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Volumn 9781597454407, Issue , 2009, Pages 517-539

Methods for structural inference and functional module identification in intracellular networks

Author keywords

Cellular networks; Inference; Mathematical methods; Modelling; Modules; Motifs

Indexed keywords

BIOLOGICAL SYSTEMS; MODELS; TOPOLOGY;

EID: 84855662104     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-59745-440-7_27     Document Type: Chapter
Times cited : (1)

References (105)
  • 1
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • Hartwell, L. H., et al., From molecular to modular cell biology. Nature, 1999.402(6761 Suppl): p. C47-52.
    • (1999) Nature , vol.402 , Issue.6761 , pp. C47-C52
    • Hartwell, L.H.1
  • 2
    • 10744226222 scopus 로고    scopus 로고
    • Computational discovery of gene modules and regulatory networks
    • Bar-Joseph, Z., et al., Computational discovery of gene modules and regulatory networks. Nat Biotechnol, 2003. 21(11):p. 1337-1342.
    • (2003) Nat Biotechnol , vol.21 , Issue.11 , pp. 1337-1342
    • Bar-Joseph, Z.1
  • 3
    • 28644449917 scopus 로고    scopus 로고
    • How does gene expression clustering work?
    • D'Haeseleer, P., How does gene expression clustering work? Nat Biotechnol, 2005. 23(12):p. 1499-1501.
    • (2005) Nat Biotechnol , vol.23 , Issue.12 , pp. 1499-1501
    • D'Haeseleer, P.1
  • 4
    • 34248572623 scopus 로고    scopus 로고
    • Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data
    • Martin, S., et al., Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data. Bioinformatics, 2007.
    • (2007) Bioinformatics
    • Martin, S.1
  • 5
    • 33746353952 scopus 로고    scopus 로고
    • Applying dynamic Bayesian networks to perturbed gene expression data
    • Dojer, N., et al., Applying dynamic Bayesian networks to perturbed gene expression data. BMC Bioinformatics, 2006. 7: p. 249.
    • (2006) BMC Bioinformatics , vol.7 , pp. 249
    • Dojer, N.1
  • 6
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • Hartwell, L. H., et al., From molecular to modular cell biology. Nature, 1999.402(6761 Suppl): p. C47-52.
    • (1999) Nature , vol.402 , Issue.6761 , pp. C47-C52
    • Hartwell, L.H.1
  • 7
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman, S. A., Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor. Biol., 1969. 22(3):p. 437-467.
    • (1969) J Theor. Biol. , vol.22 , Issue.3 , pp. 437-467
    • Kauffman, S.A.1
  • 8
    • 33749597951 scopus 로고    scopus 로고
    • Relevant components in critical random Boolean networks
    • Drossel, V. K.a. B., Relevant components in critical random Boolean networks. New J. Phys., 2006. 8 (228).
    • (2006) New J. Phys. , vol.8 , Issue.228
    • Drossel, V.K.B.1
  • 9
    • 84956252965 scopus 로고
    • Random networks of automata: A simple annealed approximation
    • 1 2: p. 45-49
    • Derrida, B.a. P., Y., Random networks of automata: A simple annealed approximation. Europhys. Lett., 1(2):45-49., 1986. 1(2):p. 45-49.
    • (1986) Europhys. Lett. , vol.1 , Issue.2 , pp. 45-49
    • Derrida, B.P.Y.1
  • 11
    • 27144548324 scopus 로고    scopus 로고
    • Dynamics of critical Kauffman networks under asynchronous stochastic update
    • Greil, F. and B. Drossel, Dynamics of critical Kauffman networks under asynchronous stochastic update. Phys Rev Lett, 2005. 95(4):p. 048701.
    • (2005) Phys Rev Lett , vol.95 , Issue.4 , pp. 048701
    • Greil, F.1    Drossel, B.2
  • 12
    • 28844465824 scopus 로고    scopus 로고
    • Stable and unstable attractors in Boolean networks
    • Klemm, K. and S. Bornholdt, Stable and unstable attractors in Boolean networks. Phys Rev E Stat Nonlin Soft Matter Phys, 2005.72(5 Pt 2): p. 055101.
