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Volumn 15, Issue 8, 2010, Pages 5354-5368

Effects of time point measurement on the reconstruction of gene regulatory networks

Author keywords

Dynamic Bayesian networks; Gene regulatory network; Network reconstruction; Network statistics; Time points

Indexed keywords

ARABIDOPSIS; ARTICLE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; PLANT GENE; TIME;

EID: 77956115125     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules15085354     Document Type: Article
Times cited : (10)

References (42)
  • 1
    • 0034571146 scopus 로고    scopus 로고
    • Inferring genetic networks from DNA microarray data by multiple regression analysis
    • Kato, M.; Tsunoda, T.; Takagi, T. Inferring genetic networks from DNA microarray data by multiple regression analysis. Genome Inform. Ser. Workshop Genome Inform. 2000, 11, 118-128.
    • (2000) Genome Inform. Ser. Workshop Genome Inform. , vol.11 , pp. 118-128
    • Kato, M.1    Tsunoda, T.2    Takagi, T.3
  • 2
    • 0032611513 scopus 로고    scopus 로고
    • Modeling gene expression with differential equations
    • Chen, T.; He, H.L.; Church, G.M. Modeling gene expression with differential equations. Pac. Symp. Biocomput. 1999, 29-40.
    • (1999) Pac. Symp. Biocomput. , pp. 29-40
    • Chen, T.1    He, H.L.2    Church, G.M.3
  • 3
    • 0043130707 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations
    • de Hoon, M.J.; Imoto, S.; Kobayashi, K.; Ogasawara, N.; Miyano, S. Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac. Symp. Biocomput. 2003, 17-28.
    • (2003) Pac. Symp. Biocomput. , pp. 17-28
    • De Hoon, M.J.1    Imoto, S.2    Kobayashi, K.3    Ogasawara, N.4    Miyano, S.5
  • 5
    • 0031616241 scopus 로고    scopus 로고
    • A general reverse engineering algorithm for inference of genetic network architectures
    • Liang, S.; Fuhrman, S.; 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    Reveal, S.R.3
  • 7
    • 0344844807 scopus 로고    scopus 로고
    • Modelling regulatory pathways in E. coli from time series expression profiles
    • Ong, I.M.; Glasner, J.D.; Page, D. Modelling regulatory pathways in E. coli from time series expression profiles. Bioinformatics 2002, 18 (Suppl. 1), S241-S248.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ong, I.M.1    Glasner, J.D.2    Page, D.3
  • 8
    • 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, 71-79.
    • (2005) Bioinformatics , vol.21 , pp. 71-79
    • Zou, M.1    Conzen, S.D.2
  • 9
    • 34249862287 scopus 로고    scopus 로고
    • Learning causal networks from systems biology time course data: An effective model selection procedure for the vector autoregressive process
    • Opgen-Rhein, R.; Strimmer, K. Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process. BMC Bioinformatics 2007, 8 Suppl 2, S3.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL 2
    • Opgen-Rhein, R.1    Strimmer, K.2
  • 10
    • 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, 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
  • 13
    • 2442691914 scopus 로고    scopus 로고
    • Modeling gene expression from microarray expression data with state-space equations
    • Wu, F.X.; Zhang, W.J.; Kusalik, A.J. Modeling gene expression from microarray expression data with state-space equations. Pac. Symp. Biocomput. 2004, 581-592.
    • (2004) Pac. Symp. Biocomput. , pp. 581-592
    • Wu, F.X.1    Zhang, W.J.2    Kusalik, A.J.3
  • 14
