메뉴 건너뛰기




Volumn 57, Issue , 2006, Pages 105-115

Bioinformatics approaches to integrate metabolomics and other systems biology data

Author keywords

[No Author keywords available]

Indexed keywords


EID: 85014049276     PISSN: 0934943X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/3-540-29782-0_8     Document Type: Chapter
Times cited : (24)

References (48)
  • 1
    • 0038699591 scopus 로고    scopus 로고
    • High-throughput classification of yeast mutants for functional genomics using metabolic footprinting
    • Allen J, Davey HM, Broadhurst D et al. (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21:692-696
    • (2003) Nat Biotechnol , vol.21 , pp. 692-696
    • Allen, J.1    Davey, H.M.2    Broadhurst, D.3
  • 2
    • 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. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 3
    • 13444273448 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt).
    • Bairoch A, Apweiler R, Wu CH et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res 33:D154-D159
    • (2005) Nucleic Acids Res , vol.33 , pp. D154-D159
    • Bairoch, A.1    Apweiler, R.2    Wu, C.H.3
  • 4
    • 4444309760 scopus 로고    scopus 로고
    • Potential of metabolomics as a functional genomics tool
    • Bino RJ, Hall RD, Fiehn O et al. (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9:418-425
    • (2004) Trends Plant Sci , vol.9 , pp. 418-425
    • Bino, R.J.1    Hall, R.D.2    Fiehn, O.3
  • 5
    • 18344396568 scopus 로고    scopus 로고
    • Minimum information about a microarray experiment (MIAME) -toward standards for microarray data
    • Brazma A, Hingamp P, Quackenbush J et al. (2001) Minimum information about a microarray experiment (MIAME) -toward standards for microarray data. Nature Genet 29:365-371
    • (2001) Nature Genet , vol.29 , pp. 365-371
    • Brazma, A.1    Hingamp, P.2    Quackenbush, J.3
  • 6
    • 13244292589 scopus 로고    scopus 로고
    • Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism
    • Broeckling CD, Huhman DV, Farag MA et al. (2005) Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J Exp Bot 56:323-336
    • (2005) J Exp Bot , vol.56 , pp. 323-336
    • Broeckling, C.D.1    Huhman, D.V.2    Farag, M.A.3
  • 8
    • 11144257813 scopus 로고    scopus 로고
    • Discrimination of pathogenic clinical isolates and laboratory strains of Bacillus cereus byNMR-based metabolomic profiling
    • Bundy JG, Willey TL, Castell RS, Ellar DJ, Brindle KM (2005) Discrimination of pathogenic clinical isolates and laboratory strains of Bacillus cereus byNMR-based metabolomic profiling. FEMS Microbiol Lett 242:127-136
    • (2005) FEMS Microbiol Lett , vol.242 , pp. 127-136
    • Bundy, J.G.1    Willey, T.L.2    Castell, R.S.3    Ellar, D.J.4    Brindle, K.M.5
  • 9
    • 20344365760 scopus 로고    scopus 로고
    • The origin of correlations in metabolomics data
    • Camacho D, de la Fuente A, Mendes P (2005) The origin of correlations in metabolomics data. Metabolomics 1:53-63
    • (2005) Metabolomics , vol.1 , pp. 53-63
    • Camacho, D.1    De La Fuente, A.2    Mendes, P.3
  • 10
    • 0029436725 scopus 로고
    • Challenges in integrating biological data sources
    • Davidson SB, Overton C, Buneman P (1995) Challenges in integrating biological data sources. J Comput Biol 2:557-572
    • (1995) J Comput Biol , vol.2 , pp. 557-572
    • Davidson, S.B.1    Overton, C.2    Buneman, P.3
  • 11
    • 4243617117 scopus 로고    scopus 로고
    • The newAutomatedMass Spectrometry Deconvolution and Identification System (AMDIS). Spectroscopy
    • Davies T (1998) The newAutomatedMass Spectrometry Deconvolution and Identification System (AMDIS). Spectroscopy, Europe 10:24-27
