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Volumn 2, Issue 1, 2008, Pages 54-77

An integrative approach for biological data mining and visualisation

Author keywords

Bioinformatics; Complex networks; Data mining; Heterogeneous database integration; Systems biology

Indexed keywords


EID: 39149116367     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2008.016756     Document Type: Article
Times cited : (11)

References (53)
  • 1
    • 1242319556 scopus 로고    scopus 로고
    • The metabolic world of Escherichia coli is not small
    • Arita, M. (2004) 'The metabolic world of Escherichia coli is not small', Proc. Natl. Acad. Sci. USA, Vol. 101, pp.1543-1547.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 1543-1547
    • Arita, M.1
  • 3
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The biomolecular interaction network database
    • Bader, G.D., Betel, D. and Hogue, C.W.V. (2003) 'BIND: The biomolecular interaction network database', Nucl. Acids Res., Vol. 31, pp.248-250.
    • (2003) Nucl. Acids Res , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.V.3
  • 5
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization'
    • Barabasi, A-L. and Oltvai, Z.N. (2004) 'Network biology: Understanding the cell's functional organization', Nat. Rev. Genet., Vol. 5, pp.101-113.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 101-113
    • Barabasi, A.-L.1    Oltvai, Z.N.2
  • 6
    • 1542290452 scopus 로고    scopus 로고
    • Ontologies in biology: Design, applications and future challenges
    • Bard, J.B.L. and Rhee, S.Y. (2004) 'Ontologies in biology: Design, applications and future challenges', Nat. Rev. Genet., Vol. 5, pp.213-222.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 213-222
    • Bard, J.B.L.1    Rhee, S.Y.2
  • 7
    • 0345863927 scopus 로고    scopus 로고
    • The unified medical language system (UMLS): Integrating biomedical terminology
    • Bodenreider, O. (2004) 'The unified medical language system (UMLS): integrating biomedical terminology', Nucl. Acids Res., Vol. 32, pp.D267-270.
    • (2004) Nucl. Acids Res , vol.32
    • Bodenreider, O.1
  • 9
    • 39149110778 scopus 로고    scopus 로고
    • BiopathwayBuilder: Nested 3D visualization system for complex molecular interactions
    • Changsu Lee, J.P. and Park, J.C. (2002) 'BiopathwayBuilder: Nested 3D visualization system for complex molecular interactions', Genome Informatics, Vol. 13, pp.447, 448.
    • (2002) Genome Informatics , vol.13
    • Changsu Lee, J.P.1    Park, J.C.2
  • 10
    • 0033198259 scopus 로고    scopus 로고
    • Kleisli: A new tool for data integration in biology
    • Chung, S.Y. and Wong, L. (1999) 'Kleisli: A new tool for data integration in biology', Trends Biotechnol., Vol. 17, pp.351-355.
    • (1999) Trends Biotechnol , vol.17 , pp. 351-355
    • Chung, S.Y.1    Wong, L.2
  • 12
    • 22744458472 scopus 로고    scopus 로고
    • Pathways to analysis of microarray data
    • Curtis, K., Oresic, M. and Vidal-Puig, A. (2005) 'Pathways to analysis of microarray data', Trends Biotechnol, Vol. 8, pp.429-435.
    • (2005) Trends Biotechnol , vol.8 , pp. 429-435
    • Curtis, K.1    Oresic, M.2    Vidal-Puig, A.3
  • 13
    • 0036578644 scopus 로고    scopus 로고
    • GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
    • Dahlquist, K.D., Karen Vranizan, N.S., Lawlor, S.C. and Conklin, B.R. (2002) 'GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways', Nature Genetics, Vol. 31, pp. 19, 20.
    • (2002) Nature Genetics , vol.31
    • Dahlquist, K.D.1    Karen Vranizan, N.S.2    Lawlor, S.C.3    Conklin, B.R.4
  • 15
    • 0030736375 scopus 로고    scopus 로고
    • Curvilinear component analysis: A self-organizing neural network for nonlinear mapping of data sets
    • Demartines, P. and Hérault, J. (1997) 'Curvilinear component analysis: A self-organizing neural network for nonlinear mapping of data sets', IEEE Trans. Neur. Netw., Vol. 8, pp.148-154.
