메뉴 건너뛰기




Volumn 8, Issue 5, 2011, Pages 1170-1182

A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention

Author keywords

breast cancer; cell proliferation; Dynamic Bayesian network; genetic intervention; genetic network; phenotype prediction; systems biology

Indexed keywords

BREAST CANCER; DYNAMIC BAYESIAN NETWORK; GENETIC INTERVENTION; GENETIC NETWORK; PHENOTYPE PREDICTION; SYSTEMS BIOLOGY;

EID: 79960897495     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.18     Document Type: Article
Times cited : (36)

References (52)
  • 1
    • 0001185873 scopus 로고    scopus 로고
    • An essay towards solving a problem in the doctrine of chances
    • T. Bayes, "An Essay Towards Solving a Problem in the Doctrine of Chances," Philosophical Trans. Royal Soc. of London, vol. 53, pp. 370-418, 1763.
    • Philosophical Trans. Royal Soc. of London , vol.53 , Issue.1763 , pp. 370-418
    • Bayes, T.1
  • 2
    • 13844253637 scopus 로고    scopus 로고
    • A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
    • DOI 10.1093/bioinformatics/bti014
    • M.J. Beal, F. Falciani, Z. Ghahramani, C. Rangel, and D.L. Wild, "A Bayesian Approach to Reconstructing Genetic Regulatory Networks with Hidden Factors," Bioinformatics, vol. 21, pp. 349-356, 2005. (Pubitemid 40246606)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 349-356
    • Beal, M.J.1    Falciani, F.2    Ghahramani, Z.3    Rangel, C.4    Wild, D.L.5
  • 4
    • 47649116839 scopus 로고    scopus 로고
    • Consistent modeling, integration and simulation of molecular interaction networks in space-time dimension
    • R. Chang, "Consistent Modeling, Integration and Simulation of Molecular Interaction Networks in Space-Time Dimension," Proc. Seventh IEEE Int'l Conf. Bioinformatics and Bioengineering (BIBE '07), pp. 1254-1259, 2007.
    • (2007) Proc. Seventh IEEE Int'l Conf. Bioinformatics and Bioengineering (BIBE '07) , pp. 1254-1259
    • Chang, R.1
  • 5
    • 40649103609 scopus 로고    scopus 로고
    • Modeling semantics of inconsistent qualitative knowledge for quantitative Bayesian network inference
    • R. Chang, W. Brauer, and M. Stetter, "Modeling Semantics of Inconsistent Qualitative Knowledge for Quantitative Bayesian Network Inference," Neural Networks, vol. 21, nos. 2-3, pp. 182-192, 2008.
    • (2008) Neural Networks , vol.21 , Issue.2-3 , pp. 182-192
    • Chang, R.1    Brauer, W.2    Stetter, M.3
  • 6
    • 55949104584 scopus 로고    scopus 로고
    • Quantitative inference by qualitative semantic knowledge mining with Bayesian model averaging
    • Dec.
    • R. Chang, M. Stetter, and W. Brauer, "Quantitative Inference by Qualitative Semantic Knowledge Mining with Bayesian Model Averaging," IEEE Trans. Knowledge and Data Eng., vol. 20, no. 12, pp. 1587-1600, Dec. 2008.