    • (1998) Europe , vol.10 , pp. 24-27
    • Davies, T.1
  • 12
    • 6044249965 scopus 로고    scopus 로고
    • Saccharomyces genome database: Underlying principles and organisation
    • Dwight SS, Balakrishnan R, Christie KR et al. (2004) Saccharomyces genome database: underlying principles and organisation. Brief Bioinform 5:9-22
    • (2004) Brief Bioinform , vol.5 , pp. 9-22
    • Dwight, S.S.1    Balakrishnan, R.2    Christie, K.R.3
  • 14
    • 0037163864 scopus 로고    scopus 로고
    • Physiological variation in metabolic phenotyping and functional genomic studies: Use of orthogonal signal correction and PLS-DA
    • Gavaghan CL, Wilson ID, Nicholson JK (2002) Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA. FEBS Lett 530:191-196
    • (2002) FEBS Lett , vol.530 , pp. 191-196
    • Gavaghan, C.L.1    Wilson, I.D.2    Nicholson, J.K.3
  • 15
    • 13244279624 scopus 로고    scopus 로고
    • Making sense of the metabolome using evolutionary computation: Seeing the wood with the trees
    • Goodacre R (2005) Making sense of the metabolome using evolutionary computation: seeing the wood with the trees. J Exp Bot 56:245-254
    • (2005) J Exp Bot , vol.56 , pp. 245-254
    • Goodacre, R.1
  • 16
    • 0033970940 scopus 로고    scopus 로고
    • Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy
    • Goodacre R, Shann B, Gilbert RJ et al. (2000) Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy. Anal Chem 72:119-127
    • (2000) Anal Chem , vol.72 , pp. 119-127
    • Goodacre, R.1    Shann, B.2    Gilbert, R.J.3
  • 18
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): Amedium for representation and exchange of biochemical network models
    • Hucka M, Beale M, Fiehn O et al. (2003) The systems biology markup language (SBML): amedium for representation and exchange of biochemical network models. Bioinformatics 19:524-531
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Beale, M.2    Fiehn, O.3
  • 19
    • 19944398727 scopus 로고    scopus 로고
    • A proposed framework for the description of plant metabolomics experiments and their results
    • Jenkins H, Hardy N, Beckmann M, et al. (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol 22:1601-1606
    • (2004) Nat Biotechnol , vol.22 , pp. 1601-1606
    • Jenkins, H.1    Hardy, N.2    Beckmann, M.3
  • 21
    • 1542408614 scopus 로고    scopus 로고
    • A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS
    • Jonsson P, Broadhurst D, Goodacre R et al. (2004) A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Anal Chem 76:1738-1745
    • (2004) Anal Chem , vol.76 , pp. 1738-1745
    • Jonsson, P.1    Broadhurst, D.2    Goodacre, R.3
  • 23
    • 2942676743 scopus 로고    scopus 로고
    • Metabolomics and systems biology: Making sense of the soup
    • Kell DB (2004) Metabolomics and systems biology: Making sense of the soup. CurrOpin Microbiol 7:296-307
    • (2004) Curropin Microbiol , vol.7 , pp. 296-307
    • Kell, D.B.1
  • 24
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano H (2002) Systems biology: a brief overview. Science 295:1662-1664
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 25
    • 0346494819 scopus 로고    scopus 로고
    • MetaCyc: A multiorganism database of metabolic pathways and enzymes
    • Krieger CJ, Zhang P, Mueller LA et al. (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 32:D438-D442
    • (2004) Nucleic Acids Res , vol.32 , pp. D438-D442
    • Krieger, C.J.1    Zhang, P.2    Mueller, L.A.3
  • 26
    • 13444312027 scopus 로고    scopus 로고
    • Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps
