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Volumn 23, Issue 20, 2007, Pages 2775-2783

Mining biological networks for unknown pathways

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME;

EID: 35748980569     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm409     Document Type: Article
Times cited : (26)

References (46)
  • 2
    • 0031966808 scopus 로고    scopus 로고
    • Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
    • Bono,H. et al. (1998) Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res., 8, 203-210.
    • (1998) Genome Res , vol.8 , pp. 203-210
    • Bono, H.1
  • 3
    • 35748972495 scopus 로고    scopus 로고
    • Mining biological networks for unknown pathways
    • Technical report full version, Available at
    • Cakmak,A. and Ozsoyoglu,G. (2007) Mining biological networks for unknown pathways. Technical report (full version). Available at http://cakmak.case.edu/PFT.
    • (2007)
    • Cakmak, A.1    Ozsoyoglu, G.2
  • 4
    • 3142667582 scopus 로고    scopus 로고
    • A signaling mucin at the head of the Cdc42- and MAPK-dependent filamentous growth pathway in yeast
    • Cullen,P.J. et al. (2004) A signaling mucin at the head of the Cdc42- and MAPK-dependent filamentous growth pathway in yeast. Genes Dev., 18, 1695-1708.
    • (2004) Genes Dev , vol.18 , pp. 1695-1708
    • Cullen, P.J.1
  • 5
    • 0036119364 scopus 로고    scopus 로고
    • Comparative genome analysis and pathway reconstruction
    • Dandekar,T. and Sauerborn,R. (2002) Comparative genome analysis and pathway reconstruction. Pharmacogenomics, 3, 245-256.
    • (2002) Pharmacogenomics , vol.3 , pp. 245-256
    • Dandekar, T.1    Sauerborn, R.2
  • 6
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • Derisi,J.L. et al. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
    • (1997) Science , vol.278 , pp. 680-686
    • Derisi, J.L.1
  • 7
    • 0346801873 scopus 로고    scopus 로고
    • The GO database and informatics resource
    • Gene Ontology Consortium
    • Gene Ontology Consortium (2004) The GO database and informatics resource. Nucleic Acids Res., 32, D258-D261.
    • (2004) Nucleic Acids Res , vol.32
  • 8
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green,M. and Karp,P. (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 9, 76.
    • (2004) BMC Bioinformatics , vol.9 , pp. 76
    • Green, M.1    Karp, P.2
  • 10
    • 57149143536 scopus 로고    scopus 로고
    • Mining coherent dense subgraphs across massive biological networks for functional discovery
    • Ann Arbor, MI
    • Hu,H. et al. (2005) Mining coherent dense subgraphs across massive biological networks for functional discovery. In Proceedings of ISMB Ann Arbor, MI.
    • (2005) Proceedings of ISMB
    • Hu, H.1
  • 11
    • 78149328300 scopus 로고    scopus 로고
    • Efficient mining of frequent subgraphs in the presence of isomorphism
    • IEEE Computer Society, Washington DC, p
    • Huan,J. et al. (2003) Efficient mining of frequent subgraphs in the presence of isomorphism. In Proceedings of International Conference on Data Mining. IEEE Computer Society, Washington DC, p. 549.
    • (2003) Proceedings of International Conference on Data Mining , pp. 549
    • Huan, J.1
  • 12
    • 12244294770 scopus 로고    scopus 로고
    • SPIN: Mining maximal frequent subgraphs from graph databases
    • Huan,J. et al. (2004) SPIN: Mining maximal frequent subgraphs from graph databases. In Proceedings of KDD.
    • (2004) Proceedings of KDD
    • Huan, J.1
  • 13
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen,R. et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 17, 449-453.
    • (2003) Science , vol.17 , pp. 449-453
    • Jansen, R.1
  • 14
    • 13444259844 scopus 로고    scopus 로고
    • Reactome: A knowledgebase of biological pathways
    • Joshi-Tope,G. et al. (2005) Reactome: A knowledgebase of biological pathways. Nucleic Acids Res., 33, D428-D432.
    • (2005) Nucleic Acids Res , vol.33
