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Volumn 40, Issue 6, 2012, Pages

An integer linear programming approach for finding deregulated subgraphs in regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN;

EID: 84859365473     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1227     Document Type: Article
Times cited : (48)

References (61)
  • 5
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker, T., Ozier, O., Schwikowski, B. and Siegel, A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240 (Pubitemid 41185658)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 6
    • 15944402798 scopus 로고    scopus 로고
    • Inferring pathways from gene lists using a literature-derived network of biological relationships
    • DOI 10.1093/bioinformatics/bti069
    • Rajagopalan, D. and Agarwal, P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793 (Pubitemid 40439415)
    • (2005) Bioinformatics , vol.21 , Issue.6 , pp. 788-793
    • Rajagopalan, D.1    Agarwal, P.2
  • 7
    • 20844450402 scopus 로고    scopus 로고
    • Differential network expression during drug and stress response
    • DOI 10.1093/bioinformatics/bti440
    • Cabusora, L., Sutton, E., Fulmer, A. and Forst, C.V. (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905 (Pubitemid 40862290)
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2898-2905
    • Cabusora, L.1    Sutton, E.2    Fulmer, A.3    Forst, C.V.4
  • 8
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • DOI 10.1093/bioinformatics/btm019
    • Nacu, S., Critchley-Thorne, R., Lee, P. and Holmes, S. (2007) Gene expression network analysis and applications to immunology. Bioinformatics, 23, 850-858 (Pubitemid 47049919)
    • (2007) Bioinformatics , vol.23 , Issue.7 , pp. 850-858
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3    Holmes, S.4
  • 9
    • 47249120912 scopus 로고    scopus 로고
    • Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles
    • Springer, Berlin/Heidelberg
    • Ulitsky, I., Karp, R. and Shamir, R. (2008) Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles. In Research in Computational Molecular Biology. Springer, Berlin/Heidelberg, pp. 347-359
    • (2008) Research in Computational Molecular Biology , pp. 347-359
    • Ulitsky, I.1    Karp, R.2    Shamir, R.3
  • 10
    • 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. and Aihara, K. (2008) Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res., 36, e48
    • (2008) Nucleic Acids Res. , vol.36
    • Zhao, X.M.1    Wang, R.S.2    Chen, L.3    Aihara, K.4
  • 11
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: An integrated exact approach
    • DOI 10.1093/bioinformatics/btn161
    • Dittrich, M.T., Klau, G.W., Rosenwald, A., Dandekar, T. and Muller, T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231 (Pubitemid 351911677)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Muller, T.5
  • 12
    • 79959392210 scopus 로고    scopus 로고
    • Optimally discriminative subnetwork markers predict response to hemotherapy
    • Dao, P., Wang, K., Collins, C., Ester, M., Lapuk, A. and Sahinalp, S.C. (2011) Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics, 27, i205-i213
    • (2011) Bioinformatics , vol.27
    • Dao, P.1    Wang, K.2    Collins, C.3    Ester, M.4    Lapuk, A.5    Sahinalp, S.C.6
  • 13
    • 79952389826 scopus 로고    scopus 로고
    • Algorithms for detecting significantly mutated pathways in cancer
    • Vandin, F., Upfal, E. and Raphael, B.J. (2011) Algorithms for detecting significantly mutated pathways in cancer. J. Comput. Biol., 18, 507-522
    • (2011) J. Comput. Biol. , vol.18 , pp. 507-522
    • Vandin, F.1    Upfal, E.2    Raphael, B.J.3
  • 14
    • 70350701855 scopus 로고    scopus 로고
    • A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
    • Keller, A., Backes, C., Gerasch, A., Kaufmann, M., Kohlbacher, O., Meese, E. and Lenhof, H.P. (2009) A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics, 25, 2787-2794
    • (2009) Bioinformatics , vol.25 , pp. 2787-2794
    • Keller, A.1    Backes, C.2    Gerasch, A.3    Kaufmann, M.4    Kohlbacher, O.5    Meese, E.6    Lenhof, H.P.7
  • 16
    • 35548988505 scopus 로고    scopus 로고
    • Computation of significance scores of unweighted gene set enrichment analyses
    • Keller, A., Backes, C. and Lenhof, H.P. (2007) Computation of significance scores of unweighted gene set enrichment analyses. BMC Bioinformatics, 8