    • (2005) Phys Rev E Stat Nonlin Soft Matter Phys , vol.72 , Issue.5 , pp. 055101
    • Klemm, K.1    Bornholdt, S.2
  • 13
    • 0036400724 scopus 로고    scopus 로고
    • Dynamics of Boolean networks controlled by biologically meaningful functions
    • Raeymaekers, L., Dynamics of Boolean networks controlled by biologically meaningful functions. J Theor Biol, 2002. 218(3):p. 331-341.
    • (2002) J Theor Biol , vol.218 , Issue.3 , pp. 331-341
    • Raeymaekers, L.1
  • 14
    • 4344706221 scopus 로고    scopus 로고
    • Activities and sensitivities in boolean network models
    • Shmulevich, I. and S. A. Kauffman, Activities and sensitivities in boolean network models. Phys Rev Lett, 2004. 93(4):p. 048701.
    • (2004) Phys Rev Lett , vol.93 , Issue.4 , pp. 048701
    • Shmulevich, I.1    Kauffman, S.A.2
  • 15
    • 33847650979 scopus 로고    scopus 로고
    • Robustness and evolvability in genetic regulatory networks
    • Aldana, M., et al., Robustness and evolvability in genetic regulatory networks. J Theor Biol, 2007. 245(3):p. 433-448.
    • (2007) J Theor Biol , vol.245 , Issue.3 , pp. 433-448
    • Aldana, M.1
  • 16
    • 0031630211 scopus 로고    scopus 로고
    • Genomic regulation modeled as a network with basins of attraction
    • Wuensche, A., Genomic regulation modeled as a network with basins of attraction. Pac Symp Biocomput, 1998: p. 89-102.
    • (1998) Pac Symp Biocomput , pp. 89-102
    • Wuensche, A.1
  • 17
    • 2342444140 scopus 로고    scopus 로고
    • External control in Markovian genetic regulatory networks: The imperfect information case
    • Datta, A., et al., External control in Markovian genetic regulatory networks: the imperfect information case. Bioinformatics, 2004. 20(6):p. 924-930.
    • (2004) Bioinformatics , vol.20 , Issue.6 , pp. 924-930
    • Datta, A.1
  • 18
    • 0031635563 scopus 로고    scopus 로고
    • Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": Their application for understanding carcinogenesis and assessing therapeutic strategies
    • Szallasi, Z. and S. Liang, Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": their application for understanding carcinogenesis and assessing therapeutic strategies. Pac Symp Biocomput, 1998: p. 66-76.
    • (1998) Pac Symp Biocomput , pp. 66-76
    • Szallasi, Z.1    Liang, S.2
  • 19
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks
    • Shmulevich, I., et al., Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics, 2002. 18(2):p. 261-274.
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 261-274
    • Shmulevich, I.1
  • 20
    • 33747874092 scopus 로고    scopus 로고
    • Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
    • Faure, A., et al., Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics, 2006. 22(14):p. e124-131.
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. e124-e131
    • Faure, A.1
  • 21
    • 33745178476 scopus 로고    scopus 로고
    • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
    • Herrgard, M. J., et al., Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res, 2006. 16(5):p. 627-635.
    • (2006) Genome Res , vol.16 , Issue.5 , pp. 627-635
    • Herrgard, M.J.1
  • 22
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • Akutsu, T., S. Miyano, and S. Kuhara, Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac Symp Biocomput, 1999: p. 17-28.
    • (1999) Pac Symp Biocomput , pp. 17-28
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 23
    • 0000419877 scopus 로고    scopus 로고
    • Error-free and Best-fit extensions of partially defined boolean functions
    • Boros, E. and T. Ibaraki, Error-free and Best-fit extensions of partially defined boolean functions. Information and Computation 1998. 140(2):p. 254-283.
    • (1998) Information and Computation , vol.140 , Issue.2 , pp. 254-283
    • Boros, E.1    Ibaraki, T.2
  • 24
    • 33749005690 scopus 로고    scopus 로고
    • An efficient top-down search algorithm for learning Boolean networks of gene expression
    • Nam, D. S., Seunghyun; Kim, Sangsoo, An efficient top-down search algorithm for learning Boolean networks of gene expression. Machine Learning, 2006. 65(1):p. 229-245.
