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Volumn 3, Issue 6, 2009, Pages 475-486

Identifying differentially expressed pathways via a mixed integer linear programming model

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CENTRAL PROBLEMS; HIGH THROUGHPUT EXPERIMENTS; HUMAN DATA; MICROARRAY TECHNOLOGIES; MIXED INTEGER LINEAR PROGRAMMING MODEL; MIXED INTEGER LINEAR PROGRAMMING PROBLEMS; SYSTEMS BIOLOGY;

EID: 71949118375     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2008.0155     Document Type: Article
Times cited : (20)

References (41)
  • 1
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with DNA microarrays
    • Brown, P.O. Botstein, D.: 'Exploring the new world of the genome with DNA microarrays', , Nat. Genet., 1999, 21, (1 Suppl), p. 33-37
    • (1999) Nat. Genet. , vol.21 , Issue.1 SUPPL , pp. 33-37
    • Brown, P.O.1    Botstein, D.2
  • 2
    • 10744224197 scopus 로고    scopus 로고
    • Development of human protein reference database as an initial platform for approaching systems biology in humans
    • Peri, S. Navarro, J.D. Amanchy, R.: et al. 'Development of human protein reference database as an initial platform for approaching systems biology in humans', , Genome Res., 2003, 13, (10), p. 2363
    • (2003) Genome Res. , vol.13 , Issue.10 , pp. 2363
    • Peri, S.1    Navarro, J.D.2    Amanchy, R.3
  • 3
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of dna binding proteins
    • 0036-8075
    • Ren, B. Robert, F. Wyrick, J.J.: et al. 'Genome-wide location and function of dna binding proteins', , Science, 2000, 290, (5500), p. 2306-2309, 0036-8075
    • (2000) Science , vol.290 , Issue.5500 , pp. 2306-2309
    • Ren, B.1    Robert, F.2    Wyrick, J.J.3
  • 4
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    • 0027-8424
    • Alon, U. Barkai, N. Notterman, D.A.: et al. 'Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays', , Proc. Natl. Acad. Sci. USA, 1999, 96, (12), p. 6745-6750, 0027-8424
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , Issue.12 , pp. 6745-6750
    • Alon, U.1    Barkai, N.2    Notterman, D.A.3
  • 5
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • 0027-8424
    • Eisen, M.B. Spellman, P.T. Brown, P.O. Botstein, D.: 'Cluster analysis and display of genome-wide expression patterns', , Proc. Natl. Acad. Sci. USA, 1998, 95, (25), p. 14863-14868, 0027-8424
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 6
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • Segal, E. Wang, H. Koller, D.: 'Discovering molecular pathways from protein interaction and gene expression data', , Bioinformatics, 2003, 19, (Suppl. 1), p. 264-272
    • (2003) Bioinformatics , vol.19 SUPPL. 1 , pp. 264-272
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 7
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A.J. Dongen Van, S. Ouzounis, C.A.: 'An efficient algorithm for large-scale detection of protein families', , Nucleic. Acids. Res., 2002, 30, (7), p. 1575-1584
    • (2002) Nucleic. Acids. Res. , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Dongen Van, S.2    Ouzounis, C.A.3
  • 8
    • 44349093750 scopus 로고    scopus 로고
    • Uncovering signal transduction networks from high-throughput data by integer linear programming
    • Zhao, X.M. Wang, R.S. Chen, L. Aihara, K.: 'Uncovering signal transduction networks from high-throughput data by integer linear programming', , Nucleic. Acids. Res., 2008, 36, (9), p. e48
    • (2008) Nucleic. Acids. Res. , vol.36 , Issue.9
    • Zhao, X.M.1    Wang, R.S.2    Chen, L.3    Aihara, K.4
  • 9
    • 70349331032 scopus 로고    scopus 로고
    • Identifying responsive functional modules from protein-protein interaction network
    • Wu, Z.K. Zhao, X.M. Chen, L.: 'Identifying responsive functional modules from protein-protein interaction network', , Mol. Cells, 2009, 27, (3), p. 271-277
    • (2009) Mol. Cells , vol.27 , Issue.3 , pp. 271-277
    • Wu, Z.K.1    Zhao, X.M.2    Chen, L.3
  • 10
    • 0037263812 scopus 로고    scopus 로고
    • MAPPFinder: using gene ontology and GenMAPP to create a global gene-expression profile from microarray data