    • (1997) IEEE Trans. Neur. Netw , vol.8 , pp. 148-154
    • Demartines, P.1    Hérault, J.2
  • 18
    • 0036181973 scopus 로고    scopus 로고
    • Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: The NOD model of Type 1 diabetes
    • Eaves, I.A., Wicker, L.S., Ghandour, G., Lyons, P.A., Peterson, L.B., Todd, J.A. and Glynne, R.J. (2002) 'Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: The NOD model of Type 1 diabetes', Genome Research, pp.232-243.
    • (2002) Genome Research , pp. 232-243
    • Eaves, I.A.1    Wicker, L.S.2    Ghandour, G.3    Lyons, P.A.4    Peterson, L.B.5    Todd, J.A.6    Glynne, R.J.7
  • 19
    • 0027457706 scopus 로고
    • SRS - an indexing and retrieval tool for flat file data libraries
    • Etzold, T. and Argos, P. (1993) 'SRS - an indexing and retrieval tool for flat file data libraries', CABIOS, Vol. 9, pp.49-57.
    • (1993) CABIOS , vol.9 , pp. 49-57
    • Etzold, T.1    Argos, P.2
  • 20
    • 0029967362 scopus 로고    scopus 로고
    • SRS: Information retrieval system for molecular biology data banks
    • Etzold, T., Ulyanov, A. and Argos, P. (1996) 'SRS: Information retrieval system for molecular biology data banks', Meth. Enzymology, pp.114-128.
    • (1996) Meth. Enzymology , pp. 114-128
    • Etzold, T.1    Ulyanov, A.2    Argos, P.3
  • 22
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Förster, J., Famili, I., Fu, P., Palsson, B.O. and Nielsen, J. (2003) 'Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network', Genome Res., Vol. 13, pp.244-253.
    • (2003) Genome Res , vol.13 , pp. 244-253
    • Förster, J.1    Famili, I.2    Fu, P.3    Palsson, B.O.4    Nielsen, J.5
  • 24
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Gene Ontology Consortium
    • Gene Ontology Consortium (2000) 'Gene ontology: Tool for the unification of biology', Nature Genetics, Vol. 25, pp.25-29.
    • (2000) Nature Genetics , vol.25 , pp. 25-29
  • 25
    • 29144514388 scopus 로고    scopus 로고
    • Gopalacharyulu, P.V., Lindfors, E., Bounsaythip, C., Kivioja, T., Yetukuri, L., Hollmen, J. and Oresic, M. (2005) 'Data integration and visualization system for enabling conceptual biology', Bioinformatics 21, pp.i177-185.
    • Gopalacharyulu, P.V., Lindfors, E., Bounsaythip, C., Kivioja, T., Yetukuri, L., Hollmen, J. and Oresic, M. (2005) 'Data integration and visualization system for enabling conceptual biology', Bioinformatics Vol. 21, pp.i177-185.
  • 27
    • 0036081122 scopus 로고    scopus 로고
    • LIGAND: Database of chemical compounds and reactions in biological pathways
    • Goto, S., Okuno, Y., Hattori, M., Nishioka, T. and Kanehisa, M. (2002) 'LIGAND: Database of chemical compounds and reactions in biological pathways', Nucl. Acids Res., Vol. 30, pp.402-404.
    • (2002) Nucl. Acids Res , vol.30 , pp. 402-404
    • Goto, S.1    Okuno, Y.2    Hattori, M.3    Nishioka, T.4    Kanehisa, M.5
  • 28
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • Guimera, R. and Amaral, L.A.N. (2005) 'Functional cartography of complex metabolic networks', Nature, Vol. 433, pp.895-900.
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimera, R.1    Amaral, L.A.N.2
  • 30
    • 0034952253 scopus 로고    scopus 로고
    • Hass, L.M., Schwartz, P.M. and Kodali, P. (2001) 'Discovery Link: A system for integrated access to life science data sources', IBM Systems Journal, 40, pp.489-51 1.
