Res. 2014;3:145.
    • (2014) F1000Res , vol.3 , pp. 145
    • Nersisyan, L.1    Samsonyan, R.2    Arakelyan, A.3
  • 46
    • 84908659098 scopus 로고    scopus 로고
    • KEGGscape: a Cytoscape app for pathway data integration
    • Nishida K, Ono K, Kanaya S, Takahashi K. KEGGscape: a Cytoscape app for pathway data integration. F1000Res. 2014;3:144.
    • (2014) F1000Res , vol.3 , pp. 144
    • Nishida, K.1    Ono, K.2    Kanaya, S.3    Takahashi, K.4
  • 47
    • 84881109408 scopus 로고    scopus 로고
    • A network module-based method for identifying cancer prognostic signatures
    • Wu G, Stein L. A network module-based method for identifying cancer prognostic signatures. Genome Biol. 2012;13(12):R112.
    • (2012) Genome Biol , vol.13 , Issue.12
    • Wu, G.1    Stein, L.2
  • 48
    • 84874741556 scopus 로고    scopus 로고
    • CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
    • Bindea G, Galon J, Mlecnik B. CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics. 2013;29(5):661-663.
    • (2013) Bioinformatics , vol.29 , Issue.5 , pp. 661-663
    • Bindea, G.1    Galon, J.2    Mlecnik, B.3
  • 49
    • 84941117508 scopus 로고    scopus 로고
    • VirHostNet 2.0: surfing on the web of virus/host molecular interactions data
    • Guirimand T, Delmotte S, Navratil V. VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. Nucleic Acids Res. 2015;43(Database issue):D583-D587.
    • (2015) Nucleic Acids Res , vol.43 , Issue.DATABASE ISSUE , pp. D583-D587
    • Guirimand, T.1    Delmotte, S.2    Navratil, V.3
  • 50
    • 84940078165 scopus 로고    scopus 로고
    • Sigma.js [homepage on the Internet], Accessed March 31
    • Sigma.js [homepage on the Internet]. Available from: http://sigmajs.org/. Accessed March 31, 2015.
    • (2015)
  • 51
    • 84940078166 scopus 로고    scopus 로고
    • Cytoscape.js [homepage on the Internet], Accessed March 31
    • Cytoscape.js [homepage on the Internet]. Available from: https://github.com/cytoscape/cytoscape.js. Accessed March 31, 2015.
    • (2015)
  • 52
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Complex Systems:1695
    • Csardi G, Nepusz T. The igraph software package for complex network research. Inter Journal. 2006;Complex Systems:1695.
    • (2006) Inter Journal
    • Csardi, G.1    Nepusz, T.2
  • 54
    • 77956664073 scopus 로고    scopus 로고
    • The BioPAX community standard for pathway data sharing
    • Demir E, Cary MP, Paley S, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010;28(9):935-942.
    • (2010) Nat Biotechnol , vol.28 , Issue.9 , pp. 935-942
    • Demir, E.1    Cary, M.P.2    Paley, S.3
  • 55
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-29.
    • (2000) Nat Genet , vol.25 , Issue.1 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 56
    • 35348976204 scopus 로고    scopus 로고
    • Broadening the horizon -level 2.5 of the HUPO-PSI format for molecular interactions
    • Kerrien S, Orchard S, Montecchi-Palazzi L, et al. Broadening the horizon - level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007;5:44.
    • (2007) BMC Biol , vol.5 , pp. 44
    • Kerrien, S.1    Orchard, S.2    Montecchi-Palazzi, L.3
  • 57
    • 84884679902 scopus 로고    scopus 로고
    • Using biological pathway data with paxtools
    • Demir E, Babur O, Rodchenkov I, et al. Using biological pathway data with paxtools. PLoS Comput Biol. 2013;9(9):e1003194.
    • (2013) PLoS Comput Biol , vol.9 , Issue.9
    • Demir, E.1    Babur, O.2    Rodchenkov, I.3
  • 58
  • 60
    • 84940078168 scopus 로고    scopus 로고
    • Cytoscape App Store [homepage on the Internet], Accessed
    • Cytoscape App Store [homepage on the Internet]. Available from: http://apps.cytoscape.org/apps/cypath2. Accessed.
