Transcriptional coordination of the metabolic network in Arabidopsis

Plant Physiology

Volumn 142, Issue 2, 2006, Pages 762-774

  Wei, Hairong ^a   Persson, Staffan ^c   Mehta, Tapan ^a   Srinivasasainagendra, Vinodh ^a   Chen, Lang ^a   Page, Grier P ^a   Somerville, Chris ^c,d   Loraine, Ann ^a,b  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^c GEOPHYSICAL LABORATORY   (United States)

^d STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COORDINATION REACTIONS; GENES; PLANT CELL CULTURE;

ARABIDOPSIS; CROSS PATHWAY TRANSCRIPTIONAL CONTROL; GENE DUPLICATION; METABOLIC PATHWAYS;

METABOLISM;

CELLS; GENES; GENETIC ENGINEERING; METABOLISM; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 33750063171     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.106.080358     Document Type: Article

References (35)

1. Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118:4947-4957
2. Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382
3. Carlson MR, Zhang B, Fang Z, