메뉴 건너뛰기




Volumn 90, Issue 11, 2002, Pages 1793-1802

Visualizing metabolic pathways: Comparative genomics and expression analysis

Author keywords

Bioinformatics; Comparative genomics; Expression; Metabolic maps; Microarrays

Indexed keywords

BIOTECHNOLOGY; CELLS; DATABASE SYSTEMS; ENZYMES; INTERNET;

EID: 3042859147     PISSN: 00189219     EISSN: None     Source Type: Journal    
DOI: 10.1109/JPROC.2002.804687     Document Type: Article
Times cited : (11)

References (40)
  • 1
    • 0037129228 scopus 로고    scopus 로고
    • Microbial genomes multiply
    • Apr.
    • R. F. Doolittle, "Microbial genomes multiply," Nature, vol. 416, pp. 697-700, Apr. 2002.
    • (2002) Nature , vol.416 , pp. 697-700
    • Doolittle, R.F.1
  • 3
    • 0031966808 scopus 로고    scopus 로고
    • Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
    • Mar.
    • H. Bono, H. Ogata, S. Goto, and M. Kanehisa, "Reconstruction of amino acid biosynthesis pathways from the complete genome sequence," Genome Research, vol. 8, pp. 203-210, Mar. 1998.
    • (1998) Genome Research , vol.8 , pp. 203-210
    • Bono, H.1    Ogata, H.2    Goto, S.3    Kanehisa, M.4
  • 4
    • 84858877427 scopus 로고    scopus 로고
    • Rockville, MD. [Online]
    • The Institute for Genomic Research (TIGR) Comprehensive Microbial Resource., Rockville, MD. [Online]. Available: http://www.tigr.org/tigr-scripts/ CMR2/GenePieChart.spl?db=CMR
  • 5
    • 0035860545 scopus 로고    scopus 로고
    • Pathway databases: A case study in computational symbolic theories
    • Sept.
    • P. D. Karp, "Pathway databases: A case study in computational symbolic theories," Science, vol. 293, pp. 2040-2044, Sept. 2001.
    • (2001) Science , vol.293 , pp. 2040-2044
    • Karp, P.D.1
  • 6
    • 0344134874 scopus 로고    scopus 로고
    • Analysis of binary relations and hierarchies of enzymes in the metabolic pathways
    • Dec.
    • H. Ogata, H. Bono, W. Fujibuchi, S. Goto, and M. Kanehisa, "Analysis of binary relations and hierarchies of enzymes in the metabolic pathways," Genome Informatics, vol. 10, pp. 128-136, Dec. 1996.
    • (1996) Genome Informatics , vol.10 , pp. 128-136
    • Ogata, H.1    Bono, H.2    Fujibuchi, W.3    Goto, S.4    Kanehisa, M.5
  • 8
    • 84858871982 scopus 로고    scopus 로고
    • [Online]
    • BioCyc Knowledge Library. [Online]. Available: http://biocyc.org/
  • 10
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Jan.
    • M. Kanehisa and S. Goto, "KEGG: Kyoto Encyclopedia of Genes and Genomes," Nucleic Acids Res., vol. 28, pp. 27-30, Jan. 2000.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 11
    • 0036084127 scopus 로고    scopus 로고
    • The EcoCyc database
    • Jan.
    • P. D. Karp et al., "The EcoCyc database," Nucleic Acids Research, vol. 30, pp. 56-58, Jan. 2002.
    • (2002) Nucleic Acids Research , vol.30 , pp. 56-58
    • Karp, P.D.1
  • 13
    • 0036086784 scopus 로고    scopus 로고
    • Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
    • May
    • S. M. Paley and P. D. Karp, "Evaluation of computational metabolic-pathway predictions for Helicobacter pylori," Bioinformatics, vol. 18, pp. 715-724, May 2002.
    • (2002) Bioinformatics , vol.18 , pp. 715-724
    • Paley, S.M.1    Karp, P.D.2
  • 14
    • 0037192115 scopus 로고    scopus 로고