    • (2008) IEEE Trans. Knowledge and Data Eng. , vol.20 , Issue.12 , pp. 1587-1600
    • Chang, R.1    Stetter, M.2    Brauer, W.3
  • 8
    • 0035970035 scopus 로고    scopus 로고
    • Defective repression of c-myc in breast cancer cells: A loss at the core of the transforming growth factor β growth arrest program
    • DOI 10.1073/pnas.98.3.992
    • C.-R. Chen, Y. Kang, and J. Massagué, "Defective Repression of c-MYC in Breast Cancer Cells: A Loss at the Core of the Transforming Growth Factor β Growth Arrest Program," Proc. Nat'l Academy of Sciences USA, vol. 98, no. 3, pp. 992-999, http://www.pnas.org/content/98/3/992.abstract, 2001. (Pubitemid 32121175)
    • (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.3 , pp. 992-999
    • Chen, C.-R.1    Kang, Y.2    Massague, J.3
  • 9
    • 0037067653 scopus 로고    scopus 로고
    • E2F4/5 and p107 as Smad cofactors linking the TGFβ receptor to c-myc repression
    • DOI 10.1016/S0092-8674(02)00801-2
    • C.-R. Chen, Y. Kang, P.M. Siegel, and J. Massague, "E2F4/5 and p107 as Smad Cofactors Linking the TGF-beta Receptor to c-myc Repression," Cell, vol. 110, pp. 19-32, 2002. (Pubitemid 34874603)
    • (2002) Cell , vol.110 , Issue.1 , pp. 19-32
    • Chen, C.-R.1    Kang, Y.2    Siegel, P.M.3    Massague, J.4
  • 10
    • 0029073142 scopus 로고
    • Transforming growth factor beta induces the cyclin-dependent kinase inhibitor p21 through a p53-independent mechanism
    • M.B. Datto, Y. Li, J. Panus, D.J. Howe, Y. Xiong, and X.-F. Wang, "Transforming Growth Factor Beta Induces the Cyclin-Dependent Kinase Inhibitor p21 through a p53-Independent Mechanism," Proc. Nat'l Academy of Science USA, vol. 92, pp. 5545-5549, 1995.
    • (1995) Proc. Nat'l Academy of Science USA , vol.92 , pp. 5545-5549
    • Datto, M.B.1    Li, Y.2    Panus, J.3    Howe, D.J.4    Xiong, Y.5    Wang, X.-F.6
  • 11
    • 84990553353 scopus 로고
    • A model for reasoning about persistence and causation
    • T. Dean and K. Kanazawa, "A Model for Reasoning about Persistence and Causation," Computational Intelligence, vol. 5, pp. 142-150, 1989.
    • (1989) Computational Intelligence , vol.5 , pp. 142-150
    • Dean, T.1    Kanazawa, K.2
  • 12
    • 3042742432 scopus 로고    scopus 로고
    • Involvement of ras activation in human breast cancer cell signaling, invasion, and anoikis
    • DOI 10.1158/0008-5472.CAN-04-0396
    • L.B. Eckert, G.A. Repasky, A.S. Ulku, A. McFall, H. Zhou, C.I. Sartor, and C.J. Der, "Involvement of Ras Activation in Human Breast Cancer Cell Signaling, Invasion, and Anoikis," Cancer Research, vol. 64, pp. 4585-4592, 2004. (Pubitemid 38856932)
    • (2004) Cancer Research , vol.64 , Issue.13 , pp. 4585-4592
    • Eckert, L.B.1    Repasky, G.A.2    Ulku, A.S.3    McFall, A.4    Zhou, H.5    Sartor, C.I.6    Der, C.J.7
  • 13
    • 33748679908 scopus 로고    scopus 로고
    • A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer
    • DOI 10.1101/gad.1446006
    • J. Eeckhoute, J.S. Carroll, T.R. Geistlinger, M.I. Torres-Arzayus, and M. Brown, "A Cell-Type-Specific Transcriptional Network Required for Estrogen Regulation of Cyclin D1 and Cell Cycle Progression in Breast Cancer," Genes & Development, vol. 20, no. 18, pp. 2513-2526, http://dx.doi.org/10. 1101/gad.1446006, Sept. 2006. (Pubitemid 44396837)
    • (2006) Genes and Development , vol.20 , Issue.18 , pp. 2513-2526
    • Eeckhoute, J.1    Carroll, J.S.2    Geistlinger, T.R.3    Torres-Arzayus, M.I.4    Brown, M.5
  • 14
    • 0001586968 scopus 로고    scopus 로고
    • Learning belief networks in the presence of missing values and hidden variables
    • N. Friedman, "Learning Belief Networks in the Presence of Missing Values and Hidden Variables," Proc. 14th Int'l Conf. Machine Learning (ICML '97), pp. 125-133, 1997.
    • (1997) Proc. 14th Int'l Conf. Machine Learning (ICML '97) , pp. 125-133
    • Friedman, N.1
  • 15
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • DOI 10.1126/science.1094068
    • N. Friedman, "Inferring Cellular Networks Using Probabilistic Graphical Models," Science, vol. 303, pp. 799-805, 2004. (Pubitemid 38174650)
    • (2004) Science , vol.303 , Issue.5659 , pp. 799-805
    • Friedman, N.1
  • 18
    • 34548538013 scopus 로고    scopus 로고
    • Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
    • article no. 11
    • F. Geier, J. Timmer, and C. Fleck1, "Reconstructing Gene-Regulatory Networks from Time Series, Knock-Out Data, and Prior Knowledge," BMC Systems Biology, vol. 1, article no. 11, 2007.
