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Volumn 76, Issue SUPPL. 3, 2007, Pages

Inferring gene regulatory networks by integrating static and dynamic data

Author keywords

Data interpretation; Gene regulatory networks; Genetic algorithm; Machine learning; Microarray analysis of gene expression

Indexed keywords

DATA REDUCTION; GENE EXPRESSION; GENETIC ALGORITHMS; MICROARRAYS;

EID: 35449002487     PISSN: 13865056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijmedinf.2007.07.005     Document Type: Article
Times cited : (9)

References (52)
  • 1
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: from co-expression clustering to reverse engineering
    • D'haeseleer P., Liang S., and Somogyi R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16 (2000) 707-726
    • (2000) Bioinformatics , vol.16 , pp. 707-726
    • D'haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 2
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 (2002) 67-103
    • (2002) J. Comput. Biol. , vol.9 , pp. 67-103
    • de Jong, H.1
  • 3
    • 0031616241 scopus 로고    scopus 로고
    • Reveal, a general reverse engineering algorithm for inference of genetic network architectures
    • Liang S., Fuhrman S., and Somogyi R. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. (1998) 18-29
    • (1998) Pac. Symp. Biocomput. , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 4
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • Akutsu T., Miyano S., and Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. Biocomput. (1999) 17-28
    • (1999) Pac. Symp. Biocomput. , pp. 17-28
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 5
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
    • Shmulevich I., Dougherty E.R., Kim S., and Zhang W. Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18 (2002) 261-274
    • (2002) Bioinformatics , vol.18 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.R.2    Kim, S.3    Zhang, W.4
  • 7
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling
    • Tegner J., Yeung M.K., Hasty J., and Collins J.J. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc. Natl. Acad. Sci. USA 100 (2003) 5944-5949
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.K.2    Hasty, J.3    Collins, J.J.4
  • 11
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Friedman N. Inferring cellular networks using probabilistic graphical models. Science 303 (2004) 799-805
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 12
    • 34547788797 scopus 로고    scopus 로고
    • Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks
    • Ferrazzi F., Sebastiani P., Ramoni M.F., and Bellazzi R. Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks. BMC Bioinformatics 8 Suppl. 5 (2007) S2
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 5
    • Ferrazzi, F.1    Sebastiani, P.2    Ramoni, M.F.3    Bellazzi, R.4
  • 14
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D., and Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34 (2003) 166-176
    • (2003) Nat. Genet. , vol.34 , 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
  • 15
    • 0242490789 scopus 로고    scopus 로고
    • Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network
    • Zak D.E., Gonye G.E., Schwaber J.S., and Doyle III F.J. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Res. 13 (2003) 2396-2405
    • (2003) Genome Res. , vol.13 , pp. 2396-2405
    • Zak, D.E.1    Gonye, G.E.2    Schwaber, J.S.3    Doyle III, F.J.4
  • 19
    • 33646360604 scopus 로고    scopus 로고
    • Modelling in molecular biology: describing transcription regulatory networks at different scales
    • Schlitt T., and Brazma A. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361 (2006) 483-494
    • (2006) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.361 , pp. 483-494
    • Schlitt, T.1    Brazma, A.2
  • 20
    • 0345928693 scopus 로고    scopus 로고
    • Building and analysing genome-wide gene disruption networks
    • Rung J., Schlitt T., Brazma A., Freivalds K., and Vilo J. Building and analysing genome-wide gene disruption networks. Bioinformatics 18 Suppl. 2 (2002) S202-S210