    • Metabolic pathway analysis in trypanosomes and malaria parasites
    • Jan.
    • A. H. Fairlamb, "Metabolic pathway analysis in trypanosomes and malaria parasites," Phil. Trans. R. Soc. Land., vol. 357, pp. 101-107, Jan. 2002.
    • (2002) Phil. Trans. R. Soc. Land. , vol.357 , pp. 101-107
    • Fairlamb, A.H.1
  • 15
    • 0033168258 scopus 로고    scopus 로고
    • Integrated pathway-genome databases and their role in drug discovery
    • July
    • P. D. Karp, M. Krummenacker, S. Paley, and J. Wagg, "Integrated pathway-genome databases and their role in drug discovery," TIBTECH, vol. 17, pp. 275-281, July 1999.
    • (1999) TIBTECH , vol.17 , pp. 275-281
    • Karp, P.D.1    Krummenacker, M.2    Paley, S.3    Wagg, J.4
  • 16
    • 0034118607 scopus 로고    scopus 로고
    • Rickettsia prowazekii and Bartonella henselae: Differences in the intracellular life styles revisited
    • May
    • S. G. E. Andersson and C. Dehio, "Rickettsia prowazekii and Bartonella henselae: Differences in the intracellular life styles revisited," Int. J. Med. Microbiol., vol. 290, pp. 135-141, May 2000.
    • (2000) Int. J. Med. Microbiol. , vol.290 , pp. 135-141
    • Andersson, S.G.E.1    Dehio, C.2
  • 17
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Sept.
    • F. R. Blattner et al., "The complete genome sequence of Escherichia coli K-12," Science, vol. 277, pp. 1453-1474, Sept. 1997.
    • (1997) Science , vol.277 , pp. 1453-1474
    • Blattner, F.R.1
  • 18
    • 0037039357 scopus 로고    scopus 로고
    • The genome sequence of the facultative intracellular pathogen Brucella melitensis
    • Jan.
    • V. G. Del Vecchio et al., "The genome sequence of the facultative intracellular pathogen Brucella melitensis," Proc. Nat. Acad. Sci. USA, vol. 99, pp. 443-448, Jan. 2002.
    • (2002) Proc. Nat. Acad. Sci. USA , vol.99 , pp. 443-448
    • Del Vecchio, V.G.1
  • 19
    • 0032512051 scopus 로고    scopus 로고
    • The genome sequence of Rickettsia prowazekii and the origin of mitochondria
    • Nov.
    • S. G. E. Andersson et al., "The genome sequence of Rickettsia prowazekii and the origin of mitochondria," Nature, vol. 396, pp. 133-140, Nov. 1998.
    • (1998) Nature , vol.396 , pp. 133-140
    • Andersson, S.G.E.1
  • 20
    • 0032744302 scopus 로고    scopus 로고
    • Evolution of metabolisms: A new method for the comparison of metabolic pathways using genomics information
    • Fall-Winter
    • C. V. Forst and K. Schulten, "Evolution of metabolisms: A new method for the comparison of metabolic pathways using genomics information," J. Comput. Biol., vol. 6, pp. 343-360, Fall-Winter 1999.
    • (1999) J. Comput. Biol. , vol.6 , pp. 343-360
    • Forst, C.V.1    Schulten, K.2
  • 21
    • 0034991456 scopus 로고    scopus 로고
    • Phylogenetic analysis of metabolic pathways
    • June
    • _, "Phylogenetic analysis of metabolic pathways," J. Mol. Evol., vol. 52, pp. 471-489, June 2001.
    • (2001) J. Mol. Evol. , vol.52 , pp. 471-489
  • 22
    • 0035144693 scopus 로고    scopus 로고
    • Microarrays under the microscope
    • Feb.
    • S. E. Wildsmith and F. J. Elcock, "Microarrays under the microscope," Mol. Pathol., vol. 54, pp. 8-16, Feb. 2001.
    • (2001) Mol. Pathol. , vol.54 , pp. 8-16
