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Volumn 7, Issue 5, 2013, Pages 143-152

Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data

Author keywords

[No Author keywords available]

Indexed keywords

COMPREHENSIVE INFORMATION; CONSISTENCY MEASUREMENT; DYNAMIC BAYESIAN NETWORKS; FUNCTIONAL RELATIONSHIP; GAUSSIAN GRAPHICAL MODELS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; TIME-COURSE GENE EXPRESSION PROFILES;

EID: 84893156375     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2012.0062     Document Type: Article
Times cited : (16)

References (32)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi, A., Oltvai, Z.: 'Network biology: understanding the cell's functional organization', Nat. Rev. Genet., 2004, 5, pp. 101-113
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.1    Oltvai, Z.2
  • 2
    • 84889418078 scopus 로고    scopus 로고
    • Biomolecular networks: methods and applications in systems biology
    • (John Wiley & Sons, New York, 2009)
    • Chen, L., Wang, R.S., Zhang, X.S.: 'Biomolecular networks: methods and applications in systems biology' (John Wiley & Sons, New York, 2009)
    • Chen, L.1    Wang, R.S.2    Zhang, X.S.3
  • 3
    • 54049146919 scopus 로고    scopus 로고
    • Network evaluation from the consistency of the graph structure with the measured data
    • Saito, S., Aburatani, S., Horimoto, K.: 'Network evaluation from the consistency of the graph structure with the measured data', BMC Syst. Biol., 2008, 2, pp. 84
    • (2008) BMC Syst. Biol. , vol.2 , pp. 84
    • Saito, S.1    Aburatani, S.2    Horimoto, K.3
  • 4
    • 33750016109 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from multiple microarray datasets
    • Wang, Y., Joshi, T., Zhang, X.S., Xu, D., Chen, L.: 'Inferring gene regulatory networks from multiple microarray datasets', Bioinformatics, 2006, 22, pp. 2413-2420
    • (2006) Bioinformatics , vol.22 , pp. 2413-2420
    • Wang, Y.1    Joshi, T.2    Zhang, X.S.3    Xu, D.4    Chen, L.5
  • 5
    • 84855160951 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
    • Zhang, X., Zhao, X., He, K., et al.: 'Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information', Bioinformatics, 2012, 28, pp. 98-104
    • (2012) Bioinformatics , vol.28 , pp. 98-104
    • Zhang, X.1    Zhao, X.2    He, K.3
  • 7
    • 0242574985 scopus 로고    scopus 로고
    • Reconciling gene expression data with known genome-scale regulatory network structures?
    • Herrgard, M.J., Covert, M.W., Palsson, B.O.: 'Reconciling gene expression data with known genome-scale regulatory network structures', Genome Res., 2003, 13, pp. 2423-2434
    • (2003) Genome Res. , vol.13 , pp. 2423-2434
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.O.3
  • 8
    • 38549126643 scopus 로고    scopus 로고
    • KEGG for linking genomes to life and the environment
    • Kanehisa, M., Araki, M., Goto, S., et al.: 'KEGG for linking genomes to life and the environment', Nucleic Acids Res., 2008, 36, pp. D480-D484
    • (2008) Nucleic Acids Res. , vol.36
    • Kanehisa, M.1    Araki, M.2    Goto, S.3
  • 9
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response.
    • Tusher, V.G., Tibshirani, R., Chu, G.: 'Significance analysis of microarrays applied to the ionizing radiation response'. Proc. Natl. Acad. Sci., 2001, vol. 98, pp. 5116-5621
    • (2001) Proc. Natl. Acad. Sci , vol.98 , pp. 5116-5621
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 10
    • 14644430468 scopus 로고    scopus 로고
    • Calculating the statistical significance of changes in pathway activity from gene expression data
    • Rahnenfuhrer, J., Domingues, F.S., Maydt, J., Lengauer, T.: 'Calculating the statistical significance of changes in pathway activity from gene expression data', Stat. Appl. Genet. Mol. Biol., 2004, 3, p. 16