    • (2006) Machine Learning , vol.65 , Issue.1 , pp. 229-245
    • Nam, D.S.1    Seunghyun2    Kim, S.3
  • 25
    • 0031616241 scopus 로고    scopus 로고
    • Reveal, a general reverse engineering algorithm for inference of genetic network architectures
    • Liang, S., S. Fuhrman, and R. Somogyi, Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput, 1998: p. 18-29.
    • (1998) Pac Symp Biocomput , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 26
    • 33847260655 scopus 로고    scopus 로고
    • Boolean networks using the chi-square test for inferring large-scale gene regulatory networks
    • Kim, H., J. K. Lee, and T. Park, Boolean networks using the chi-square test for inferring large-scale gene regulatory networks. BMC Bioinformatics, 2007. 8: p. 37.
    • (2007) BMC Bioinformatics , vol.8 , pp. 37
    • Kim, H.1    Lee, J.K.2    Park, T.3
  • 27
    • 0038047901 scopus 로고    scopus 로고
    • On Learning Gene Regulatory Networks under the Boolean Network Model
    • Lahdesmaki, H., On Learning Gene Regulatory Networks under the Boolean Network Model. Machine Learning, 2002. 52: p. 147-163.
    • (2002) Machine Learning , vol.52 , pp. 147-163
    • Lahdesmaki, H.1
  • 28
    • 0000005079 scopus 로고    scopus 로고
    • A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions
    • Akutsu, T., et al., A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions. Genome Inform Ser Workshop Genome Inform, 1998. 9: p. 151-160.
    • (1998) Genome Inform Ser Workshop Genome Inform , vol.9 , pp. 151-160
    • Akutsu, T.1
  • 29
    • 24944466553 scopus 로고    scopus 로고
    • Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks
    • 2005, Springer Berlin/Heidelberg
    • Osamu Hirose, N. N., Yoshinori Tamada, Hideo Bannai, Seiya Imoto and Satoru Miyano, Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks, in Computational Science and Its Applications - ICCSA 2005. 2005, Springer Berlin/Heidelberg. p. 349-356.
    • (2005) Computational Science and its Applications - ICCSA , pp. 349-356
    • Osamu Hirose, N.N.1    Tamada, Y.2    Bannai, H.3    Imoto, S.4    Miyano, S.5
  • 30
    • 34248572623 scopus 로고    scopus 로고
    • Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data
    • Martin, S., et al., Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data. Bioinformatics, 2007.
    • (2007) Bioinformatics
    • Martin, S.1
  • 31
    • 16344368806 scopus 로고    scopus 로고
    • Intervention in context-sensitive probabilistic Boolean networks
    • Pal, R., et al., Intervention in context-sensitive probabilistic Boolean networks. Bioinformatics, 2005. 21(7):p. 1211-1218.
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1211-1218
    • Pal, R.1
  • 32
    • 0029267491 scopus 로고
    • Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
    • Thomas, R., D. Thieffry, and M. Kaufman, Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull Math Biol, 1995. 57(2):p. 247-276.
    • (1995) Bull Math Biol , vol.57 , Issue.2 , pp. 247-276
    • Thomas, R.1    Thieffry, D.2    Kaufman, M.3
  • 33
    • 0007712725 scopus 로고    scopus 로고
    • Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior
    • Thomas, R. and M. Kaufman, Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos, 2001. 11(1):p. 170-179.
    • (2001) Chaos , vol.11 , Issue.1 , pp. 170-179
    • Thomas, R.1    Kaufman, M.2
  • 34
    • 0035582202 scopus 로고    scopus 로고
    • Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits
    • Thomas, R. and M. Kaufman, Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits. Chaos, 2001. 11(1):p. 180-195.
    • (2001) Chaos , vol.11 , Issue.1 , pp. 180-195
    • Thomas, R.1    Kaufman, M.2
  • 35
    • 0015823097 scopus 로고
    • Boolean formalization of genetic control circuits
    • Thomas, R., Boolean formalization of genetic control circuits. J Theor Biol, 1973. 42(3):p. 563-585.