    • (2007) BMC Systems Biology , vol.1
    • Geier, F.1    Timmer, J.2    Fleck, C.3
  • 21
    • 0028168242 scopus 로고
    • Pl5INK4B is a potential effector of TGF-[beta]-induced cell cycle arrest
    • G.J. Hannon and D. Beach, "pl5INK4B is a Potential Effector of TGF-[Beta]-Induced Cell Cycle Arrest," Nature, vol. 371, pp. 257-261, 1994.
    • (1994) Nature , vol.371 , pp. 257-261
    • Hannon, G.J.1    Beach, D.2
  • 22
    • 0036366689 scopus 로고    scopus 로고
    • Combining location and expression data for principled discovery of genetic regulatory network models
    • A.J. Hartemink, D.K. Gifford, T. Jaakkola, and R.A. Young, "Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models," Proc. Pacific Symp. Biocomputing, pp. 437-449, 2002.
    • (2002) Proc. Pacific Symp. Biocomputing , pp. 437-449
    • Hartemink, A.J.1    Gifford, D.K.2    Jaakkola, T.3    Young, R.A.4
  • 23
    • 9944259646 scopus 로고
    • Learning Bayesian networks: The combination of knowledge and statistical data
    • technical report
    • D. Heckerman, "Learning Bayesian Networks: The Combination of Knowledge and Statistical Data," technical report, KDD Workshop, 1994.
    • (1994) KDD Workshop
    • Heckerman, D.1
  • 24
    • 0003846041 scopus 로고    scopus 로고
    • A tutorial on learning with bayesian networks
    • technical report
    • D. Heckerman, "A Tutorial on Learning with Bayesian Networks," technical report, Microsoft Research, 1996.
    • (1996) Microsoft Research
    • Heckerman, D.1
  • 25
    • 0033525188 scopus 로고    scopus 로고
    • RhoA stimulates p27(Kip) degradation through its regulation of cyclin E/CDK2 activity
    • DOI 10.1074/jbc.274.6.3396
    • W. Hu, C.J. Bellone, and J.J. Baldassare, "RhoA Stimulates p27Kip Degradation through Its Regulation of Cyclin E/CDK2 Activity," J. Biological Chemistry, vol. 274, pp. 3396-3401, 1999. (Pubitemid 29077177)
    • (1999) Journal of Biological Chemistry , vol.274 , Issue.6 , pp. 3396-3401
    • Hu, W.1    Bellone, C.J.2    Baldassare, J.J.3
  • 26
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • G. Karlebach and R. Shamir, "Modelling and Analysis of Gene Regulatory Networks," Nature Rev. Molecular Cell Biology, vol. 9, pp. 770-780, 2008.
    • (2008) Nature Rev. Molecular Cell Biology , vol.9 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 29
    • 0842309206 scopus 로고    scopus 로고
    • Inferring gene networks from time series microarray data using dynamic Bayesian networks
    • S.Y. Kim, S. Imoto, and S. Miyano, "Inferring Gene Networks from Time Series Microarray Data Using Dynamic Bayesian Networks," Briefings in Bioinformatics, vol. 4, pp. 228-235, 2003.
    • (2003) Briefings in Bioinformatics , vol.4 , pp. 228-235
    • Kim, S.Y.1    Imoto, S.2    Miyano, S.3
  • 30
    • 22144460567 scopus 로고    scopus 로고
    • STEPP - Search Tool for Exploration of Petri net Paths: A new tool for petri net-based path analysis in biochemical networks
    • 0014
    • I. Koch, M. Schueler, and M. Heiner, "STEPP-Search Tool for Exploration of Petri Net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks," In Silico Biology, vol. 5, pp. 129-137, 2005. (Pubitemid 40983547)
    • (2005) Silico Biology , vol.5 , Issue.2 , pp. 129-137
    • Koch, I.1    Schuler, M.2    Heiner, M.3
  • 31
    • 0033670135 scopus 로고    scopus 로고
    • Pathway analysis in metabolic databases via differential metabolic display (DMD)
    • R. Kuffner, R. Zimmer, and T. Lengauer, "Pathway Analysis in Metabolic Databases via Differential Metabolic Display (DMD)," Bioinformatics, vol. 16, pp. 825-836, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 825-836
    • Kuffner, R.1    Zimmer, R.2    Lengauer, T.3
  • 32
    • 0001006209 scopus 로고
    • Local computations with probabilities on graphical structures and their application to expert systems
    • S. Lauritzen and D. Spiegelhalter, "Local Computations with Probabilities on Graphical Structures and Their Application to Expert Systems," J. Royal Statistical Soc. Series B, vol. 50, pp. 157-224, 1988.