    • (2007) BMC Bioinformatics , vol.8
    • Keller, A.1    Backes, C.2    Lenhof, H.P.3
  • 17
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. (2000) Kegg: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30 (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 19
    • 75549090213 scopus 로고    scopus 로고
    • Kegg for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M. (2010) Kegg for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360
    • (2010) Nucleic Acids Res. , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 22
    • 76549121309 scopus 로고    scopus 로고
    • Reversing hoxa9 oncogene activation by pi3k inhibition: Epigenetic mechanism and prognostic significance in human glioblastoma
    • Costa, B.M., Smith, J.S., Chen, Y., Chen, J., Phillips, H.S., Aldape, K.D., Zardo, G., Nigro, J., James, C.D., Fridlyand, J. et al. (2010) Reversing hoxa9 oncogene activation by pi3k inhibition: epigenetic mechanism and prognostic significance in human glioblastoma. Cancer Res., 70, 453-462
    • (2010) Cancer Res. , vol.70 , pp. 453-462
    • Costa, B.M.1    Smith, J.S.2    Chen, Y.3    Chen, J.4    Phillips, H.S.5    Aldape, K.D.6    Zardo, G.7    Nigro, J.8    James, C.D.9    Fridlyand, J.10
  • 24
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • DOI 10.1093/bioinformatics/19.2.185
    • Bolstad, B., Irizarry, R., Astrand, M. and Speed, T. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193 (Pubitemid 36181903)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 27
    • 84859307628 scopus 로고    scopus 로고
    • 7 December 2011, date last accessed
    • IBM ILOG CPLEX Optimize. http://www-01.ibm. com/software/integration/ optimization/cplex-optimizer/(7 December 2011, date last accessed)
    • IBM ILOG CPLEX Optimize
  • 31
    • 33747884345 scopus 로고    scopus 로고
    • Gene expression omnibus: Microarray data storage, submission, retrieval, and analysis
    • DOI 10.1016/S0076-6879(06)11019-8, PII S0076687906110198, DNA Microarrays, Part B: Databases and Statistics
    • Barrett, T. and Edgar, R. (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol., 411, 352-369 (Pubitemid 44291435)
    • (2006) Methods in Enzymology , vol.411 , pp. 352-369
    • Barrett, T.1    Edgar, R.2
  • 32
    • 77951972600 scopus 로고    scopus 로고
    • BioNet: An R-package for the functional analysis of biological networks
    • Beisser, D., Klau, G.W., Dandekar, T., Müller, T. and Dittrich, M.T. (2010) BioNet: an R-package for the functional analysis of biological networks. Bioinformatics, 26, 1129-1130
    • (2010) Bioinformatics , vol.26 , pp. 1129-1130
    • Beisser, D.1    Klau, G.W.2    Dandekar, T.3    Müller, T.4    Dittrich, M.T.5
  • 39
    • 70349682197 scopus 로고    scopus 로고
    • BRCA1 tumours correlate with a HIF-1[alpha] phenotype and have a poor prognosis through modulation of hydroxylase enzyme profile expression
    • Yan, M., Rayoo, M., Takano, E.A., Thorne, H. and Fox, S.B. (2009) BRCA1 tumours correlate with a HIF-1[alpha] phenotype and have a poor prognosis through modulation of hydroxylase enzyme profile expression. Br. J. Cancer, 101, 1168-1174
    • (2009) Br. J. Cancer , vol.101 , pp. 1168-1174
    • Yan, M.1    Rayoo, M.2    Takano, E.A.3    Thorne, H.4    Fox, S.B.5
  • 41
    • 10044269621 scopus 로고    scopus 로고
    • Increased GADD gene expression in human colon epithelial cells exposed to deoxycholate
    • DOI 10.1002/jcp.20135
    • Scott, D.W., Mutamba, S., Hopkins, R.G. and Loo, G. (2005) Increased GADD gene expression in human colon epithelial cells exposed to deoxycholate. J. Cell Physiol., 202, 295-303 (Pubitemid 39603387)
    • (2005) Journal of Cellular Physiology , vol.202 , Issue.1 , pp. 295-303
    • Scott, D.W.1    Mutamba, S.2    Hopkins, R.G.3    Loo, G.4
  • 42
    • 0035863111 scopus 로고    scopus 로고
    • Peroxynitrite induces GADD34, 45, and 153 via p38 MAPK in human neuroblastoma SH-SY5Y cells
    • DOI 10.1016/S0891-5849(00)00461-5, PII S0891584900004615
    • Oh-Hashi, K., Maruyama, W. and Isobe, K. (2001) Peroxynitrite induces GADD34, 45, and 153 VIA p38 MAPK in human neuroblastoma SH-SY5Y cells. Free Radic. Biol. Med., 30, 213-221 (Pubitemid 32121799)
    • (2001) Free Radical Biology and Medicine , vol.30 , Issue.2 , pp. 213-221