    • (1973) J Theor Biol , vol.42 , Issue.3 , pp. 563-585
    • Thomas, R.1
  • 36
    • 0032879544 scopus 로고    scopus 로고
    • Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis
    • Mendoza, L., D. Thieffry, and E. R. Alvarez-Buylla, Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinformatics, 1999.15(7-8): p. 593-606.
    • (1999) Bioinformatics , vol.15 , Issue.7-8 , pp. 593-606
    • Mendoza, L.1    Thieffry, D.2    Alvarez-Buylla, E.R.3
  • 37
    • 0041344607 scopus 로고    scopus 로고
    • Dynamical modelling of pattern formation during embryonic development
    • Thieffry, D. and L. Sanchez, Dynamical modelling of pattern formation during embryonic development. Curr Opin Genet Dev, 2003. 13(4):p. 326-330.
    • (2003) Curr Opin Genet Dev , vol.13 , Issue.4 , pp. 326-330
    • Thieffry, D.1    Sanchez, L.2
  • 38
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman, N., et al., Using Bayesian networks to analyze expression data. J Comput Biol, 2000.7(3-4): p. 601-620.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1
  • 39
    • 0035221560 scopus 로고    scopus 로고
    • Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
    • Hartemink, A. J., et al., Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput, 2001: p. 422-433.
    • (2001) Pac Symp Biocomput , pp. 422-433
    • Hartemink, A.J.1
  • 40
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen, R., et al., A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 2003. 302(5644):p. 449-453.
    • (2003) Science , vol.302 , Issue.5644 , pp. 449-453
    • Jansen, R.1
  • 41
    • 10044240790 scopus 로고    scopus 로고
    • Using prior knowledge to improve genetic network reconstruction from microarray data
    • Le Phillip, P., A. Bahl, and L. H. Ungar, Using prior knowledge to improve genetic network reconstruction from microarray data. In Silico Biol, 2004. 4(3):p. 335-353.
    • (2004) Silico Biol , vol.4 , Issue.3 , pp. 335-353
    • Le Phillip, P.1    Bahl, A.2    Ungar, L.H.3
  • 43
    • 13844253637 scopus 로고    scopus 로고
    • A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
    • Beal, M. J., et al., A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics, 2005. 21(3):p. 349-356.
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 349-356
    • Beal, M.J.1
  • 44
    • 15944361900 scopus 로고    scopus 로고
    • Informative structure priors: Joint learning of dynamic regulatory networks from multiple types of data
    • Bernard, A. and A. J. Hartemink, Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data. Pac Symp Biocomput, 2005: p. 459-470.
    • (2005) Pac Symp Biocomput , pp. 459-470
    • Bernard, A.1    Hartemink, A.J.2
  • 45
    • 33746353952 scopus 로고    scopus 로고
    • Applying dynamic Bayesian networks to perturbed gene expression data
    • Dojer, N., et al., Applying dynamic Bayesian networks to perturbed gene expression data. BMC Bioinformatics, 2006. 7: p. 249.
    • (2006) BMC Bioinformatics , vol.7 , pp. 249
    • Dojer, N.1
  • 46
    • 12744261506 scopus 로고    scopus 로고
    • A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
    • Zou, M. and S. D. Conzen, A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics, 2005. 21(1):p. 71-79.
    • (2005) Bioinformatics , vol.21 , Issue.1 , pp. 71-79
    • Zou, M.1    Conzen, S.D.2
  • 47
    • 19544364324 scopus 로고    scopus 로고
    • Selective integration of multiple biological data for supervised network inference
    • Kato, T., K. Tsuda, and K. Asai, Selective integration of multiple biological data for supervised network inference. Bioinformatics, 2005. 21(10):p. 2488-2495.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2488-2495
    • Kato, T.1    Tsuda, K.2    Asai, K.3
  • 48
    • 29144446142 scopus 로고    scopus 로고
    • Supervised enzyme network inference from the integration of genomic data and chemical information
    • Yamanishi, Y., J. P. Vert, and M. Kanehisa, Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics, 2005. 21 Suppl 1: p. 2468i477.