    • Lange BM, Ghassemian M (2005) Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps. Phytochemistry 66:413-451
    • (2005) Phytochemistry , vol.66 , pp. 413-451
    • Lange, B.M.1    Ghassemian, M.2
  • 27
    • 13444273452 scopus 로고    scopus 로고
    • The TIGR Gene Indices: Clustering and assembling EST and known genes and integration with eukaryotic genomes
    • Lee Y, Tsai J, Sunkara S et al. (2005) The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 33:D71-D74
    • (2005) Nucleic Acids Res , vol.33 , pp. D71-D74
    • Lee, Y.1    Tsai, J.2    Sunkara, S.3
  • 28
    • 0036307213 scopus 로고    scopus 로고
    • Visualizing metabolic activity on a genome-wide scale
    • Luyf AC, de Gast J, van Kampen AH (2002) Visualizing metabolic activity on a genome-wide scale. Bioinformatics 18:813-818
    • (2002) Bioinformatics , vol.18 , pp. 813-818
    • Luyf, A.C.1    De Gast, J.2    Van Kampen, A.H.3
  • 29
    • 0000718866 scopus 로고    scopus 로고
    • Modeling large scale biological systems from functional genomicdata: Parameter estimation
    • Kitano H, MIT Press, Cambridge, MA
    • Mendes P (2001) Modeling large scale biological systems from functional genomicdata: Parameter estimation. In: Kitano H (ed) Foundations of systems biology. MIT Press, Cambridge, MA, pp 163-186
    • (2001) Foundations of Systems Biology , pp. 163-186
    • Mendes, P.1
  • 30
    • 0036596887 scopus 로고    scopus 로고
    • Emerging bioinformatics for the metabolome
    • Mendes P (2002) Emerging bioinformatics for the metabolome. Brief Bioinform 3:134-145
    • (2002) Brief Bioinform , vol.3 , pp. 134-145
    • Mendes, P.1
  • 31
    • 77957055223 scopus 로고    scopus 로고
    • Bioinformatics and computational biology for plant functional genomics
    • Mendes P, de la Fuente A, Hoops S (2002) Bioinformatics and computational biology for plant functional genomics. Rec Adv Phytochem 36:1-13
    • (2002) Rec Adv Phytochem , vol.36 , pp. 1-13
    • Mendes, P.1    De La Fuente, A.2    Hoops, S.3
  • 32
    • 0038460047 scopus 로고    scopus 로고
    • AraCyc: A biochemical pathway database for Arabidopsis
    • Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453-460
    • (2003) Plant Physiol , vol.132 , pp. 453-460
    • Mueller, L.A.1    Zhang, P.2    Rhee, S.Y.3
  • 33
    • 0036331713 scopus 로고    scopus 로고
    • Functional genomics: High-throughput mRNA, protein, and metabolite analyses
    • Oliver DJ, Nikolau B, Wurtele ES (2002) Functional genomics: high-throughput mRNA, protein, and metabolite analyses. Metabolic Eng 4:98-106
    • (2002) Metabolic Eng , vol.4 , pp. 98-106
    • Oliver, D.J.1    Nikolau, B.2    Wurtele, E.S.3
  • 34
    • 1242339568 scopus 로고    scopus 로고
    • Common interchange standards for proteomics data: Public availability of tools and schema
    • Orchard S, Hermjakob H, Julian RK et al. (2004) Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics 4:490-491
    • (2004) Proteomics , vol.4 , pp. 490-491
    • Orchard, S.1    Hermjakob, H.2    Julian, R.K.3
  • 35
    • 3342906838 scopus 로고    scopus 로고
    • Discrimination models using variancestabilizing transformation of metabolomic NMR data
    • Purohit PV, Rocke DM, Viant MR, Woodruff DL (2004) Discrimination models using variancestabilizing transformation of metabolomic NMR data. Omics 8:118-130
    • (2004) Omics , vol.8 , pp. 118-130
    • Purohit, P.V.1    Rocke, D.M.2    Viant, M.R.3    Woodruff, D.L.4
  • 36
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data
    • Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2:418-427
    • (2001) Nat Rev Genet , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 37
    • 0035160371 scopus 로고    scopus 로고