    • Oh-Hashi, K.1    Maruyama, W.2    Isobe, K.3
  • 43
    • 66349110527 scopus 로고    scopus 로고
    • Oxidative stress obesity, and breast cancer risk: Results from the shanghai women's health study
    • Dai, Q., Gao, Y., Shu, X., Yang, G., Milne, G., Cai, Q., Wen, W., Rothman, N., Cai, H., Li, H. et al. (2009) Oxidative stress, obesity, and breast cancer risk: Results from the shanghai women's health study. J. Clin. Oncol., 27, 2482-2488
    • (2009) J. Clin. Oncol. , vol.27 , pp. 2482-2488
    • Dai, Q.1    Gao, Y.2    Shu, X.3    Yang, G.4    Milne, G.5    Cai, Q.6    Wen, W.7    Rothman, N.8    Cai, H.9    Li, H.10
  • 48
    • 28344456263 scopus 로고    scopus 로고
    • Roles of the Rac1 and Rac3 GTPases in human tumor cell invasion
    • DOI 10.1038/sj.onc.1208909, PII 1208909
    • Chan, A.Y., Coniglio, S.J., yu Chuang, Y., Michaelson, D., Knaus, U.G., Philips, M.R. and Symons, M. (2005) Roles of the rac1 and rac3 gtpases in human tumor cell invasion. Oncogene, 24, 7821-7829 (Pubitemid 41715188)
    • (2005) Oncogene , vol.24 , Issue.53 , pp. 7821-7829
    • Chan, A.Y.1    Coniglio, S.J.2    Chuang, Y.-Y.3    Michaelson, D.4    Knaus, U.G.5    Philips, M.R.6    Symons, M.7
  • 52
    • 34248379012 scopus 로고    scopus 로고
    • Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: Lessons from recent developments in the IARC TP53 database
    • DOI 10.1002/humu.20495
    • Petitjean, A., Mathe, E., Kato, S., Ishioka, C., Tavtigian, S.V., Hainaut, P. and Olivier, M. (2007) Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum. Mutat., 28, 622-629 (Pubitemid 46744292)
    • (2007) Human Mutation , vol.28 , Issue.6 , pp. 622-629
    • Petitjean, A.1    Mathe, E.2    Kato, S.3    Ishioka, C.4    Tavtigian, S.V.5    Hainaut, P.6    Olivier, M.7
  • 54
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software Environment for integrated models of biomolecular interaction networks
    • DOI 10.1101/gr.1239303
    • Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504 (Pubitemid 37428274)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 56
    • 78149460182 scopus 로고    scopus 로고
    • DEGAS: De novo discovery of dysregulated pathways in human diseases
    • Ulitsky, I., Krishnamurthy, A., Karp, R.M. and Shamir, R. (2010) DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One, 5, e13367
    • (2010) PLoS One , vol.5
    • Ulitsky, I.1    Krishnamurthy, A.2    Karp, R.M.3    Shamir, R.4
  • 57
    • 77349088313 scopus 로고    scopus 로고
    • Detecting disease associated modules and prioritizing active genes based on high throughput data
    • Qiu, Y., Zhang, S., Zhang, X. and Chen, L. (2010) Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics, 11, 26-26
    • (2010) BMC Bioinformatics , vol.11 , pp. 26-26
    • Qiu, Y.1    Zhang, S.2    Zhang, X.3    Chen, L.4
  • 58
    • 77957694184 scopus 로고    scopus 로고
    • Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network
    • Su, J., Yoon, B. and Dougherty, E.R. (2010) Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. BMC Bioinformatics, 11, S8-S8
    • (2010) BMC Bioinformatics , vol.11
    • Su, J.1    Yoon, B.2    Dougherty, E.R.3
  • 59
    • 77953194530 scopus 로고    scopus 로고
    • Inferring the functions of longevity genes with modular subnetwork biomarkers of caenorhabditis elegans aging
    • Fortney, K., Kotlyar, M. and Jurisica, I. (2010) Inferring the functions of longevity genes with modular subnetwork biomarkers of caenorhabditis elegans aging. Genome Biol., 11, R13-R13
    • (2010) Genome Biol. , vol.11
    • Fortney, K.1    Kotlyar, M.2    Jurisica, I.3
  • 60
    • 77956836440 scopus 로고    scopus 로고
    • A systems biology approach to identify effective cocktail drugs
    • Wu, Z., Zhao, X. and Chen, L. (2010) A systems biology approach to identify effective cocktail drugs. BMC Syst. Biol., 4, S7-S7
    • (2010) BMC Syst. Biol. , vol.4
    • Wu, Z.1    Zhao, X.2    Chen, L.3
  • 61
    • 84873051678 scopus 로고    scopus 로고
    • Identification of coordinately dysregulated subnetworks in complex phenotypes
    • Chowdhury, S.A. and Koyutrk, M. (2010) Identification of coordinately dysregulated subnetworks in complex phenotypes. Pac. Symp. Biocomput., 2010, 133-144.
    • (2010) Pac. Symp. Biocomput. , vol.2010 , pp. 133-144
    • Chowdhury, S.A.1    Koyutrk, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.