메뉴 건너뛰기




Volumn 388, Issue 2, 2009, Pages 390-414

Metabolic Pathfinding Using RPAIR Annotation

Author keywords

KEGG RPAIR; metabolic network; metabolic pathways; pathfinding; pathfinding evaluation

Indexed keywords

PYRUVIC ACID; WATER;

EID: 64449087758     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.03.006     Document Type: Article
Times cited : (53)

References (54)
  • 5
    • 38549117301 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi R., Foerster H., Fulcher C.A., Kaipa P., Krummenacker M., Latendresse M., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 36 (2008) D623-D631
    • (2008) Nucleic Acids Res. , vol.36
    • Caspi, R.1    Foerster, H.2    Fulcher, C.A.3    Kaipa, P.4    Krummenacker, M.5    Latendresse, M.6
  • 6
    • 0033670135 scopus 로고    scopus 로고
    • Pathway analysis in metabolic databases via differential metabolic display
    • Kueffner R., Zimmer R., and Lengauer T. Pathway analysis in metabolic databases via differential metabolic display. Bioinformatics 16 (2000) 825-836
    • (2000) Bioinformatics , vol.16 , pp. 825-836
    • Kueffner, R.1    Zimmer, R.2    Lengauer, T.3
  • 7
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Förster J., Famili I., Fu P., Palsson B.Ø., and Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13 (2003) 244-253
    • (2003) Genome Res. , vol.13 , pp. 244-253
    • Förster, J.1    Famili, I.2    Fu, P.3    Palsson, B.Ø.4    Nielsen, J.5
  • 8
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • Duarte N.C., Becker S.A., Jamshidi N., Thiele I., Mo M.L., Vo T.D., et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl Aced. Sci. 104 (2007) 1777-1782
    • (2007) Proc. Natl Aced. Sci. , vol.104 , pp. 1777-1782
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3    Thiele, I.4    Mo, M.L.5    Vo, T.D.6
  • 10
    • 0037881782 scopus 로고    scopus 로고
    • Metabolic reconstruction using shortest paths
    • Arita M. Metabolic reconstruction using shortest paths. Simul. Pract. Theory 8 (2000) 109-125
    • (2000) Simul. Pract. Theory , vol.8 , pp. 109-125
    • Arita, M.1
  • 11
    • 0037316239 scopus 로고    scopus 로고
    • Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
    • Ma H., and Zeng A.-P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19 (2003) 270-277
    • (2003) Bioinformatics , vol.19 , pp. 270-277
    • Ma, H.1    Zeng, A.-P.2
  • 14
    • 34248632008 scopus 로고    scopus 로고
    • Toward the automated generation of genome-scale metabolic networks in the SEED
    • DeJongh M., Formsma K., Boillot P., Gould J., Rycenga M., and Best A. Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinf. 8 (2007) 139
    • (2007) BMC Bioinf. , vol.8 , pp. 139
    • DeJongh, M.1    Formsma, K.2    Boillot, P.3    Gould, J.4    Rycenga, M.5    Best, A.6
  • 15
    • 0036086784 scopus 로고    scopus 로고
    • Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
    • Paley S.M., and Karp P.D. Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics 18 (2002) 705-714
    • (2002) Bioinformatics , vol.18 , pp. 705-714
    • Paley, S.M.1    Karp, P.D.2
  • 16
    • 24744467372 scopus 로고    scopus 로고
    • Filling gaps in a metabolic network using expression information
    • Kharchenko P., Vitkup D., and Church G.M. Filling gaps in a metabolic network using expression information. Bioinformatics 20 (2004) i178-i185
    • (2004) Bioinformatics , vol.20
    • Kharchenko, P.1    Vitkup, D.2    Church, G.M.3
  • 17
    • 33646171940 scopus 로고    scopus 로고
    • Identifying metabolic enzymes with multiple types of association evidence
    • Kharchenko P., Chen L., Freund Y., Vitkup D., and Church G.M. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinf. 7 (2006) 177
    • (2006) BMC Bioinf. , vol.7 , pp. 177
    • Kharchenko, P.1    Chen, L.2    Freund, Y.3    Vitkup, D.4    Church, G.M.5
  • 19
    • 0033764169 scopus 로고    scopus 로고
    • The small world of metabolism
    • Nature America, Inc.
    • Fell D.A., and Wagner A. The small world of metabolism. Metab. Eng. 18 (2000) 1121-1122 Nature America, Inc.
    • (2000) Metab. Eng. , vol.18 , pp. 1121-1122
    • Fell, D.A.1    Wagner, A.2
  • 20
    • 1242319556 scopus 로고    scopus 로고
    • The metabolic world of Escherichia coli is not small
    • Arita M. The metabolic world of Escherichia coli is not small. Proc. Natl Acad. Sci. 101 (2004) 1543-1547