    • (2004) Stat. Appl. Genet. Mol. Biol , vol.3 , pp. 16
    • Rahnenfuhrer, J.1    Domingues, F.S.2    Maydt, J.3    Lengauer, T.4
  • 11
    • 14844332708 scopus 로고    scopus 로고
    • Pathway information for systems biology
    • Cary, M.P., Bader, G.D., Sander, C.: 'Pathway information for systems biology', FEBS Lett., 2005, 579, pp. 1815-1820
    • (2005) FEBS Lett. , vol.579 , pp. 1815-1820
    • Cary, M.P.1    Bader, G.D.2    Sander, C.3
  • 12
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • 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., 2005, vol. 102, pp. 15545-15550
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3
  • 13
    • 35348890683 scopus 로고    scopus 로고
    • On testing the significance of sets of genes
    • Efron, B., Tibshirani, R.: 'On testing the significance of sets of genes', Ann. Appl. Stat., 2007, 1, pp. 107-129
    • (2007) Ann. Appl. Stat. , vol.1 , pp. 107-129
    • Efron, B.1    Tibshirani, R.2
  • 15
    • 58049215467 scopus 로고    scopus 로고
    • A novel signaling pathway impact analysis
    • Tarca, A.L., Draghici, S., Khatri, P., et al.: 'A novel signaling pathway impact analysis', Bioinformatics, 2009, 25, pp. 75-82
    • (2009) Bioinformatics , vol.25 , pp. 75-82
    • Tarca, A.L.1    Draghici, S.2    Khatri, P.3
  • 16
    • 34548400259 scopus 로고    scopus 로고
    • A systems biology approach for pathway level analysis
    • Draghici, S., Khatri, P., Tarca, A.L., et al.: 'A systems biology approach for pathway level analysis', Genome Res., 2007, 17, pp. 1537-1545
    • (2007) Genome Res. , vol.17 , pp. 1537-1545
    • Draghici, S.1    Khatri, P.2    Tarca, A.L.3
  • 17
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman, N., Linial, M., Nachman, I., Péer, D.: 'Using Bayesian networks to analyze expression data', J. Comput. Biol., 2000, 7, pp. 601-620
    • (2000) J. Comput. Biol. , vol.7 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Péer, D.4
  • 18
    • 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, p. e48
    • (2008) Nucleic Acids Res. , vol.36
    • Zhao, X.M.1    Wang, R.S.2    Chen, L.3    Aihara, K.4
  • 19
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A., Gerstein, M.: 'Genomic analysis of regulatory network dynamics reveals large topological changes', Nature, 2004, 431, pp. 308-312
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 20
    • 79959265839 scopus 로고    scopus 로고
    • Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression
    • Zhou, H., Saito, S., Piao, G., et al.: 'Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression', BMC Syst. Biol., 2011, 5, (Suppl 1), pp. S16
    • (2011) BMC Syst. Biol. , vol.5 , Issue.SUPPL. 1
    • Zhou, H.1    Saito, S.2    Piao, G.3
  • 21
    • 36249019789 scopus 로고    scopus 로고
    • Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference
    • Stolovitzky, G., Monroe, D., Califano, A.: 'Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference', Ann. N. Y. Acad. Sci., 2007, 1115, pp. 11-22
    • (2007) Ann. N. Y. Acad. Sci. , vol.1115 , pp. 11-22
    • Stolovitzky, G.1    Monroe, D.2    Califano, A.3
  • 22
    • 33846064113 scopus 로고    scopus 로고
    • NCBI GEO: mining tens of millions of expression profiles-database and tools update
    • Barrett, T., Troup, D.B., Wilhite, S.E., et al.: 'NCBI GEO: mining tens of millions of expression profiles-database and tools update', Nucleic Acids Res., 2007, 35, pp. D760-D765
    • (2007) Nucleic Acids Res. , vol.35
    • Barrett, T.1    Troup, D.B.2    Wilhite, S.E.3
  • 23
    • 79959351684 scopus 로고    scopus 로고
    • Light-dark oscillations in the lung transcriptome: implications for lung homeostasis, repair, metabolism, disease, and drug action