    • (2005) Bioinformatics , vol.21 , pp. 2468i477
    • Yamanishi, Y.1    Vert, J.P.2    Kanehisa, M.3
  • 49
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: From co-expression clustering to reverse engineering
    • D'Haeseleer, P., S. Liang, and R. Somogyi, Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics, 2000. 16(8):p. 707-726.
    • (2000) Bioinformatics , vol.16 , Issue.8 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 50
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal, E., et al., Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet, 2003. 34(2):p. 166-176.
    • (2003) Nat Genet , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1
  • 51
    • 10744226222 scopus 로고    scopus 로고
    • Computational discovery of gene modules and regulatory networks
    • Bar-Joseph, Z., et al., Computational discovery of gene modules and regulatory networks. Nat Biotechnol, 2003. 21(11):p. 1337-1342.
    • (2003) Nat Biotechnol , vol.21 , Issue.11 , pp. 1337-1342
    • Bar-Joseph, Z.1
  • 52
    • 33750351769 scopus 로고    scopus 로고
    • Data-driven modelling of signal-transduction networks
    • Janes, K. A. and M. B. Yaffe, Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol, 2006. 7(11):p. 820-828.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , Issue.11 , pp. 820-828
    • Janes, K.A.1    Yaffe, M.B.2
  • 53
    • 28644449917 scopus 로고    scopus 로고
    • How does gene expression clustering work?
    • D'Haeseleer, P., How does gene expression clustering work? Nat Biotechnol, 2005. 23(12):p. 1499-1501.
    • (2005) Nat Biotechnol , vol.23 , Issue.12 , pp. 1499-1501
    • D'Haeseleer, P.1
  • 54
    • 0037667290 scopus 로고    scopus 로고
    • Clustering gene-expression data with repeated measurements
    • Yeung, K. Y., M. Medvedovic, and R. E. Bumgarner, Clustering gene-expression data with repeated measurements. Genome Biol, 2003. 4(5):p. R34.
    • (2003) Genome Biol , vol.4 , Issue.5 , pp. R34
    • Yeung, K.Y.1    Medvedovic, M.2    Bumgarner, R.E.3
  • 55
    • 0033452362 scopus 로고    scopus 로고
    • Prediction of gene function by genome-scale expression analysis: Prostate cancer-associated genes
    • Walker, M. G., et al., Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. Genome Res, 1999. 9(12):p. 1198-1203.
    • (1999) Genome Res , vol.9 , Issue.12 , pp. 1198-1203
    • Walker, M.G.1
  • 56
    • 0036796327 scopus 로고    scopus 로고
    • Identification and confirmation of a module of coexpressed genes
    • Thompson, H. G., et al., Identification and confirmation of a module of coexpressed genes. Genome Res, 2002. 12(10):p. 1517-1522.
    • (2002) Genome Res , vol.12 , Issue.10 , pp. 1517-1522
    • Thompson, H.G.1
  • 57
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen, M. B., et al., Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A, 1998. 95(25):p. 14863-14868.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1
  • 58
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie, S., et al., Systematic determination of genetic network architecture. Nat Genet, 1999. 22(3):p. 281-285.
    • (1999) Nat Genet , vol.22 , Issue.3 , pp. 281-285
    • Tavazoie, S.1
  • 59
    • 0032837252 scopus 로고    scopus 로고
    • Computational methods for the identification of differential and coordinated gene expression
    • Claverie, J. M., Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet, 1999. 8(10):p. 1821-1832.
    • (1999) Hum Mol Genet , vol.8 , Issue.10 , pp. 1821-1832
    • Claverie, J.M.1
  • 60
    • 0031616361 scopus 로고    scopus 로고
    • Cluster analysis and data visualization of large-scale gene expression data
    • Michaels, G. S., et al., Cluster analysis and data visualization of large-scale gene expression data. Pac Symp Biocomput, 1998: p. 42-53.
    • (1998) Pac Symp Biocomput , pp. 42-53
    • Michaels, G.S.1
  • 61
    • 0032728081 scopus 로고    scopus 로고
    • Clustering gene expression patterns
    • Ben-Dor, A., R. Shamir, and Z. Yakhini, Clustering gene expression patterns. J Comput Biol, 1999.6(3-4): p. 281-297.