    • Doniger, S.W. Salomonis, N. Dahlquist, K.D.: et al. 'MAPPFinder: using gene ontology and GenMAPP to create a global gene-expression profile from microarray data', , Genome Biol., 2003, 4, (1), p. R7
    • (2003) Genome Biol. , vol.4 , Issue.1
    • Doniger, S.W.1    Salomonis, N.2    Dahlquist, K.D.3
  • 11
    • 0038054341 scopus 로고    scopus 로고
    • Pgc-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V.K. Lindgren, C.M. Eriksson, K.F.: et al. 'Pgc-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes', , Nat. Genet., 2003, 34, (3), p. 267-273
    • (2003) Nat. Genet. , vol.34 , Issue.3 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3
  • 12
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • 0027-8424
    • Subramanian, A. Tamayo, P. Mootha, V.K.: et al. 'Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles', , Proc. Natl. Acad. Sci. USA, 2005, 102, (43), p. 15545-15550, 0027-8424
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.43 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3
  • 13
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: tool for the unification of biology
    • 'Gene Ontology: tool for the unification of biology', , Nat. Genet., 2000, 25, p. 25-29
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
  • 14
    • 33644874819 scopus 로고    scopus 로고
    • From genomics to chemical genomics: new developments in KEGG
    • Kanehisa, M. Goto, S. Hattori, M.: et al. 'From genomics to chemical genomics: new developments in KEGG', , Nucleic. Acids. Res., 2006, 34, p. D354 (database issue)
    • (2006) Nucleic. Acids. Res. , vol.34
    • Kanehisa, M.1    Goto, S.2    Hattori, M.3
  • 15
    • 0036578644 scopus 로고    scopus 로고
    • GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
    • Dahlquist, K.D. Salomonis, N. Vranizan, K. Lawlor, S.C. Conklin, B.R.: 'GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways', , Nat. Genet., 2002, 31, (1), p. 19-20
    • (2002) Nat. Genet. , vol.31 , Issue.1 , pp. 19-20
    • Dahlquist, K.D.1    Salomonis, N.2    Vranizan, K.3    Lawlor, S.C.4    Conklin, B.R.5
  • 16
    • 22744458472 scopus 로고    scopus 로고
    • Pathways to the analysis of microarray data
    • Curtis, R.K. Orešič, M. Vidal-Puig, A.: 'Pathways to the analysis of microarray data', , Trends Biotechnol., 2005, 23, (8), p. 429-435
    • (2005) Trends Biotechnol. , vol.23 , Issue.8 , pp. 429-435
    • Curtis, R.K.1    Orešič, M.2    Vidal-Puig, A.3
  • 17
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker, T. Ozier, O. Schwikowski, B. Siegel, A.F.: 'Discovering regulatory and signalling circuits in molecular interaction networks', , Bioinformatics, 2002, 18, (Suppl. 1), p. 233-240
    • (2002) Bioinformatics , vol.18 SUPPL. , Issue.1 , pp. 233-240
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 18
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • Nacu, S. Critchley-Thorne, R. Lee, P. Holmes, S.: 'Gene expression network analysis and applications to immunology', , Bioinformatics, 2007, 23, (7), p. 850
    • (2007) Bioinformatics , vol.23 , Issue.7 , pp. 850
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3    Holmes, S.4
  • 19
    • 34548583420 scopus 로고    scopus 로고
    • Edge-based scoring and searching method for identifying condition-responsive protein protein interaction sub-network
    • Guo, Z. Li, Y. Gong, X.: et al. 'Edge-based scoring and searching method for identifying condition-responsive protein protein interaction sub-network', , Bioinformatics, 2007, 23, (16), p. 2121
    • (2007) Bioinformatics , vol.23 , Issue.16 , pp. 2121
    • Guo, Z.1    Li, Y.2    Gong, X.3
  • 20
    • 36849021779 scopus 로고    scopus 로고
    • Discovering regulated networks during HIV-1 latency and reactivation
    • Bandyopadhyay, S. Kelley, R. Ideker, T.: 'Discovering regulated networks during HIV-1 latency and reactivation', , Pacific Symp. Biocomput., 2006, 11, p. 354-366
    • (2006) Pacific Symp. Biocomput. , vol.11 , pp. 354-366
    • Bandyopadhyay, S.1    Kelley, R.2    Ideker, T.3
  • 21
