Using biologically interrelated experiments to identify pathway genes in arabidopsis

Bioinformatics

Volumn 28, Issue 6, 2012, Pages 815-822

  Kim, Kyungpil ^a   Jiang, Keni ^b   Teng, Siew Leng ^c   Feldman, Lewis J ^b   Huang, Haiyan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS;

ALGORITHM; ARABIDOPSIS; ARTICLE; GENETICS; METABOLISM; PLANT GENE; REGRESSION ANALYSIS;

ALGORITHMS; ARABIDOPSIS; GENES, PLANT; METABOLIC NETWORKS AND PATHWAYS; REGRESSION ANALYSIS;

EID: 84859073880     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts038     Document Type: Article

References (27)

1. Bolouri, H. and Davidson, E. H. (2002) Modeling transcriptional regulatory networks. BioEssays, 24, 1118-1129.
2. Butte, A. J. and Kohane, I. S. (2000) Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements. Pac. Sympos. Biocomput., 24, 418-429.
3. De la Fuente, A. et al. (2004) Discovery of meaningful relationships in genomic data using partial correlation coefficients. Bioinformatics, 20, 3565-3574.
4. Dobra, A. et al. (2004) Sparse graphical models for exploring gene expression data. J. Multivar. Anal., 90, 196-212.
5. Edwards, D. (1995) Introduction to Graphical Modeling. Springer-Verlag New York, Inc.
6. Eisen, M. B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
7. Friedman, F. et al. (2000) Using Bayesian networks to analyze expression data. J. Comput. Biol., 7, 601-620.
8. Gachon, C. M. M. et al. (2005) Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. PlantMol. Biol., 58, 229-245.
9. Gigolashvili, T. et al. (2009) The plastidic bile acid transporter 5 is required for the biosynthesis of methionine-derived glucosinolates in arabidopsis thaliana. Plant Cell, 21, 1813-1829.
10. Hammond-Kosack, K. and Jones, J. D. G. (2001) Responses to plant pathogens. In Buchanan, B. B. et al. (eds) Biochemistry and Molecular Biology of Plants. American Society of Plant Physiologists, Rockville, pp. 1114-1115.
11. Hirai, M. Y. et al. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl Acad. Sci. USA, 104, 6478-6483.
12. Lauritzen, S. (1996) Graphical models. Clarendon Press, Oxford.
13. Magwene, P. M. and Kim, J. (2004) Estimating genomic coexpression networks using first-order conditional independence. Genome Biol., 5, R100.
14. Matsuno, T. et al. (2006) Graphical gaussian modeling for gene association structures based on expression deviation patterns induced by various chemical stimuli. IEICE Trans. Inf. Syst., E89D, 1563-1573.
15. Naoumkina, M. A. et al. (2010) Genome-wide analysis of phenylpropanoid defence pathways. Mol. Plant Pathol., 11, 829-846.
16. Opgen-Rhein, R. and Strimmer, K. (2007) From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst. Biol., 1, 37.
17. Schäfer, J. and Strimmer, K. (2005a)An empirical bayes approach to inferring large-scale gene association networks. Bioinformatics, 21, 754-764.
18. Schäfer, J. and Strimmer, K. (2005b) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat. Appl. Genet. Mol. Biol., 3, 32.
19. Sønderby, I. E. et al. (2010) Biosynthesis of glucosinolates - gene discovery and beyond. Trends Plant Sci., 15, 283-290.
20. Taylor, L. P. and Grotewold, E. (2005) Flavonoids as developmental regulators. Curr. Opin. Plant Biol., 8, 317-323.
21. Teng, S. L. and Huang, H. (2009) A statistical framework to infer functional gene relationships from biologically interrelated microarray experiments. J. Am. Stat. Assoc., 104, 465-473.
22. Verkerk, R. et al. (2009) Glucosinolates in Brassica vegetables: the influence of the food supply chain on intake, bioavailability and human health. Mol. Nutr. Food. Res., 53 (Suppl. 2), S219.
23. Wille, A. et al. (2004) Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis Thaliana. Genome Biol., 5, R92.
24. Wille, A. and Bühlmann, P. (2006) Low-order conditional independence graphs for inferring genetic networks. Stat. Appl. Genet. Mol. Biol., 5, 1.
25. Woo, H. et al. (2005) Flavonoids: from cell cycle regulation to biotechnology. Biotechnol. Lett., 27, 365-374.
26. Yan, X. and Chen, S. (2007) Regulation of plant glucosinolate metabolism. Planta, 226, 1343-1352.
27. Yonekura-Sakakibara, K. et al. (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding genemetabolite correlations in arabidopsis. Plant Cell, 20, 2160-2176.