    • A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations
    • Raamsdonk LM, Teusink B, Broadhurst D et al. (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnol 19:45-50
    • (2001) Nature Biotechnol , vol.19 , pp. 45-50
    • Raamsdonk, L.M.1    Teusink, B.2    Broadhurst, D.3
  • 38
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3
  • 39
    • 7044229934 scopus 로고    scopus 로고
    • Development of biomarkers based on diet-dependentmetabolic serotypes: Practical issues in development of expert system-based classification models in metabolomic studies
    • Shi H, Paolucci U, Vigneau-Callahan KE, Milbury PE, Matson WR, Kristal BS (2004) Development of biomarkers based on diet-dependentmetabolic serotypes: practical issues in development of expert system-based classification models in metabolomic studies. Omics 8:197-208
    • (2004) Omics , vol.8 , pp. 197-208
    • Shi, H.1    Paolucci, U.2    Vigneau-Callahan, K.E.3    Milbury, P.E.4    Matson, W.R.5    Kristal, B.S.6
  • 40
    • 0038281453 scopus 로고    scopus 로고
    • Observing and interpreting correlations in metabolomic networks
    • Steuer R, Kurths J, Fiehn O, Weckwerth W (2003) Observing and interpreting correlations in metabolomic networks. Bioinformatics 19:1019-1026
    • (2003) Bioinformatics , vol.19 , pp. 1019-1026
    • Steuer, R.1    Kurths, J.2    Fiehn, O.3    Weckwerth, W.4
  • 41
    • 0345270397 scopus 로고    scopus 로고
    • Plant metabolomics: Large-scale phytochemistry in the functional genomics era
    • Sumner LW, Mendes P, Dixon RA (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62:817-836
    • (2003) Phytochemistry , vol.62 , pp. 817-836
    • Sumner, L.W.1    Mendes, P.2    Dixon, R.A.3
  • 42
    • 0037337307 scopus 로고    scopus 로고
    • A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    • Taylor CF, Paton NW, Garwood KL et al. (2003) A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 21:247-254
    • (2003) Nat Biotechnol , vol.21 , pp. 247-254
    • Taylor, C.F.1    Paton, N.W.2    Garwood, K.L.3
  • 43
    • 12144291195 scopus 로고    scopus 로고
    • MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    • Thimm O, Blasing O, Gibon Y et al. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914-939
    • (2004) Plant J , vol.37 , pp. 914-939
    • Thimm, O.1    Blasing, O.2    Gibon, Y.3
  • 44
    • 4444363957 scopus 로고    scopus 로고
    • Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis
    • Verhoeckx KC, Bijlsma S, Jespersen S et al. (2004) Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis. Int Immunopharmacol 4:1499-1514
    • (2004) Int Immunopharmacol , vol.4 , pp. 1499-1514
    • Verhoeckx, K.C.1    Bijlsma, S.2    Jespersen, S.3
  • 45
    • 0345701915 scopus 로고    scopus 로고
    • Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles
    • Wagner C, Sefkow M, Kopka J (2003) Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry 62:887-900
    • (2003) Phytochemistry , vol.62 , pp. 887-900
    • Wagner, C.1    Sefkow, M.2    Kopka, J.3
  • 46
    • 0142040405 scopus 로고    scopus 로고
    • Metabolomics in systems biology
    • Weckwerth W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54:669-689
    • (2003) Annu Rev Plant Biol , vol.54 , pp. 669-689
    • Weckwerth, W.1
  • 47
    • 0035348948 scopus 로고    scopus 로고
    • Analysis and comparison of metabolic pathway databases
    • Wittig U, de Beuckelaer A (2001) Analysis and comparison of metabolic pathway databases. Brief Bioinform 2:126-142
    • (2001) Brief Bioinform , vol.2 , pp. 126-142
    • Wittig, U.1    De Beuckelaer, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.