    • Sukumaran, S., Jusko, W.J., Dubois, D.C., Almon, R.R.: 'Light-dark oscillations in the lung transcriptome: implications for lung homeostasis, repair, metabolism, disease, and drug action', J. Appl. Physiol., 2011, 110, pp. 1732-1747
    • (2011) J. Appl. Physiol. , vol.110 , pp. 1732-1747
    • Sukumaran, S.1    Jusko, W.J.2    Dubois, D.C.3    Almon, R.R.4
  • 24
    • 77958067872 scopus 로고    scopus 로고
    • Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology
    • Sukumaran, S., Xue, B., Jusko, W.J., DuBois, D.C., Almon, R.R.: 'Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology', Physiol. Genomics, 2010, 42A, pp. 141-152
    • (2010) Physiol. Genomics , vol.42 A , pp. 141-152
    • Sukumaran, S.1    Xue, B.2    Jusko, W.J.3    DuBois, D.C.4    Almon, R.R.5
  • 25
    • 0036191190 scopus 로고    scopus 로고
    • Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
    • Toh, H., Horimoto, K.: 'Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling', Bioinformatics, 2002, 18, pp. 287-297
    • (2002) Bioinformatics , vol.18 , pp. 287-297
    • Toh, H.1    Horimoto, K.2
  • 26
    • 13844253637 scopus 로고    scopus 로고
    • A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
    • Beal, M.J., Falciani, F., Ghahramani, Z., Rangel, C., Wild, D.L.: 'A Bayesian approach to reconstructing genetic regulatory networks with hidden factors', Bioinformatics, 2005, 21, pp. 349-356
    • (2005) Bioinformatics , vol.21 , pp. 349-356
    • Beal, M.J.1    Falciani, F.2    Ghahramani, Z.3    Rangel, C.4    Wild, D.L.5
  • 27
    • 12744261506 scopus 로고    scopus 로고
    • A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
    • Zou, M., Conzen, S.D.: 'A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data', Bioinformatics, 2005, 21, pp. 71-79
    • (2005) Bioinformatics , vol.21 , pp. 71-79
    • Zou, M.1    Conzen, S.D.2
  • 28
    • 69249154268 scopus 로고    scopus 로고
    • A network biology study on circadian rhythm by integrating various Omics data
    • Wang, Y., Zhang, X.S., Chen, L.: 'A network biology study on circadian rhythm by integrating various Omics data', OMICS, 2009, 13, pp. 313-324
    • (2009) OMICS , vol.13 , pp. 313-324
    • Wang, Y.1    Zhang, X.S.2    Chen, L.3
  • 29
    • 77956850355 scopus 로고    scopus 로고
    • Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains
    • Liu, Z.P., Wang, Y., Zhang, X.S., Chen, L.: 'Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains', BMC Syst. Biol., 2010, 4, (Suppl 2), p. S11
    • (2010) BMC Syst. Biol. , vol.4 , Issue.SUPPL. 2
    • Liu, Z.P.1    Wang, Y.2    Zhang, X.S.3    Chen, L.4
  • 30
    • 84863128658 scopus 로고    scopus 로고
    • Identifying disease genes and module biomarkers with differential interactions
    • Liu, X., Liu, Z.P., Zhao, X., Chen, L.: 'Identifying disease genes and module biomarkers with differential interactions', J. Am. Med. Inform. Assoc., 2012, 19, pp. 241-248
    • (2012) J. Am. Med. Inform. Assoc. , vol.19 , pp. 241-248
    • Liu, X.1    Liu, Z.P.2    Zhao, X.3    Chen, L.4
  • 31
    • 84859741480 scopus 로고    scopus 로고
    • Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers
    • Chen, L., Liu, R., Liu, Z.P., Li, M., Aihara, K.: 'Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers', Sci. Rep., 2012, 2, p. 342
    • (2012) Sci. Rep. , vol.2 , pp. 342
    • Chen, L.1    Liu, R.2    Liu, Z.P.3    Li, M.4    Aihara, K.5
  • 32
    • 84861893428 scopus 로고    scopus 로고
    • Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma
    • He, D., Liu, Z.P., Honda, M., Kaneko, S., Chen, L.: 'Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma', J. Mol. Cell. Biol., 2012, 4, pp. 140-152
    • (2012) J. Mol. Cell. Biol. , vol.4 , pp. 140-152
    • He, D.1    Liu, Z.P.2    Honda, M.3    Kaneko, S.4    Chen, L.5


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