  • 61
    • 68449103579 scopus 로고    scopus 로고
    • The systems biology graphical notation
    • Accessed March 31, 2015
    • Le Novère N, Hucka M, Mi H, et al. The systems biology graphical notation. Nat Biotechnol. 2009;27(8):735-741. Accessed March 31, 2015.
    • (2009) Nat Biotechnol , vol.27 , Issue.8 , pp. 735-741
    • Le Novère, N.1    Hucka, M.2    Mi, H.3
  • 62
    • 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
  • 63
    • 58149186477 scopus 로고    scopus 로고
    • PID: the pathway interaction database
    • Schaefer CF, Anthony K, Krupa S, et al. PID: the pathway interaction database. Nucleic Acids Res. 2009;37(Database issue):D674-D679.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE , pp. D674-D679
    • Schaefer, C.F.1    Anthony, K.2    Krupa, S.3
  • 64
    • 79959846617 scopus 로고    scopus 로고
    • PSICQUIC and PSISCORE: accessing and scoring molecular interactions
    • Aranda B, Blankenburg H, Kerrien S, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011;8(7): 528-529.
    • (2011) Nat Methods , vol.8 , Issue.7 , pp. 528-529
    • Aranda, B.1    Blankenburg, H.2    Kerrien, S.3
  • 65
    • 75549087047 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2010
    • Aranda B, Achuthan P, Alam-Faruque Y, et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2010;38(Database issue):D525-D531.
    • (2010) Nucleic Acids Res , vol.38 , Issue.DATABASE ISSUE , pp. D525-D531
    • Aranda, B.1    Achuthan, P.2    Alam-Faruque, Y.3
  • 66
    • 13444249988 scopus 로고    scopus 로고
    • STRING: known and predicted protein-protein associations, integrated and transferred across organisms
    • von Mering C, Jensen LJ, Snel B, et al. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 2005;33(Database issue):D433-D437.
    • (2005) Nucleic Acids Res , vol.33 , Issue.DATABASE ISSUE , pp. D433-D437
    • von Mering, C.1    Jensen, L.J.2    Snel, B.3
  • 67
    • 23944492134 scopus 로고    scopus 로고
    • Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    • Omenn GS, States DJ, Adamski M, et al. Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 2005; 5(13):3226-3245.
    • (2005) Proteomics , vol.5 , Issue.13 , pp. 3226-3245
    • Omenn, G.S.1    States, D.J.2    Adamski, M.3
  • 68
    • 38449100072 scopus 로고    scopus 로고
    • The protein identifier cross-referencing (PICR) service: reconciling protein identifiers across multiple source databases
    • Côté RG, Jones P, Martens L, et al. The protein identifier cross-referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics. 2007;8:401.
    • BMC Bioinformatics , vol.2007 , pp. 401
    • Côté, R.G.1    Jones, P.2    Martens, L.3
  • 69
    • 75849153303 scopus 로고    scopus 로고
    • The universal protein resource (UniProt) in 2010
    • UniProt Consortium. The universal protein resource (UniProt) in 2010. Nucleic Acids Res. 2010;38(Database):D142-D148.
    • (2010) Nucleic Acids Res , vol.38 , Issue.DATABASE , pp. D142-D148
  • 70
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 71
    • 84897584818 scopus 로고    scopus 로고
    • Edge bundling in information visualization
    • Zhou H, Xu P, Yuan X, Qu H. Edge bundling in information visualization. Tsinghua Sci Technol. 2013;18(2):145-156.
    • (2013) Tsinghua Sci Technol , vol.18 , Issue.2 , pp. 145-156
    • Zhou, H.1    Xu, P.2    Yuan, X.3    Qu, H.4
  • 72
    • 68549085159 scopus 로고    scopus 로고
    • Force-directed edge bundling for graph visualization
    • Holten D, van Wijk JJ. Force-directed edge bundling for graph visualization. Comput Graph Forum. 2009;28(3):983-990.
    • (2009) Comput Graph Forum , vol.28 , Issue.3 , pp. 983-990
    • Holten, D.1    van Wijk, J.J.2
  • 74
    • 68549126815 scopus 로고    scopus 로고
    • Scalable, versatile and simple constrained graph layout
    • Dwyer T. Scalable, versatile and simple constrained graph layout. Comput Graph Forum. 2009;1:991-998.