    • Joshi-Tope, G.1
  • 15
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • Kanehisa,M. et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
    • (2004) Nucleic Acids Res , vol.32
    • Kanehisa, M.1
  • 16
    • 3442886313 scopus 로고    scopus 로고
    • PathBLAST: A tool for alignment of protein interaction networks
    • Kelley,B.P. et al. (2004) PathBLAST: A tool for alignment of protein interaction networks. Nucleic Acids Res., 32, W83-W88.
    • (2004) Nucleic Acids Res , vol.32
    • Kelley, B.P.1
  • 17
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • USA
    • Kelley,P. et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad Sci., pp. 11394-11399, USA.
    • (2003) Proc. Natl. Acad Sci , pp. 11394-11399
    • Kelley, P.1
  • 18
    • 13444262374 scopus 로고    scopus 로고
    • Eco-Cyc: A comprehensive database resource for Escherichia coli
    • Keseler,I.M. et al. (2005) Eco-Cyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334-D337.
    • (2005) Nucleic Acids Res , vol.33
    • Keseler, I.M.1
  • 19
    • 24744467372 scopus 로고    scopus 로고
    • Filling gaps in a metabolic network using expression information
    • Kharchenko,P. et al. (2004) Filling gaps in a metabolic network using expression information. Bioinformatics, 20, 449-453.
    • (2004) Bioinformatics , vol.20 , pp. 449-453
    • Kharchenko, P.1
  • 20
    • 33846194268 scopus 로고    scopus 로고
    • Detecting conserved interaction patterns in biological networks
    • Koyuturk,M. et al. (2006) Detecting conserved interaction patterns in biological networks. J. Comput. Biol., 13, 1299-1322.
    • (2006) J. Comput. Biol , vol.13 , pp. 1299-1322
    • Koyuturk, M.1
  • 22
    • 0005180705 scopus 로고    scopus 로고
    • An information-theoretic definition of similarity
    • Morgan Kaufmann, San Fransisco, pp
    • Lin,D. (1998) An information-theoretic definition of similarity. International Conference on Machine Learning. Morgan Kaufmann, San Fransisco, pp. 296-304.
    • (1998) International Conference on Machine Learning , pp. 296-304
    • Lin, D.1
  • 23
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the Gene Ontology
    • Lord,W. et al. (2003) Investigating semantic similarity measures across the Gene Ontology. Bioinformatics, 19, 1275-1283.
    • (2003) Bioinformatics , vol.19 , pp. 1275-1283
    • Lord, W.1
  • 24
    • 0348184963 scopus 로고    scopus 로고
    • ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex
    • Mizuguchi,G. et al. (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science, 303, 343-348.
    • (2004) Science , vol.303 , pp. 343-348
    • Mizuguchi, G.1
  • 25
    • 33745113181 scopus 로고    scopus 로고
    • Discovery of biological networks from diverse functional genomic data
    • Myers,C.L. et al. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol., 6, R114.
    • (2005) Genome Biol , vol.6
    • Myers, C.L.1
  • 26
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: A comparative genomics approach
    • Osterman,A. and Overbeek,R. (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol., 7, 238-251.
    • (2003) Curr. Opin. Chem. Biol , vol.7 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 27
    • 33746217026 scopus 로고    scopus 로고
    • Genomic pathways database and biological data management
    • Ozsoyoglu,M. et al. (2006) Genomic pathways database and biological data management. Animal Genet., 37 (Suppl. 1), 41-47.
    • (2006) Animal Genet , vol.37 , Issue.SUPPL. 1 , pp. 41-47
    • Ozsoyoglu, M.1
  • 28
    • 0036086784 scopus 로고    scopus 로고
    • Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
    • Paley,S. and Karp,P.D. (2002) Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics 18, 715-724.
    • (2002) Bioinformatics , vol.18 , pp. 715-724
    • Paley, S.1    Karp, P.D.2
  • 29
    • 24044488288 scopus 로고    scopus 로고
    • Alignment of metabolic pathways
    • Pinter,R. et al. (2005) Alignment of metabolic pathways. Bioinformatics, 21, 3401-3408.