    • 14744275289 scopus 로고    scopus 로고
    • Diurnal changes in the transcriptome encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves
    • Smith, S.M.; Fulton, D.C.; Chia, T.; Thorneycroft, D.; Chapple, A.; Dunstan, H.; Hylton, C.; Zeeman, S.C.; Smith, A.M. Diurnal changes in the transcriptome encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves. Plant Physiol. 2004, 136, 2687-2699.
    • (2004) Plant Physiol. , vol.136 , pp. 2687-2699
    • Smith, S.M.1    Fulton, D.C.2    Chia, T.3    Thorneycroft, D.4    Chapple, A.5    Dunstan, H.6    Hylton, C.7    Zeeman, S.C.8    Smith, A.M.9
  • 15
    • 0034928217 scopus 로고    scopus 로고
    • Growth stage-based phenotypic analysis of Arabidopsis: A model for high throughput functional genomics in plants
    • Boyes, D.C.; Zayed, A.M.; Ascenzi, R.; McCaskill, A.J.; Hoffman, N.E.; Davis, K.R.; Gorlach, J. Growth stage-based phenotypic analysis of Arabidopsis: A model for high throughput functional genomics in plants. Plant Cell 2001, 13, 1499-1510.
    • (2001) Plant Cell , vol.13 , pp. 1499-1510
    • Boyes, D.C.1    Zayed, A.M.2    Ascenzi, R.3    McCaskill, A.J.4    Hoffman, N.E.5    Davis, K.R.6    Gorlach, J.7
  • 18
    • 84866934189 scopus 로고    scopus 로고
    • Inferring dynamic genetic networks with low order independencies
    • LÃb̈re, S. Inferring Dynamic Genetic Networks with Low Order Independencies. Stat. Appl. Genet. Mol. Biol. 2009, 8, 9.
    • (2009) Stat. Appl. Genet. Mol. Biol. , vol.8 , pp. 9
    • Lãb̈re, S.1
  • 20
    • 33745320292 scopus 로고    scopus 로고
    • Bounded search for de novo identification of degenerate cis-regulatory elements
    • Carlson, J.M.; Chakravarty, A.; Khetani, R.S.; Gross, R.H. Bounded search for de novo identification of degenerate cis-regulatory elements. BMC Bioinformatics 2006, 7, 254.
    • (2006) BMC Bioinformatics , vol.7 , pp. 254
    • Carlson, J.M.1    Chakravarty, A.2    Khetani, R.S.3    Gross, R.H.4
  • 25
    • 77953311470 scopus 로고    scopus 로고
    • Mathematical methods to analysis of topology, functional variability and evolution of metabolic systems based on different decomposition concepts
    • Mrabet, Y.; Semmar, N. Mathematical methods to analysis of topology, functional variability and evolution of metabolic systems based on different decomposition concepts. Curr. Drug Metab. 2010 11, 315-341.
    • (2010) Curr. Drug Metab. , vol.11 , pp. 315-341
    • Mrabet, Y.1    Semmar, N.2
  • 26
    • 77952868004 scopus 로고    scopus 로고
    • Graphic rule for drug metabolism systems
    • Chou, K.C. Graphic rule for drug metabolism systems. Curr. Drug Metab. 2010, 11, 369-378.
    • (2010) Curr. Drug Metab. , vol.11 , pp. 369-378
    • Chou, K.C.1
  • 27
    • 77953304189 scopus 로고    scopus 로고
    • Network topological indices, drug metabolism, and distribution
    • Gonzalez-Diaz, H. Network topological indices, drug metabolism, and distribution. Curr. Drug Metab. 2010, 11, 283-284.
    • (2010) Curr. Drug Metab. , vol.11 , pp. 283-284
    • Gonzalez-Diaz, H.1
  • 28
    • 77953301845 scopus 로고    scopus 로고
    • Review of MARCH-INSIDE & complex networks prediction of drugs: ADMET, anti-parasite activity, metabolizing enzymes and cardiotoxicity proteome biomarkers
    • Gonzalez-Diaz, H.; Duardo-Sanchez, A.; Ubeira, F.M.; Prado-Prado, F.; Perez-Montoto, L.G.; Concu, R.; Podda, G.; Shen, B. Review of MARCH-INSIDE & complex networks prediction of drugs: ADMET, anti-parasite activity, metabolizing enzymes and cardiotoxicity proteome biomarkers. Curr. Drug Metab. 2010, 11, 379-406.