    • (1999) J Comput Biol , vol.6 , Issue.3-4 , pp. 281-297
    • Ben-Dor, A.1    Shamir, R.2    Yakhini, Z.3
  • 62
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    • Alon, U., 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 U S A, 1999. 96(12):p. 6745-6750.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , Issue.12 , pp. 6745-6750
    • Alon, U.1
  • 63
    • 33847657554 scopus 로고    scopus 로고
    • Measuring similarities between gene expression profiles through new data transformations
    • Kim, K., et al., Measuring similarities between gene expression profiles through new data transformations. BMC Bioinformatics, 2007. 8: p. 29.
    • (2007) BMC Bioinformatics , vol.8 , pp. 29
    • Kim, K.1
  • 64
    • 33947159574 scopus 로고    scopus 로고
    • Evaluation of stability of k-means cluster ensembles with respect to random initialization
    • Kuncheva, L. I. and D. P. Vetrov, Evaluation of stability of k-means cluster ensembles with respect to random initialization. IEEE Trans Pattern Anal Mach Intell, 2006. 28(11):p. 1798-1808.
    • (2006) IEEE Trans Pattern Anal Mach Intell , vol.28 , Issue.11 , pp. 1798-1808
    • Kuncheva, L.I.1    Vetrov, D.P.2
  • 65
    • 13244255357 scopus 로고    scopus 로고
    • Incremental genetic k-means algorithm and its application in gene expression data analysis
    • Lu, Y., et al., Incremental genetic k-means algorithm and its application in gene expression data analysis. BMC Bioinformatics, 2004. 5: p. 172.
    • (2004) BMC Bioinformatics , vol.5 , pp. 172
    • Lu, Y.1
  • 67
    • 2942511784 scopus 로고    scopus 로고
    • Clustering of the SOM easily reveals distinct gene expression patterns: Results of a reanalysis of lymphoma study
    • Wang, J., et al., Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics, 2002. 3: p. 36.
    • (2002) BMC Bioinformatics , vol.3 , pp. 36
    • Wang, J.1
  • 68
    • 0042863923 scopus 로고    scopus 로고
    • Analysis of gene expression data using self-organizing maps
    • Toronen, P., et al., Analysis of gene expression data using self-organizing maps. FEBS Lett, 1999. 451(2):p. 142-146.
    • (1999) FEBS Lett , vol.451 , Issue.2 , pp. 142-146
    • Toronen, P.1
  • 69
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Tamayo, P., et al., Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A, 1999. 96(6):p. 2907-2912.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , Issue.6 , pp. 2907-2912
    • Tamayo, P.1
  • 70
    • 0036069214 scopus 로고    scopus 로고
    • Interactive exploration of microarray gene expression patterns in a reduced dimensional space
    • Misra, J., et al., Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res, 2002. 12(7):p. 1112-1120.
    • (2002) Genome Res , vol.12 , Issue.7 , pp. 1112-1120
    • Misra, J.1
  • 71
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter, O., P. O. Brown, and D. Botstein, Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA, 2000. 97(18):p. 10101-10106.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.18 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 72
    • 23744491001 scopus 로고    scopus 로고
    • Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach
    • Boulesteix, A. L. and K. Strimmer, Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theor Biol Med Model, 2005. 2: p. 23.
    • (2005) Theor Biol Med Model , vol.2 , pp. 23
    • Boulesteix, A.L.1    Strimmer, K.2
  • 73
    • 0035184506 scopus 로고    scopus 로고
    • Exploring relationships in gene expressions: A partial least squares approach
    • Datta, S., Exploring relationships in gene expressions: a partial least squares approach. Gene Expr, 2001. 9(6):p. 249-255.
    • (2001) Gene Expr , vol.9 , Issue.6 , pp. 249-255
    • Datta, S.1
  • 74
    • 0030882391 scopus 로고    scopus 로고
    • Robust multivariate statistics and the prediction of protein secondary structure content
    • Clementi, M., et al., Robust multivariate statistics and the prediction of protein secondary structure content. Protein Eng, 1997. 10(7):p. 747-749.