    • (2005) Bioinformatics , vol.21 , pp. 3401-3408
    • Pinter, R.1
  • 31
    • 14844326483 scopus 로고    scopus 로고
    • Computational prediction of human metabolic pathways from the complete genome
    • Romero,P. et al. (2005) Computational prediction of human metabolic pathways from the complete genome. Genome Biol., 6 R2.
    • (2005) Genome Biol , vol.6
    • Romero, P.1
  • 32
    • 0002016474 scopus 로고    scopus 로고
    • Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language
    • Resnik,P. (1999) Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. J. Artif. Intell. Res., 11, 95-130.
    • (1999) J. Artif. Intell. Res , vol.11 , pp. 95-130
    • Resnik, P.1
  • 33
    • 13844314048 scopus 로고    scopus 로고
    • Conserved patterns of protein interaction in multiple species
    • Sharan,R. et al. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA, 102, 1974-1979.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1974-1979
    • Sharan, R.1
  • 34
    • 33646347364 scopus 로고    scopus 로고
    • QPath: A method for querying pathways in a protein-protein interaction network
    • Shlomi,J. et al. (2006) QPath: A method for querying pathways in a protein-protein interaction network. BMC Bioinformatics, 7, 199.
    • (2006) BMC Bioinformatics , vol.7 , pp. 199
    • Shlomi, J.1
  • 35
    • 33644873683 scopus 로고    scopus 로고
    • The YEASTRACT: A tool for the analysis of transcription regulatory associations in S. cerevisiae
    • Teixeira,M. et al. (2006) The YEASTRACT: A tool for the analysis of transcription regulatory associations in S. cerevisiae. Nucleic Acids Res., 34, D446-D451.
    • (2006) Nucleic Acids Res , vol.34
    • Teixeira, M.1
  • 37
    • 33747880011 scopus 로고    scopus 로고
    • An integrative approach for causal gene identification and gene regulatory pathway inference
    • Tu,Z. et al. (2006) An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics 22, e489-e496.
    • (2006) Bioinformatics , vol.22
    • Tu, Z.1
  • 38
    • 10944233962 scopus 로고    scopus 로고
    • Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair
    • Van Attikum,H. et al. (2004) Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell, 119, 777-788.
    • (2004) Cell , vol.119 , pp. 777-788
    • Van Attikum, H.1
  • 40
    • 0033604609 scopus 로고    scopus 로고
    • Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast
    • Wyrick,J. et al. (1999) Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418-421.
    • (1999) Nature , vol.402 , pp. 418-421
    • Wyrick, J.1
  • 41
  • 42
    • 34247374704 scopus 로고    scopus 로고
    • Prediction of missing enzyme genes in a bacterial metabolic network
    • Yamanishi,Y. et al. (2007) Prediction of missing enzyme genes in a bacterial metabolic network. FEBS J., 274, 2262-2273.
    • (2007) FEBS J , vol.274 , pp. 2262-2273
    • Yamanishi, Y.1
  • 43
    • 78149333073 scopus 로고    scopus 로고
    • gSpan: Graph-based substructure pattern mining, Technical Report
    • Yan,X. and Han,J. (2002) gSpan: Graph-based substructure pattern mining. In International Conference on Data Mining, Technical Report.
    • (2002) International Conference on Data Mining
    • Yan, X.1    Han, J.2
  • 44
    • 35748971296 scopus 로고    scopus 로고
    • Substructure similarity search in graph database, SIGMOD, June 14-16
    • Yan,X. et al. (2005) Substructure similarity search in graph database. Substructure Similarity search in Graph Database, SIGMOD, June 14-16, 2005.
    • (2005) Substructure Similarity search in Graph Database
    • Yan, X.1
  • 45
    • 27144524216 scopus 로고    scopus 로고
    • Automatic detection of subsystem/pathway variants in genome analysis
    • Ye,Y. et al. (2005) Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics, (Suppl. 1), i478-i486.
    • (2005) Bioinformatics , Issue.SUPPL. 1
    • Ye, Y.1
  • 46


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