    • (1988) J. Royal Statistical Soc. Series B , vol.50 , pp. 157-224
    • Lauritzen, S.1    Spiegelhalter, D.2
  • 34
  • 36
    • 34547844132 scopus 로고    scopus 로고
    • Connecting quantitative regulatory-network models to the genome
    • Y. Pan, T. Durfee, J. Bockhorst, and M. Craven, "Connecting Quantitative Regulatory-Network Models to the Genome," Bioinformatics, vol. 23, pp. 367-376, 2007.
    • (2007) Bioinformatics , vol.23 , pp. 367-376
    • Pan, Y.1    Durfee, T.2    Bockhorst, J.3    Craven, M.4
  • 39
    • 0030026495 scopus 로고    scopus 로고
    • Qualitative analysis of biochemical reaction systems
    • DOI 10.1016/0010-4825(95)00042-9
    • V.N. Reddy, M.N. Liebman, and M.L. Mavrovouniotis, "Qualitative Analysis of Biochemical Reaction Systems," Computers in Biology and Medicine, vol. 26, pp. 9-24, 1996. (Pubitemid 26046739)
    • (1996) Computers in Biology and Medicine , vol.26 , Issue.1 , pp. 9-24
    • Reddy, V.N.1    Liebman, M.N.2    Mavrovouniotis, M.L.3
  • 40
    • 0029153609 scopus 로고
    • Kip/cip and Ink4 Cdk inhibitors cooperate to induce cell cycle arrest in response to TGF-beta
    • I. Reynisdottir, K. Polyak, A. Iavarone, and J. Massague, "Kip/Cip and Ink4 Cdk Inhibitors Cooperate to Induce Cell Cycle Arrest in Response to TGF-Beta," Genes and Development, vol. 9, pp. 1831-1845, 1995.
    • (1995) Genes and Development , vol.9 , pp. 1831-1845
    • Reynisdottir, I.1    Polyak, K.2    Iavarone, A.3    Massague, J.4
  • 41
    • 0033012926 scopus 로고    scopus 로고
    • Transforming growth factor-β1 up-regulates p15, p21 and p27 and blocks cell cycling in G1 in human prostate epithelium
    • DOI 10.1677/joe.0.1600257
    • C.N. Robson, V. Gnanapragasam, R.L. Byrne, and A.T. Collins, "Transforming Growth Factor-Beta1 Up-Regulates p15, p21 and p27 and Blocks Cell Cycling in G1 in Human Prostate Epithelium," J. Endocrinology, vol. 160, pp. 257-266, 1999. (Pubitemid 29074696)
    • (1999) Journal of Endocrinology , vol.160 , Issue.2 , pp. 257-266
    • Robson, C.N.1    Gnanapragasam, V.2    Byrne, R.L.3    Collins, A.T.4    Neal, D.E.5
  • 42
    • 17644427718 scopus 로고    scopus 로고
    • Causal protein-signaling networks derived from multiparameter single-cell data
    • DOI 10.1126/science.1105809
    • K. Sachs, O. Perez, D. Peer, D.A. Lauffenburger, and G.P. Nolan, "Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data," Science, vol. 308, pp. 523-529, 2005. (Pubitemid 40570578)
    • (2005) Science , vol.308 , Issue.5721 , pp. 523-529
    • Sachs, K.1    Perez, O.2    Pe'er, D.3    Lauffenburger, D.A.4    Nolan, G.P.5
  • 43
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • DOI 10.1038/ng1165
    • E. Segal, M. Shapira, R. A, D. Pe'er, D. Botstein, D. Koller, and N. Friedman, "Module Networks: Identifying Regulatory Modules and Their Condition-Specific Regulators from Gene Expression Data," Nature Genetics, vol. 34, pp. 166-176, 2003. (Pubitemid 36666927)
    • (2003) Nature Genetics , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 44
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • E. Segal, H. Wang, and D. Koller, "Discovering Molecular Pathways from Protein Interaction and Gene Expression Data," Bioinformatics, vol. 19, pp. 264-272, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 264-272