    • (2004) Proc. Natl Acad. Sci. , vol.101 , pp. 1543-1547
    • Arita, M.1
  • 21
    • 30344456708 scopus 로고    scopus 로고
    • Inferring meaningful pathways in weighted metabolic networks
    • Croes D., Couche F., Wodak S., and van Helden J. Inferring meaningful pathways in weighted metabolic networks. J. Mol. Biol. 356 (2006) 222-236
    • (2006) J. Mol. Biol. , vol.356 , pp. 222-236
    • Croes, D.1    Couche, F.2    Wodak, S.3    van Helden, J.4
  • 23
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
    • Schuster S., Dandekar T., and Fell D.A. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. TIBTECH 17 (1999) 53-60
    • (1999) TIBTECH , vol.17 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 24
    • 33846015888 scopus 로고    scopus 로고
    • Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
    • Teusink B., Wiersma A., Molenaar D., Francke C., de Vos W.M., Siezen R.J., and Smid E.J. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 281 (2006) 40041-40048
    • (2006) J. Biol. Chem. , vol.281 , pp. 40041-40048
    • Teusink, B.1    Wiersma, A.2    Molenaar, D.3    Francke, C.4    de Vos, W.M.5    Siezen, R.J.6    Smid, E.J.7
  • 25
    • 2942579562 scopus 로고    scopus 로고
    • Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions
    • Edwards J.S., and Palsson B.Ø. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinf. 1 (2001) 1
    • (2001) BMC Bioinf. , vol.1 , pp. 1
    • Edwards, J.S.1    Palsson, B.Ø.2
  • 28
    • 0242574984 scopus 로고    scopus 로고
    • In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism
    • Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 13 (2003) 2455-2466
    • (2003) Genome Res. , vol.13 , pp. 2455-2466
    • Arita, M.1
  • 29
    • 0141850380 scopus 로고    scopus 로고
    • PathMiner: predicting metabolic pathways by heuristic search
    • McShan D.C., Rao S., and Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 19 (2003) 1692-1698
    • (2003) Bioinformatics , vol.19 , pp. 1692-1698
    • McShan, D.C.1    Rao, S.2    Shah, I.3
  • 30
    • 2942516004 scopus 로고    scopus 로고
    • Ab initio reconstruction of metabolic pathways
    • Boyer F., and Viari A. Ab initio reconstruction of metabolic pathways. Bioinformatics 19 (2003) ii26-ii34
    • (2003) Bioinformatics , vol.19
    • Boyer, F.1    Viari, A.2
  • 31
    • 16344376028 scopus 로고    scopus 로고
    • Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
    • Rahman S.A., Advani P., Schunk R., Schrader R., and Schomburg D. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 21 (2004) 1189-1193
    • (2004) Bioinformatics , vol.21 , pp. 1189-1193
    • Rahman, S.A.1    Advani, P.2    Schunk, R.3    Schrader, R.4    Schomburg, D.5
  • 32
    • 47549099578 scopus 로고    scopus 로고
    • Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks
    • Blum T., and Kolhbalcher O. Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. J. Comput. Biol. 15 (2008) 565-576
    • (2008) J. Comput. Biol. , vol.15 , pp. 565-576
    • Blum, T.1    Kolhbalcher, O.2
  • 34
    • 45249101693 scopus 로고    scopus 로고
    • RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions
    • Kotera M., Hattori M., Oh M.-A., Yamamoto R., Komeno T., Yabuzaki J., et al. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Inf. 15 (2004) P062
    • (2004) Genome Inf. , vol.15
    • Kotera, M.1    Hattori, M.2    Oh, M.-A.3    Yamamoto, R.4    Komeno, T.5    Yabuzaki, J.6
  • 35
    • 11444249446 scopus 로고    scopus 로고
    • Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions
    • Kotera M., Okuno Y., Hattori M., Goto S., and Kanehisa M. Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc. 126 (2004) 16487-16498
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 16487-16498
    • Kotera, M.1    Okuno, Y.2    Hattori, M.3    Goto, S.4    Kanehisa, M.5
  • 36
    • 34547691000 scopus 로고    scopus 로고
    • Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways
    • Oh M., Yamada T., Hattori M., Goto S., and Kanehisa M. Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf. Model 47 (2007) 1702-1712
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1702-1712
    • Oh, M.1    Yamada, T.2    Hattori, M.3    Goto, S.4    Kanehisa, M.5
  • 37
    • 23144466440 scopus 로고    scopus 로고
    • Metabolic PathFinding: inferring relevant pathways in biochemical networks