    • (1997) Protein Eng , vol.10 , Issue.7 , pp. 747-749
    • Clementi, M.1
  • 75
    • 0242290935 scopus 로고    scopus 로고
    • Reconstructing genetic networks in yeast
    • Zhang, Z. and M. Gerstein, Reconstructing genetic networks in yeast. Nat Biotechnol, 2003. 21(11):p. 1295-1297.
    • (2003) Nat Biotechnol , vol.21 , Issue.11 , pp. 1295-1297
    • Zhang, Z.1    Gerstein, M.2
  • 76
    • 29244482315 scopus 로고    scopus 로고
    • Barriers to progress in Systems Biology
    • Cassman, M., Barriers to progress in Systems Biology. Nature, 2005. 438(7071):p. 1079.
    • (2005) Nature , vol.438 , Issue.7071 , pp. 1079
    • Cassman, M.1
  • 77
    • 33745128746 scopus 로고    scopus 로고
    • Inferring transcriptional modules from ChIP-chip, motif and microarray data
    • Lemmens, K., et al., Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol, 2006. 7(5):p. R37.
    • (2006) Genome Biol , vol.7 , Issue.5 , pp. R37
    • Lemmens, K.1
  • 78
    • 1542357674 scopus 로고    scopus 로고
    • Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
    • Tanay, A., et al., Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A, 2004. 101(9):p. 2981-2986.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.9 , pp. 2981-2986
    • Tanay, A.1
  • 79
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., et al., Lethality and centrality in protein networks. Nature, 2001. 411(6833):p. 41-42.
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1
  • 80
    • 0037059461 scopus 로고    scopus 로고
    • A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
    • Tong, A. H., et al., A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 2002. 295(5553):p. 321-324.
    • (2002) Science , vol.295 , Issue.5553 , pp. 321-324
    • Tong, A.H.1
  • 81
    • 3042848952 scopus 로고    scopus 로고
    • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    • Han, J. D., et al., Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 2004. 430(6995):p. 88-93.
    • (2004) Nature , vol.430 , Issue.6995 , pp. 88-93
    • Han, J.D.1
  • 82
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong, H., et al., The large-scale organization of metabolic networks. Nature, 2000. 407(6804):p. 651-654.
    • (2000) Nature , vol.407 , Issue.6804 , pp. 651-654
    • Jeong, H.1
  • 83
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • Guimera, R. and L. A. Nunes Amaral, Functional cartography of complex metabolic networks. Nature, 2005. 433(7028):p. 895-900.
    • (2005) Nature , vol.433 , Issue.7028 , pp. 895-900
    • Guimera, R.1    Amaral, L.A.N.2
  • 84
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart, J. M., et al., A gene-coexpression network for global discovery of conserved genetic modules. Science, 2003. 302(5643):p. 249-255.
    • (2003) Science , vol.302 , Issue.5643 , pp. 249-255
    • Stuart, J.M.1
  • 85
    • 10744230485 scopus 로고    scopus 로고
    • Global mapping of the yeast genetic interaction network
    • Tong, A. H., et al., Global mapping of the yeast genetic interaction network. Science, 2004. 303(5659):p. 808-813.
    • (2004) Science , vol.303 , Issue.5659 , pp. 808-813
    • Tong, A.H.1
  • 86
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee, T. I., et al., Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 2002. 298(5594):p. 799-804.
    • (2002) Science , vol.298 , Issue.5594 , pp. 799-804
    • Lee, T.I.1
  • 87
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E., et al., Hierarchical organization of modularity in metabolic networks. Science, 2002. 297(5586):p. 15511555.
    • (2002) Science , vol.297 , Issue.5586 , pp. 15511555
    • Ravasz, E.1
  • 88
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • Schilling, C. H., D. Letscher, and B. O. Palsson, Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol, 2000. 203(3):p. 229-248.
    • (2000) J Theor Biol , vol.203 , Issue.3 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 89
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster, S., D. A. Fell, and T. Dandekar, A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol, 2000. 18(3):p. 326-332.
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 90
    • 1242274402 scopus 로고    scopus 로고
    • Flux coupling analysis of genome-scale metabolic network reconstructions
    • Burgard, A. P., et al., Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res, 2004. 14(2):p. 301-312.