    • Wildsmith, S.E.1    Elcock, F.J.2
  • 23
    • 0035032570 scopus 로고    scopus 로고
    • Statistical design and the analysis of gene expression microarray data
    • Apr.
    • M. K. Kerr and G. A. Churchill, "Statistical design and the analysis of gene expression microarray data," Genet. Res., vol. 77, pp. 123-128, Apr. 2001.
    • (2001) Genet. Res. , vol.77 , pp. 123-128
    • Kerr, M.K.1    Churchill, G.A.2
  • 24
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with DNA microarrays
    • Suppl. 33-37, Jan.
    • P. O. Brown and D. Botstein, "Exploring the new world of the genome with DNA microarrays," Nat. Genet., vol. 21, no. 1, pp. Suppl. 33-37, Jan. 1999.
    • (1999) Nat. Genet. , vol.21 , Issue.1
    • Brown, P.O.1    Botstein, D.2
  • 26
    • 0034710992 scopus 로고    scopus 로고
    • DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli
    • Oct.
    • A. B. Khodursky et al., "DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli," in Proc. Nat. Acad. Sci. USA 2000, vol. 97, Oct. 2000, pp. 12 170-12175.
    • (2000) Proc. Nat. Acad. Sci. USA 2000 , vol.97 , pp. 12170-12175
    • Khodursky, A.B.1
  • 27
    • 0002146392 scopus 로고    scopus 로고
    • Genome-scale gene expression analysis and pathway reconstruction in KEGG
    • Dec.
    • M. Nakao, H. Bono, S. Kawashima, T. Kamiya, and K. Sato et al., "Genome-scale gene expression analysis and pathway reconstruction in KEGG," Genome Informatics, vol. 10, pp. 94-103, Dec. 1999.
    • (1999) Genome Informatics , vol.10 , pp. 94-103
    • Nakao, M.1    Bono, H.2    Kawashima, S.3    Kamiya, T.4    Sato, K.5
  • 28
    • 33646755951 scopus 로고    scopus 로고
    • KEGG/EXPRESSION: A database for browsing and analysing microarray expression data
    • Dec.
    • S. Goto et al., "KEGG/EXPRESSION: A database for browsing and analysing microarray expression data," Genome Informatics, vol. 11, pp. 222-223, Dec. 2000.
    • (2000) Genome Informatics , vol.11 , pp. 222-223
    • Goto, S.1
  • 29
    • 0036061833 scopus 로고    scopus 로고
    • Pathway Processor: A tool for integrating whole-genome expression results into metabolic networks
    • July
    • P. Grosu, J. P. Townsend, D. L. Haitl, and D. Cavalieri, "Pathway Processor: A tool for integrating whole-genome expression results into metabolic networks," Genome Res., vol. 12, pp. 1121-1126, July 2002.
    • (2002) Genome Res. , vol.12 , pp. 1121-1126
    • Grosu, P.1    Townsend, J.P.2    Haitl, D.L.3    Cavalieri, D.4
  • 30
    • 0036369840 scopus 로고    scopus 로고
    • Genome-wide patheway analysys and visualization using gene expression data
    • Jan.
    • M. P. Kurhekar, S. Adak, S. Jhunjhunwala, and K. Raghupathy, "Genome-wide patheway analysys and visualization using gene expression data," in Pac. Symp, Biocomp., Jan. 2002, pp. 462-473.
    • (2002) Pac. Symp, Biocomp. , pp. 462-473
    • Kurhekar, M.P.1    Adak, S.2    Jhunjhunwala, S.3    Raghupathy, K.4
  • 31
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale in yeast
    • Oct.
    • J. L. DeRisi, V. R. Iyer, and P. O. Brown, "Exploring the metabolic and genetic control of gene expression on a genomic scale in yeast," Science, vol. 278, pp. 680-686, Oct. 1997.
    • (1997) Science , vol.278 , pp. 680-686
    • Derisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 32