    • 34347326247 scopus 로고    scopus 로고
    • Network-based analysis of affected biological processes in Type 2 diabetes models
    • Liu, M. Liberzon, A. Kong, S.W. Lai, W.R. Park, P.J. Kerr, K.: 'Network-based analysis of affected biological processes in Type 2 diabetes models', , PLoS Genet., 2007, 3, (6), p. e96
    • (2007) PLoS Genet. , vol.3 , Issue.6
    • Liu, M.1    Liberzon, A.2    Kong, S.W.3    Lai, W.R.4    Park, P.J.5    Kerr, K.6
  • 22
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from saccharomyces cerevisiae
    • Ge, H. Liu, Z. Church, G.M. Vidal, M.: 'Correlation between transcriptome and interactome mapping data from saccharomyces cerevisiae', , Nat. Genet., 2001, 29, (4), p. 482-486
    • (2001) Nat. Genet. , vol.29 , Issue.4 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 23
    • 0035805255 scopus 로고    scopus 로고
    • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
    • 0036-8075
    • Ideker, T. Thorsson, V. Ranish, J.A.: et al. 'Integrated genomic and proteomic analyses of a systematically perturbed metabolic network', , Science, 2001, 292, (5518), p. 929, 0036-8075
    • (2001) Science , vol.292 , Issue.5518 , pp. 929
    • Ideker, T.1    Thorsson, V.2    Ranish, J.A.3
  • 24
    • 13844310310 scopus 로고    scopus 로고
    • Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
    • Wang, Y. Klijn, J.G.M. Zhang, Y.: et al. 'Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer', , Lancet, 2005, 365, (9460), p. 671-679
    • (2005) Lancet , vol.365 , Issue.9460 , pp. 671-679
    • Wang, Y.1    Klijn, J.G.M.2    Zhang, Y.3
  • 25
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
    • 0036-8075
    • Golub, T.R. Slonim, D.K. Tamayo, P.: et al. 'Molecular classification of cancer: class discovery and class prediction by gene expression monitoring', , Science, 1999, 286, (5439), p. 531, 0036-8075
    • (1999) Science , vol.286 , Issue.5439 , pp. 531
    • Golub, T.R.1    Slonim, D.K.2    Tamayo, P.3
  • 26
    • 0347201147 scopus 로고    scopus 로고
    • Multiclass cancer diagnosis using tumor gene expression signatures
    • 0027-8424
    • Ramaswamy, S. Tamayo, P. Rifkin, R.: et al. 'Multiclass cancer diagnosis using tumor gene expression signatures', , Proc. Natl. Acad. Sci. USA, 2001, 98, (26), p. 15149, 0027-8424
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , Issue.26 , pp. 15149
    • Ramaswamy, S.1    Tamayo, P.2    Rifkin, R.3
  • 27
    • 0030270966 scopus 로고    scopus 로고
    • Algorithms for the constrained maximum-weight connected graph problem
    • Lee, H.F. Dooly, D.R.: 'Algorithms for the constrained maximum-weight connected graph problem', , Nav. Res. Log., 1996, 43, p. 985-1008
    • (1996) Nav. Res. Log. , vol.43 , pp. 985-1008
    • Lee, H.F.1    Dooly, D.R.2
  • 28
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon, P. Markiel, A. Ozier, O.: et al. 'Cytoscape: a software environment for integrated models of biomolecular interaction networks', , Genome Res., 2003, 13, (11), p. 2498
    • (2003) Genome Res. , vol.13 , Issue.11 , pp. 2498
    • Shannon, P.1    Markiel, A.2    Ozier, O.3
  • 29
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere, S. Heymans, K. Kuiper, M.: 'BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks', , Bioinformatics, 2005, 21, (16), p. 3448-3449
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 30
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • Chuang, H.Y. Lee, E. Liu, Y.T. Lee, D. Ideker, T.: 'Network-based classification of breast cancer metastasis', , Mol. Syst. Biol., 2007, 3, (140)
    • (2007) Mol. Syst. Biol. , vol.3 , Issue.140
    • Chuang, H.Y.1    Lee, E.2    Liu, Y.T.3    Lee, D.4    Ideker, T.5
  • 31
    • 18544389716 scopus 로고    scopus 로고
    • CHEK2-breast cancer consortium. Low-penetrance susceptibility to breast cancer due to CHEK2 (*) 1100delC in noncarriers of BRCA1 or BRCA2 mutations
    • Meijers-Heijboer, H. van den Ouweland, A. Klijn, J.: et al. 'CHEK2-breast cancer consortium. Low-penetrance susceptibility to breast cancer due to CHEK2 (*) 1100delC in noncarriers of BRCA1 or BRCA2 mutations', , Nat. Genet., 2002, 31, p. 55-59