    • (2004) Genome Res , vol.14 , Issue.2 , pp. 301-312
    • Burgard, A.P.1
  • 91
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • Kuepfer, L., U. Sauer, and L. M. Blank, Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res, 2005. 15(10):p. 1421-1430.
    • (2005) Genome Res , vol.15 , Issue.10 , pp. 1421-1430
    • Kuepfer, L.1    Sauer, U.2    Blank, L.M.3
  • 92
    • 5044245707 scopus 로고    scopus 로고
    • Gene co-expression network topology provides a framework for molecular characterization of cellular state
    • Carter, S. L., et al., Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics, 2004. 20(14):p. 2242-2250.
    • (2004) Bioinformatics , vol.20 , Issue.14 , pp. 2242-2250
    • Carter, S.L.1
  • 93
    • 13244264814 scopus 로고    scopus 로고
    • Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
    • Ma, H. W., J. Buer, and A. P. Zeng, Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics, 2004. 5: p. 199.
    • (2004) BMC Bioinformatics , vol.5 , pp. 199
    • Ma, H.W.1    Buer, J.2    Zeng, A.P.3
  • 94
    • 33646347144 scopus 로고    scopus 로고
    • The origins and evolution of functional modules: Lessons from protein complexes
    • Pereira-Leal, J. B., E. D. Levy, and S. A. Teichmann, The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci, 2006. 361(1467):p. 507-517.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , Issue.1467 , pp. 507-517
    • Pereira-Leal, J.B.1    Levy, E.D.2    Teichmann, S.A.3
  • 96
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal, J. B., A. J. Enright, and C. A. Ouzounis, Detection of functional modules from protein interaction networks. Proteins, 2004. 54(1):p. 49-57.
    • (2004) Proteins , vol.54 , Issue.1 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3
  • 97
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • Rives, A. W. and T. Galitski, Modular organization of cellular networks. Proc Natl Acad Sci U S A, 2003. 100(3):p. 1128-1133.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , Issue.3 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 98
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • Arnau, V., S. Mars, and I. Marin, Iterative cluster analysis of protein interaction data. Bioinformatics, 2005. 21(3):p. 364-378.
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Marin, I.3
  • 99
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • Milo, R., et al., Network motifs: simple building blocks of complex networks. Science, 2002. 298(5594):p. 824-827.
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1
  • 100
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S. S., et al., Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet, 2002. 31(1):p. 64-68.
    • (2002) Nat Genet , vol.31 , Issue.1 , pp. 64-68
    • Shen-Orr, S.S.1
  • 101
    • 13544269611 scopus 로고    scopus 로고
    • An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
    • Ma, H. W., et al., An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res, 2004. 32(22):p. 6643-6649.
    • (2004) Nucleic Acids Res , vol.32 , Issue.22 , pp. 6643-6649
    • Ma, H.W.1
  • 102
    • 33847051248 scopus 로고    scopus 로고
    • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
    • Zhang, L. V., et al., Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol, 2005. 4(2):p. 6.
    • (2005) J Biol , vol.4 , Issue.2 , pp. 6
    • Zhang, L.V.1
  • 103
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituents in the yeast protein interaction network
    • Wuchty, S., Z. N. Oltvai, and A. L. Barabasi, Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet, 2003. 35(2):p. 176-179.
    • (2003) Nat Genet , vol.35 , Issue.2 , pp. 176-179
    • Wuchty, S.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 104
    • 0037743679 scopus 로고    scopus 로고
    • Convergent evolution of gene circuits
    • Conant, G. C. and A. Wagner, Convergent evolution of gene circuits. Nat Genet, 2003. 34(3):p. 264-266.
    • (2003) Nat Genet , vol.34 , Issue.3 , pp. 264-266
    • Conant, G.C.1    Wagner, A.2
  • 105
    • 1542286745 scopus 로고    scopus 로고
    • Quantifying modularity in the evolution of biomolecular systems
    • Snel, B. and M. A. Huynen, Quantifying modularity in the evolution of biomolecular systems. Genome Res, 2004. 14(3):p. 391-397.
    • (2004) Genome Res , vol.14 , Issue.3 , pp. 391-397
    • Snel, B.1    Huynen, M.A.2


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