    • 84858880985 scopus 로고    scopus 로고
    • [Online]
    • NCBI Gene Expression Omnibus. [Online], GEO accession GSE28. Available: http://www.ncbi.nlm.nih.gov/geo/.
    • GEO Accession GSE28
  • 33
    • 0035281870 scopus 로고    scopus 로고
    • Metabolic modeling of microbial strains in silico
    • Mar.
    • M. W. Covert et al., "Metabolic modeling of microbial strains in silico," Trends in Biochemical Sciences, vol. 26, pp. 179-186, Mar. 2001.
    • (2001) Trends in Biochemical Sciences , vol.26 , pp. 179-186
    • Covert, M.W.1
  • 34
    • 0033136109 scopus 로고    scopus 로고
    • Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era
    • May-June
    • C. Schilling, S. Schuster, B. O. Palsson, and R. Heinrich, "Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era," Biotechnol. Prog., vol. 15, pp. 296-303, May-June 1999.
    • (1999) Biotechnol. Prog. , vol.15 , pp. 296-303
    • Schilling, C.1    Schuster, S.2    Palsson, B.O.3    Heinrich, R.4
  • 35
    • 0033136116 scopus 로고    scopus 로고
    • Toward metabolic phenomics: Analysis of genomic data using flux balances
    • May-June
    • C. H. Schilling, J. S. Edwards, and B. O. Palsson, "Toward metabolic phenomics: Analysis of genomic data using flux balances," Biotechnol. Prog., vol. 15, pp. 288-295, May-June 1999.
    • (1999) Biotechnol. Prog. , vol.15 , pp. 288-295
    • Schilling, C.H.1    Edwards, J.S.2    Palsson, B.O.3
  • 36
    • 0036273832 scopus 로고    scopus 로고
    • Genomics to fluxomics and physiomics - Pathway engineering
    • May
    • K. Sanford, P. Soucaille, G. Whited, and G. Chotani, "Genomics to fluxomics and physiomics - Pathway engineering," Curr. Opin. Microbiol., vol. 5, pp. 318-322, May 2002.
    • (2002) Curr. Opin. Microbiol. , vol.5 , pp. 318-322
    • Sanford, K.1    Soucaille, P.2    Whited, G.3    Chotani, G.4
  • 37
    • 0035874957 scopus 로고    scopus 로고
    • How to make a superior cell
    • June
    • G. Stephanopoulos and J. Kelleher, "How to make a superior cell," Science, vol. 292, pp. 2024-2025, June 2001.
    • (2001) Science , vol.292 , pp. 2024-2025
    • Stephanopoulos, G.1    Kelleher, J.2
  • 38
    • 0037177589 scopus 로고    scopus 로고
    • Maneuvering in the complex path from genotype to phenotype
    • Apr.
    • R. Strohman, "Maneuvering in the complex path from genotype to phenotype," Science, vol. 296, pp. 701-703, Apr. 2002.
    • (2002) Science , vol.296 , pp. 701-703
    • Strohman, R.1
  • 39
    • 0034959944 scopus 로고    scopus 로고
    • Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks
    • Apr.
    • O. Fiehn, "Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks," Comp. Funct. Genom., vol. 2, pp. 155-168, Apr. 2002.
    • (2002) Comp. Funct. Genom. , vol.2 , pp. 155-168
    • Fiehn, O.1
  • 40
    • 0036331713 scopus 로고    scopus 로고
    • Functional genomics: High-throughput mRNA, protein and metabolite analyzes
    • Jan.
    • D. J. Oliver, B. Nikolau, and E. S. Wurtele, "Functional genomics: High-throughput mRNA, protein and metabolite analyzes," Metabolic Eng., vol. 4, pp. 98-106, Jan. 2002.
    • (2002) Metabolic Eng. , vol.4 , pp. 98-106
    • Oliver, D.J.1    Nikolau, B.2    Wurtele, E.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.