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 45
    • 0037126303 scopus 로고    scopus 로고
    • Cip1 Cdk inhibitor influences the outcome of the p53 response to DNA damage
    • DOI 10.1038/nature01119
    • J. Seoane, H.-V. Le, and J. Massague, "Myc Suppression of the p21Cip1 Cdk Inhibitor Influences the Outcome of the p53 Response to DNA Damage," Nature, vol. 419, pp. 729-734, 2002. (Pubitemid 35177959)
    • (2002) Nature , vol.419 , Issue.6908 , pp. 729-734
    • Seoane, J.1    Le, H.-V.2    Massague, J.3
  • 47
    • 0842320996 scopus 로고    scopus 로고
    • Cooperation of the ErbB2 receptor and transforming growth factor beta in induction of migration and invasion in mammary epithelial cells
    • S.E. Seton-Rogers, Y. Lu, L.M. Hines, M. Koundinya, J. LaBaer, S.K. Muthuswamy, and J.S. Brugge, "Cooperation of the ErbB2 Receptor and Transforming Growth Factor Beta in Induction of Migration and Invasion in Mammary Epithelial Cells," Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 1257-1262, 2003.
    • (2003) Proc. Nat'l Academy of Sciences USA , vol.101 , pp. 1257-1262
    • Seton-Rogers, S.E.1    Lu, Y.2    Hines, L.M.3    Koundinya, M.4    Labaer, J.5    Muthuswamy, S.K.6    Brugge, J.S.7
  • 48
    • 0242499448 scopus 로고    scopus 로고
    • Cytostatic and apoptotic actions of TGF-beta in homeostasis and cancer
    • P.M. Siegel and J. Massagué, "Cytostatic and Apoptotic Actions of TGF-Beta in Homeostasis and Cancer," Nature Rev. Cancer, vol. 3, no. 11, pp. 807-821, 2003.
    • (2003) Nature Rev. Cancer , vol.3 , Issue.11 , pp. 807-821
    • Siegel, P.M.1    Massagué, J.2
  • 49
    • 0032482437 scopus 로고    scopus 로고
    • 1 cyclin expression in breast cancer cells
    • K.J. Sweeney, A. Swarbrick, R.L. Sutherland, and E.A. Musgrove, "Lack of Relationship between CDK Activity and G1 Cyclin Expression in Breast Cancer Cells," Oncogene, vol. 16, pp. 2865-2878, 1998. (Pubitemid 28383271)
    • (1998) Oncogene , vol.16 , Issue.22 , pp. 2865-2878
    • Sweeney, K.J.1    Swarbrick, A.2    Sutherland, R.L.3    Musgrove, E.A.4
  • 51
    • 46049101810 scopus 로고    scopus 로고
    • Gene regulatory network reconstruction by bayesian integration of prior knowledge and/or different experimental conditions
    • DOI 10.1142/S0219720008003539, PII S0219720008003539
    • A.V. Werhli and D. Husmeier, "Gene Regulatory Network Reconstruction by Bayesian Integration of Prior Knowledge and/or Different Experimental Conditions," J. Bioinformatics and Computational Biology, vol. 6, pp. 543-572, 2008. (Pubitemid 351895193)
    • (2008) Journal of Bioinformatics and Computational Biology , vol.6 , Issue.3 , pp. 543-572
    • Werhli, A.V.1    Husmeier, D.2
  • 52
    • 0030787048 scopus 로고    scopus 로고
    • Inhibition of cyclin D expression in human breast carcinoma cells by retinoids in vitro
    • Q. Zhou, M. Stetler-Stevenson, and P.S. Steeg, "Inhibition of Cyclin D Expression in Human Breast Carcinoma Cells by Retinoids In Vitro," Oncogene, vol. 15, pp. 107-115, 1997. (Pubitemid 27348102)
    • (1997) Oncogene , vol.15 , Issue.1 , pp. 107-115
    • Zhou, Q.1    Stetler-Stevenson, M.2    Steeg, P.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.