    • (2009) Comput Graph Forum , vol.1 , pp. 991-998
    • Dwyer, T.1
  • 75
    • 84860916660 scopus 로고    scopus 로고
    • Hive plots -rational approach to visualizing networks
    • Krzywinski M, Birol I, Jones SJ, Marra MA. Hive plots - rational approach to visualizing networks. Brief Bioinform. 2012;13(5):627-644.
    • (2012) Brief Bioinform , vol.13 , Issue.5 , pp. 627-644
    • Krzywinski, M.1    Birol, I.2    Jones, S.J.3    Marra, M.A.4
  • 76
    • 35748937331 scopus 로고    scopus 로고
    • Construction, visualisation, and clustering of transcription networks from microarray expression data
    • Freeman TC, Goldovsky L, Brosch M, et al. Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol. 2007;3(10):2032-2042.
    • (2007) PLoS Comput Biol , vol.3 , Issue.10 , pp. 2032-2042
    • Freeman, T.C.1    Goldovsky, L.2    Brosch, M.3
  • 77
    • 73349116606 scopus 로고    scopus 로고
    • Network visualization and analysis of gene expression data using BioLayout Express(3D)
    • Theocharidis A, van Dongen S, Enright AJ, Freeman TC. Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc. 2009;4(10):1535-1550.
    • (2009) Nat Protoc , vol.4 , Issue.10 , pp. 1535-1550
    • Theocharidis, A.1    van Dongen, S.2    Enright, A.J.3    Freeman, T.C.4
  • 79
    • 0346882669 scopus 로고    scopus 로고
    • Metabolic pathways in three dimensions
    • Rojdestvenski I. Metabolic pathways in three dimensions. Bioinformatics. 2003;19(18):2436-2441.
    • (2003) Bioinformatics , vol.19 , Issue.18 , pp. 2436-2441
    • Rojdestvenski, I.1
  • 81
    • 80855140990 scopus 로고    scopus 로고
    • Developing and evaluating quilts for the depiction of large layered graphs
    • Bae J, Watson B. Developing and evaluating quilts for the depiction of large layered graphs. IEEE Trans Vis Comput Graph. 2011;17(12): 2268-2275.
    • (2011) IEEE Trans Vis Comput Graph , vol.17 , Issue.12 , pp. 2268-2275
    • Bae, J.1    Watson, B.2
  • 82
    • 57349127354 scopus 로고    scopus 로고
    • Exploring semantic social networks using virtual reality
    • Sheth A, Staab S, Dean M, et al., editors, Berlin, HD: Springer
    • Halpin H, Zielinski DJ, Brady R, Kelly G. Exploring semantic social networks using virtual reality. In: Sheth A, Staab S, Dean M, et al., editors. The Semantic Web - ISWC 2008. Berlin, HD: Springer; 2008: 599-614.
    • (2008) The Semantic Web -ISWC 2008 , pp. 599-614
    • Halpin, H.1    Zielinski, D.J.2    Brady, R.3    Kelly, G.4
  • 83
    • 84945320022 scopus 로고
    • Surround-Screen Projection-Based Virtual Reality: The Design and Implementation of the CAVE
    • New York, NY: ACM
    • Cruz-Neira C, Sandin DJ, DeFanti TA. Surround-Screen Projection-Based Virtual Reality: The Design and Implementation of the CAVE. New York, NY: ACM; 1993:135-142.
    • (1993) , pp. 135-142
    • Cruz-Neira, C.1    Sandin, D.J.2    DeFanti, T.A.3
  • 84
    • 84864037265 scopus 로고    scopus 로고
    • INOH: ontology-based highly structured database of signal transduction pathways
    • (Oxford), 2011 bar052
    • Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T. INOH: ontology-based highly structured database of signal transduction pathways. Database (Oxford). 2011;2011:bar052.
    • (2011) Database
    • Yamamoto, S.1    Sakai, N.2    Nakamura, H.3    Fukagawa, H.4    Fukuda, K.5    Takagi, T.6
  • 85
    • 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(1):R3.
    • (2010) Genome Biol , vol.11 , Issue.1
    • Kandasamy, K.1    Mohan, S.S.2    Raju, R.3
  • 86


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.