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Rung, J.1    Schlitt, T.2    Brazma, A.3    Freivalds, K.4    Vilo, J.5
  • 23
    • 8744307994 scopus 로고    scopus 로고
    • Multimodel inference. Understanding AIC and BIC in model selection
    • Burnham K.P., and Anderson D.R. Multimodel inference. Understanding AIC and BIC in model selection. Sociological Methods Res. 33 (2004) 261-304
    • (2004) Sociological Methods Res. , vol.33 , pp. 261-304
    • Burnham, K.P.1    Anderson, D.R.2
  • 28
    • 33847784791 scopus 로고    scopus 로고
    • Multiple levels of cyclin specificity in cell-cycle control
    • Bloom J., and Cross F.R. Multiple levels of cyclin specificity in cell-cycle control. Nat. Rev. Mol. Cell. Biol. 8 (2007) 149-160
    • (2007) Nat. Rev. Mol. Cell. Biol. , vol.8 , pp. 149-160
    • Bloom, J.1    Cross, F.R.2
  • 30
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • de Lichtenberg U., Jensen L.J., Brunak S., and Bork P. Dynamic complex formation during the yeast cell cycle. Science 307 (2005) 724-727
    • (2005) Science , vol.307 , pp. 724-727
    • de Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 32
    • 0029082391 scopus 로고
    • Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae
    • Piatti S., Lengauer C., and Nasmyth K. Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae. EMBO J. 14 (1995) 3788-3799
    • (1995) EMBO J. , vol.14 , pp. 3788-3799
    • Piatti, S.1    Lengauer, C.2    Nasmyth, K.3
  • 33
    • 0029791262 scopus 로고    scopus 로고
    • The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1
    • Knapp D., Bhoite L., Stillman D.J., and Nasmyth K. The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1. Mol. Cell. Biol 16 (1996) 5701-5707
    • (1996) Mol. Cell. Biol , vol.16 , pp. 5701-5707
    • Knapp, D.1    Bhoite, L.2    Stillman, D.J.3    Nasmyth, K.4
  • 34
    • 0031015401 scopus 로고    scopus 로고
    • The Swi5 transcription factor of Saccharomyces cerevisiae has a role in exit from mitosis through induction of the cdk-inhibitor Sic1 in telophase
    • Toyn J.H., Johnson A.L., Donovan J.D., Toone W.M., and Johnston L.H. The Swi5 transcription factor of Saccharomyces cerevisiae has a role in exit from mitosis through induction of the cdk-inhibitor Sic1 in telophase. Genetics 145 (1997) 85-96
    • (1997) Genetics , vol.145 , pp. 85-96
    • Toyn, J.H.1    Johnson, A.L.2    Donovan, J.D.3    Toone, W.M.4    Johnston, L.H.5
  • 35
    • 35448936679 scopus 로고    scopus 로고
    • "KEGG: Kyoto Encyclopedia of Genes and Genomes," http://www.genome.jp/kegg/.
  • 36
    • 0034964368 scopus 로고    scopus 로고
    • Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF
    • Cosma M.P., Panizza S., and Nasmyth K. Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. Mol. Cell 7 (2001) 1213-1220
    • (2001) Mol. Cell , vol.7 , pp. 1213-1220
    • Cosma, M.P.1    Panizza, S.2    Nasmyth, K.3
  • 37
    • 35448965981 scopus 로고    scopus 로고
    • "Saccharomyces Genome Database," http://www.yeastgenome.org/.
  • 38
    • 0036935790 scopus 로고    scopus 로고
    • KNR4 is a member of the PKC1 signalling pathway and genetically interacts with BCK2, a gene involved in cell cycle progression in Saccharomyces cerevisiae
    • Martin-Yken H., Dagkessamanskaia A., Talibi D., and Francois J. KNR4 is a member of the PKC1 signalling pathway and genetically interacts with BCK2, a gene involved in cell cycle progression in Saccharomyces cerevisiae. Curr. Genet. 41 (2002) 323-332
    • (2002) Curr. Genet. , vol.41 , pp. 323-332
    • Martin-Yken, H.1    Dagkessamanskaia, A.2    Talibi, D.3    Francois, J.4
  • 39
    • 0037425623 scopus 로고    scopus 로고
    • Periodic transcription: a cycle within a cycle
    • Breeden L.L. Periodic transcription: a cycle within a cycle. Curr. Biol. 13 (2003) R31-R38
    • (2003) Curr. Biol. , vol.13
    • Breeden, L.L.1
  • 40
    • 0030977093 scopus 로고    scopus 로고
    • A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription
    • McInerny C.J., Partridge J.F., Mikesell G.E., Creemer D.P., and Breeden L.L. A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. Genes Dev. 11 (1997) 1277-1288