    • Hass, L.M., Schwartz, P.M. and Kodali, P. (2001) 'Discovery Link: A system for integrated access to life science data sources', IBM Systems Journal, Vol. 40, pp.489-51 1.
  • 31
    • 0033872934 scopus 로고    scopus 로고
    • Graph visualization and navigation in information visualization: A survey
    • Herman, I., Melancon, G. and Marshall, M.S. (2000) 'Graph visualization and navigation in information visualization: A survey', IEEE CS Society, Vol. 6, pp.24-43.
    • (2000) IEEE CS Society , vol.6 , pp. 24-43
    • Herman, I.1    Melancon, G.2    Marshall, M.S.3
  • 33
  • 34
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N. and Barabási, A-L. (2000) 'The large-scale organization of metabolic networks', Nature Vol. 407, pp.651-654.
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    Barabási, A.-L.5
  • 35
  • 37
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano, H. (2002) 'Systems biology: A brief overview', Science, Vol. 295, pp. 1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 38
    • 0037208158 scopus 로고    scopus 로고
    • TRANSPATH: An integrated database on signal transduction and a tool for array analysis
    • Krull, M., Voss, N., Choi, C., Pistor, S., Potapov, A. and Wingender, E. (2003) 'TRANSPATH: An integrated database on signal transduction and a tool for array analysis', Nucl. Acids Res., Vol. 31, pp.97-100.
    • (2003) Nucl. Acids Res , vol.31 , pp. 97-100
    • Krull, M.1    Voss, N.2    Choi, C.3    Pistor, S.4    Potapov, A.5    Wingender, E.6
  • 39
    • 1542680971 scopus 로고    scopus 로고
    • Nonlinear projection with curvilinear distances: Isomap versus curvilinear distance analysis
    • Lee, J.A., Lendasse, A. and Verleysen, M. (2004a) 'Nonlinear projection with curvilinear distances: Isomap versus curvilinear distance analysis', Neurocomputing, Vol. 57, pp.49-76.
    • (2004) Neurocomputing , vol.57 , pp. 49-76
    • Lee, J.A.1    Lendasse, A.2    Verleysen, M.3
  • 40
    • 1342330530 scopus 로고    scopus 로고
    • A graph-theoretic modeling on GO space for biological interpretation of gene clusters
    • Lee, S.G., Hur, J.U. and Kim, Y.S. (2004b) 'A graph-theoretic modeling on GO space for biological interpretation of gene clusters', Bioinformatics, Vol. 20, pp.381-388.
    • (2004) Bioinformatics , vol.20 , pp. 381-388
    • Lee, S.G.1    Hur, J.U.2    Kim, Y.S.3
  • 41
    • 24144463983 scopus 로고    scopus 로고
    • Metabolic control through the PGC-1 family of transcription coactivators
    • Lin, J., Handschin, C. and Spiegelman, B.M. (2005) 'Metabolic control through the PGC-1 family of transcription coactivators', Cell Metab. Vol. 1, pp.361-370.
    • (2005) Cell Metab , vol.1 , pp. 361-370
    • Lin, J.1    Handschin, C.2    Spiegelman, B.M.3
  • 42
    • 4644326931 scopus 로고    scopus 로고
    • Luscombe, N.M., Madan Babu, M., Yu, H., Snyder, M., Teichmann, S.A. and Gerstein, M. (2004) Genomic Analysis of Regulatory Network Dynamics Reveals Large Topological Changes, 431, pp.308-312.
    • Luscombe, N.M., Madan Babu, M., Yu, H., Snyder, M., Teichmann, S.A. and Gerstein, M. (2004) Genomic Analysis of Regulatory Network Dynamics Reveals Large Topological Changes, Vol. 431, pp.308-312.