    • Croes D., Couche F., Wodak S., and van Helden J. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res. 33 (2005) W326-W330
    • (2005) Nucleic Acids Res. , vol.33
    • Croes, D.1    Couche, F.2    Wodak, S.3    van Helden, J.4
  • 38
    • 55749088074 scopus 로고    scopus 로고
    • Can sugars be produced from fatty acids? A test case for pathway analysis tools
    • de Figueiredo L.F., Schuster S., Kaleta C., and Fell D.A. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 24 (2008) 2615-2621
    • (2008) Bioinformatics , vol.24 , pp. 2615-2621
    • de Figueiredo, L.F.1    Schuster, S.2    Kaleta, C.3    Fell, D.A.4
  • 40
    • 28044438219 scopus 로고    scopus 로고
    • Enzymes involved in the formation and transformation of steroid hormones in the fetal and placental compartments
    • Pasqualini J.R. Enzymes involved in the formation and transformation of steroid hormones in the fetal and placental compartments. J. Steroid Biochem. Mol. Biol. 97 (2005) 401-415
    • (2005) J. Steroid Biochem. Mol. Biol. , vol.97 , pp. 401-415
    • Pasqualini, J.R.1
  • 43
    • 33845877959 scopus 로고    scopus 로고
    • Recovering metabolic pathways via optimization
    • Beasley J.E., and Planes F.J. Recovering metabolic pathways via optimization. Bioinformatics 23 (2007) 92-98
    • (2007) Bioinformatics , vol.23 , pp. 92-98
    • Beasley, J.E.1    Planes, F.J.2
  • 44
    • 2042440312 scopus 로고
    • Identification of qualitatively feasible metabolic pathways
    • American Association for Artificial Intelligence, Menlo Park, CA
    • Mavrovouniotis M.L. Identification of qualitatively feasible metabolic pathways. Artificial Intelligence and Molecular Biology (1993), American Association for Artificial Intelligence, Menlo Park, CA 325-364
    • (1993) Artificial Intelligence and Molecular Biology , pp. 325-364
    • Mavrovouniotis, M.L.1
  • 45
    • 0022971582 scopus 로고
    • MPS: an algorithm and data base for metabolic pathway synthesis
    • Seressiotis A., and Bailey J.E. MPS: an algorithm and data base for metabolic pathway synthesis. Biotechnol. Lett. 8 (1986) 837-842
    • (1986) Biotechnol. Lett. , vol.8 , pp. 837-842
    • Seressiotis, A.1    Bailey, J.E.2
  • 46
    • 49949089557 scopus 로고    scopus 로고
    • A critical examination of stoichiometric and path-finding approaches to metabolic pathways
    • Planes F.J., and Beasley J.E. A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Brief. Bioinf. 9 (2008) 422-436
    • (2008) Brief. Bioinf. , vol.9 , pp. 422-436
    • Planes, F.J.1    Beasley, J.E.2
  • 47
    • 0034564487 scopus 로고    scopus 로고
    • Analysis of gene expression data with pathway scores
    • Zien A., Kuffner R., Zimmer R., and Lengauer T. Analysis of gene expression data with pathway scores. ISMB 8 (2000) 407-417
    • (2000) ISMB , vol.8 , pp. 407-417
    • Zien, A.1    Kuffner, R.2    Zimmer, R.3    Lengauer, T.4
  • 49
    • 33747199651 scopus 로고    scopus 로고
    • Challenges to be faced in the reconstruction of metabolic networks from public databases
    • Poolman M.G., Bonde B.K., Gevorgyan A., Patel H.H., and Fell D.A. Challenges to be faced in the reconstruction of metabolic networks from public databases. IEE Proc. Syst. Biol. 153 (2006) 379-384
    • (2006) IEE Proc. Syst. Biol. , vol.153 , pp. 379-384
    • Poolman, M.G.1    Bonde, B.K.2    Gevorgyan, A.3    Patel, H.H.4    Fell, D.A.5
  • 50
    • 34548503411 scopus 로고    scopus 로고
    • Validation of metabolic pathway databases based on chemical substructure search
    • Félix L., and Valiente G. Validation of metabolic pathway databases based on chemical substructure search. Biomol. Eng. 24 (2007) 327-335
    • (2007) Biomol. Eng. , vol.24 , pp. 327-335
    • Félix, L.1    Valiente, G.2
  • 51
    • 33845398915 scopus 로고    scopus 로고
    • Correcting ligands, metabolites, and pathways
    • Ott M.A., and Vriend G. Correcting ligands, metabolites, and pathways. BMC Bioinf. 7 (2006) 517
    • (2006) BMC Bioinf. , vol.7 , pp. 517
    • Ott, M.A.1    Vriend, G.2
  • 52
  • 54
    • 0344874732 scopus 로고    scopus 로고
    • Solving group Steiner problems as Steiner problems
    • Duin C.W., Volgenant A., and Vo S. Solving group Steiner problems as Steiner problems. Eur. J. Oper. Res. 154 (2004) 323-329
    • (2004) Eur. J. Oper. Res. , vol.154 , pp. 323-329
    • Duin, C.W.1    Volgenant, A.2    Vo, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.