    • (2010) Curr. Drug Metab. , vol.11 , pp. 379-406
    • Gonzalez-Diaz, H.1    Duardo-Sanchez, A.2    Ubeira, F.M.3    Prado-Prado, F.4    Perez-Montoto, L.G.5    Concu, R.6    Podda, G.7    Shen, B.8
  • 30
    • 0003736078 scopus 로고    scopus 로고
    • 2nd ed.; Prentice Hall: Englewood Cliffs, NJ
    • West, D. Introduction to Graph Theory, 2nd ed.; Prentice Hall: Englewood Cliffs, NJ, 1996.
    • (1996) Introduction to Graph Theory
    • West, D.1
  • 31
    • 1642416044 scopus 로고    scopus 로고
    • A cytosolic glucosyltransferase is required for conversion of starch to sucrose in Arabidopsis leaves at night
    • Chia, T.; Thorneycroft, D.; Chapple, A.; Messerli, G.; Chen, J.; Zeeman, S.C.; Smith, S.M.; Smith, A.M. A cytosolic glucosyltransferase is required for conversion of starch to sucrose in Arabidopsis leaves at night. Plant J. 2004, 37, 853-863.
    • (2004) Plant J. , vol.37 , pp. 853-863
    • Chia, T.1    Thorneycroft, D.2    Chapple, A.3    Messerli, G.4    Chen, J.5    Zeeman, S.C.6    Smith, S.M.7    Smith, A.M.8
  • 32
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • Albert, R.; Barabasi, A.-L. Statistical mechanics of complex networks. Rev. Mod. Phys. 2002, 74, 47-97.
    • (2002) Rev. Mod. Phys. , vol.74 , pp. 47-97
    • Albert, R.1    Barabasi, A.-L.2
  • 33
    • 84865730611 scopus 로고
    • A set of measures of centrality based on betweenness
    • Freeman, L.C. A set of measures of centrality based on betweenness. Sociometry 1977, 40, 35-41.
    • (1977) Sociometry , vol.40 , pp. 35-41
    • Freeman, L.C.1
  • 35
    • 33750177351 scopus 로고
    • Centrality in social networks: Conceptual clarification
    • Freeman, L. Centrality in social networks: Conceptual clarification. Soc. Networks 1979, 1, 215-239.
    • (1979) Soc. Networks , vol.1 , pp. 215-239
    • Freeman, L.1
  • 36
    • 35348957264 scopus 로고    scopus 로고
    • Efficient behavior of small-world networks
    • Latora, V.; Marchiori, M. Efficient behavior of small-world networks. Phys. Rev. Lett. 2001, 87, 198701.
    • (2001) Phys. Rev. Lett. , vol.87 , pp. 198701
    • Latora, V.1    Marchiori, M.2
  • 38
    • 0031845074 scopus 로고    scopus 로고
    • The AP2/EREBP family of plant transcription factors
    • Riechmann, J.L.; Meyerowitz, E.M. The AP2/EREBP family of plant transcription factors. Biol. Chem. 1998, 379, 633-646.
    • (1998) Biol. Chem. , vol.379 , pp. 633-646
    • Riechmann, J.L.1    Meyerowitz, E.M.2
  • 39
  • 40
    • 84970866422 scopus 로고
    • Diagnostic tests. 1: Sensitivity and specificity
    • Altman, D.G.; Bland, J.M. Diagnostic tests. 1: Sensitivity and specificity. BMJ 1994, 308, 1552.
    • (1994) BMJ , vol.308 , pp. 1552
    • Altman, D.G.1    Bland, J.M.2
  • 41
    • 49549123570 scopus 로고    scopus 로고
    • Equation discovery for systems biology: Finding the structure and dynamics of biological networks from time course data
    • Dzeroski, S.; Todorovski, L. Equation discovery for systems biology: finding the structure and dynamics of biological networks from time course data. Curr. Opin. Biotechnol. 2008, 19, 360-368.
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 360-368
    • Dzeroski, S.1    Todorovski, L.2
  • 42
    • 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, 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


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