  • 44
    • 20044380758 scopus 로고    scopus 로고
    • Medina-Gomez, G., Virtue, S., Lelliott, C., Boiani, R., Campbell, M., Christodoulides, C., Perrin, C., Jimenez-Linan, M., Blount, M., Dixon, J., Zahn, D., Thresher, R.R., Aparicio, S., Carlton, M., Colledge, W.H., Kettunen, M.I., Seppanen-Laakso, T., Sethi, J.K., O'Rahilly, S., Brindle, K., Cinti, S., Oresic, M., Burcelin, R. and Vidal-Puig, A. (2005) 'The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific Peroxisome Proliferator-Activated Receptor-{gamma}2 isoform', Diabetes, 54, pp.1706-1716.
    • Medina-Gomez, G., Virtue, S., Lelliott, C., Boiani, R., Campbell, M., Christodoulides, C., Perrin, C., Jimenez-Linan, M., Blount, M., Dixon, J., Zahn, D., Thresher, R.R., Aparicio, S., Carlton, M., Colledge, W.H., Kettunen, M.I., Seppanen-Laakso, T., Sethi, J.K., O'Rahilly, S., Brindle, K., Cinti, S., Oresic, M., Burcelin, R. and Vidal-Puig, A. (2005) 'The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific Peroxisome Proliferator-Activated Receptor-{gamma}2 isoform', Diabetes, Vol. 54, pp.1706-1716.
  • 46
    • 84930064585 scopus 로고    scopus 로고
    • Hierarchical organization in complex networks
    • Ravasz, E. and Barabási, A-L. (2003) 'Hierarchical organization in complex networks', Physical Review, Vol. 67, pp.1-7.
    • (2003) Physical Review , vol.67 , pp. 1-7
    • Ravasz, E.1    Barabási, A.-L.2
  • 47
    • 84887006810 scopus 로고
    • A nonlinear mapping for data structure analysis
    • Sammon Jr., J.W. (1969) 'A nonlinear mapping for data structure analysis', IEEE Trans. Comp., Vol. C-18, pp.401-409.
    • (1969) IEEE Trans. Comp , vol.C-18 , pp. 401-409
    • Sammon Jr., J.W.1
  • 48
    • 22944451507 scopus 로고    scopus 로고
    • Visualization for biological pathways: Requirements analysis, systems evaluation and research agenda
    • Saraiya, P., North, C. and Duca, K. (2005) 'Visualization for biological pathways: Requirements analysis, systems evaluation and research agenda', IEEE Trans. Vis. Comput. Graph., Vol. 11, pp.443-456.
    • (2005) IEEE Trans. Vis. Comput. Graph , vol.11 , pp. 443-456
    • Saraiya, P.1    North, C.2    Duca, K.3
  • 49
    • 12144262660 scopus 로고    scopus 로고
    • Data integration: Challenges for drug discovery
    • Searls, D.B. (2005) 'Data integration: Challenges for drug discovery', Nat. Rev. Drug Disc., Vol. 4, pp.45-48.
    • (2005) Nat. Rev. Drug Disc , vol.4 , pp. 45-48
    • Searls, D.B.1
  • 50
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • Segal, E., Friedman, N., Koller, D. and Regev, A. (2004) 'A module map showing conditional activity of expression modules in cancer', Nat. Genetics, Vol. 36, pp.1090-1098.
    • (2004) Nat. Genetics , vol.36 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3    Regev, A.4
  • 51
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networksar interactions
    • Shannon, P.M.A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) 'Cytoscape: A software environment for integrated models of biomolecular interaction networksar interactions', Genome Research, Vol. 3, pp.2498-2504.
    • (2003) Genome Research , vol.3 , pp. 2498-2504
    • Shannon, P.M.A.1    Ozier, O.2    Baliga, N.S.3    Wang, J.T.4    Ramage, D.5    Amin, N.6    Schwikowski, B.7    Ideker, T.8
  • 52
    • 31144438390 scopus 로고    scopus 로고
    • Rescuing drug discovery: In vivo systems pathology and systems pharmacology
    • van der Greef, J. and McBurney, R. (2005) 'Rescuing drug discovery: In vivo systems pathology and systems pharmacology', Nat. Rev. Drug Disc., Vol. 4, pp.961-967.
    • (2005) Nat. Rev. Drug Disc , vol.4 , pp. 961-967
    • van der Greef, J.1    McBurney, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.