    • (2002) Nat. Genet. , vol.31 , pp. 55-59
    • Meijers-Heijboer, H.1    van den Ouweland, A.2    Klijn, J.3
  • 32
    • 0028073794 scopus 로고
    • BRCA1 mutations in primary breast and ovarian carcinomas
    • 0036-8075
    • Futreal, P.A. Liu, Q. Shattuck-Eidens, D.: et al. 'BRCA1 mutations in primary breast and ovarian carcinomas', , Science, 1994, 266, (5182), p. 120-122, 0036-8075
    • (1994) Science , vol.266 , Issue.5182 , pp. 120-122
    • Futreal, P.A.1    Liu, Q.2    Shattuck-Eidens, D.3
  • 33
    • 0028113345 scopus 로고
    • A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1
    • 0036-8075
    • Miki, Y. Swensen, J. Shattuck-Eidens, D.: et al. 'A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1', , Science, 1994, 266, (5182), p. 66-71, 0036-8075
    • (1994) Science , vol.266 , Issue.5182 , pp. 66-71
    • Miki, Y.1    Swensen, J.2    Shattuck-Eidens, D.3
  • 34
    • 0006713602 scopus 로고
    • Identification of the breast cancer susceptibility gene BRCA2
    • 0028-0836
    • Wooster, R. Bignell, G. Lancaster, J.: et al. 'Identification of the breast cancer susceptibility gene BRCA2', , Nature, 1995, 378, (6559), p. 789-792, 0028-0836
    • (1995) Nature , vol.378 , Issue.6559 , pp. 789-792
    • Wooster, R.1    Bignell, G.2    Lancaster, J.3
  • 35
    • 16644393213 scopus 로고    scopus 로고
    • The PIK3CA gene is mutated with high frequency in human breast cancers
    • Bachman, K.E. Argani, P. Samuels, Y.: et al. 'The PIK3CA gene is mutated with high frequency in human breast cancers', , Cancer Biol. Ther., 2004, 3, (8), p. 772-775
    • (2004) Cancer Biol. Ther. , vol.3 , Issue.8 , pp. 772-775
    • Bachman, K.E.1    Argani, P.2    Samuels, Y.3
  • 36
    • 7444250290 scopus 로고    scopus 로고
    • Mutation of the PIK3CA Gene in ovarian and breast cancer
    • Campbell, I.G. Russell, S.E. Choong, D.Y.H.: et al. 'Mutation of the PIK3CA Gene in ovarian and breast cancer', , Cancer Res., 2004, 64, (21), p. 7678-7681
    • (2004) Cancer Res. , vol.64 , Issue.21 , pp. 7678-7681
    • Campbell, I.G.1    Russell, S.E.2    Choong, D.Y.H.3
  • 37
    • 35349024501 scopus 로고    scopus 로고
    • Network modeling links breast cancer susceptibility and centrosome dysfunction
    • Pujana, M.A. Han, J.D. Starita, L.M.: et al. 'Network modeling links breast cancer susceptibility and centrosome dysfunction', , Nat. Genet., 2007, 39, (11), p. 1338-1349
    • (2007) Nat. Genet. , vol.39 , Issue.11 , pp. 1338-1349
    • Pujana, M.A.1    Han, J.D.2    Starita, L.M.3
  • 38
    • 33746491583 scopus 로고    scopus 로고
    • ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles
    • Renwick, A. Thompson, D. Seal, S.: et al. 'ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles', , Nat. Genet., 2006, 38, p. 873-875
    • (2006) Nat. Genet. , vol.38 , pp. 873-875
    • Renwick, A.1    Thompson, D.2    Seal, S.3
  • 39
    • 0003710380 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines
    • Software available at http://www.csie.ntu.edu.tw/cjlin/libsvm
    • Chang, C.C. Lin, C.J.: 'LIBSVM: a library for support vector machines', 2001, Software available at http://www.csie.ntu.edu.tw/cjlin/libsvm
    • (2001)
    • Chang, C.C.1    Lin, C.J.2
  • 40
    • 33644617753 scopus 로고    scopus 로고
    • Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
    • Gandhi, T.K.B. Zhong, J. Mathivanan, S.: et al. 'Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets', , Nat. Genet., 2006, 38, p. 285-293
    • (2006) Nat. Genet. , vol.38 , pp. 285-293
    • Gandhi, T.K.B.1    Zhong, J.2    Mathivanan, S.3
  • 41
    • 33751017706 scopus 로고    scopus 로고
    • Discovering disease-genes by topological features in human protein-protein interaction network
    • Xu, J. Li, Y.: 'Discovering disease-genes by topological features in human protein-protein interaction network', , Bioinformatics, 2006, 22, (22), p. 2800
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2800
    • Xu, J.1    Li, Y.2


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