    • (1997) Genes Dev. , vol.11 , pp. 1277-1288
    • McInerny, C.J.1    Partridge, J.F.2    Mikesell, G.E.3    Creemer, D.P.4    Breeden, L.L.5
  • 41
    • 0031737085 scopus 로고    scopus 로고
    • Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae
    • Mendenhall M.D., and Hodge A.E. Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 62 (1998) 1191-1243
    • (1998) Microbiol. Mol. Biol. Rev. , vol.62 , pp. 1191-1243
    • Mendenhall, M.D.1    Hodge, A.E.2
  • 42
    • 0027527033 scopus 로고
    • Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins
    • Amon A., Tyers M., Futcher B., and Nasmyth K. Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins. Cell 74 (1993) 993-1007
    • (1993) Cell , vol.74 , pp. 993-1007
    • Amon, A.1    Tyers, M.2    Futcher, B.3    Nasmyth, K.4
  • 44
    • 0027220020 scopus 로고
    • CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae
    • Schwob E., and Nasmyth K. CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. Genes Dev. 7 (1993) 1160-1175
    • (1993) Genes Dev. , vol.7 , pp. 1160-1175
    • Schwob, E.1    Nasmyth, K.2
  • 45
    • 33645124786 scopus 로고    scopus 로고
    • Functional connection between the Clb5 cyclin, the protein kinase C pathway and the Swi4 transcription factor in Saccharomyces cerevisiae
    • Queralt E., and Igual J.C. Functional connection between the Clb5 cyclin, the protein kinase C pathway and the Swi4 transcription factor in Saccharomyces cerevisiae. Genetics 171 (2005) 1485-1498
    • (2005) Genetics , vol.171 , pp. 1485-1498
    • Queralt, E.1    Igual, J.C.2
  • 46
    • 0033588106 scopus 로고    scopus 로고
    • Recovery of the yeast cell cycle from heat shock-induced G(1) arrest involves a positive regulation of G(1) cyclin expression by the S phase cyclin Clb5
    • Li X., and Cai M. Recovery of the yeast cell cycle from heat shock-induced G(1) arrest involves a positive regulation of G(1) cyclin expression by the S phase cyclin Clb5. J. Biol. Chem. 274 (1999) 24220-24231
    • (1999) J. Biol. Chem. , vol.274 , pp. 24220-24231
    • Li, X.1    Cai, M.2
  • 47
    • 35448941117 scopus 로고    scopus 로고
    • Inferring gene expression networks via static and dynamic data integration
    • Ferrazzi F., Magni P., Sacchi L., and Bellazzi R. Inferring gene expression networks via static and dynamic data integration. Stud. Health Technol. Inform. 124 (2006) 119-124
    • (2006) Stud. Health Technol. Inform. , vol.124 , pp. 119-124
    • Ferrazzi, F.1    Magni, P.2    Sacchi, L.3    Bellazzi, R.4
  • 48
    • 27544494569 scopus 로고    scopus 로고
    • Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data
    • Nariai N., Tamada Y., Imoto S., and Miyano S. Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics 21 Suppl. 2 (2005) ii206-ii212
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Nariai, N.1    Tamada, Y.2    Imoto, S.3    Miyano, S.4
  • 49
    • 3242891560 scopus 로고    scopus 로고
    • Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
    • Tamada Y., Kim S., Bannai H., Imoto S., Tashiro K., Kuhara S., and Miyano S. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics 19 Suppl. 2 (2003) II227-II236
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Tamada, Y.1    Kim, S.2    Bannai, H.3    Imoto, S.4    Tashiro, K.5    Kuhara, S.6    Miyano, S.7
  • 50
    • 33748669610 scopus 로고    scopus 로고
    • Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
    • Li S., Wu L., and Zhang Z. Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 22 (2006) 2143-2150
    • (2006) Bioinformatics , vol.22 , pp. 2143-2150
    • Li, S.1    Wu, L.2    Zhang, Z.3
  • 51
    • 34249906427 scopus 로고    scopus 로고
    • Gene functional annotation by statistical analysis of biomedical articles
    • Theodosiou T., Angelis L., Vakali A., and Thomopoulos G.N. Gene functional annotation by statistical analysis of biomedical articles. Int. J. Med. Inform. 76 (2007) 601-613
    • (2007) Int. J. Med. Inform. , vol.76 , pp. 601-613
    • Theodosiou, T.1    Angelis, L.2    Vakali, A.3    Thomopoulos, G.N.4


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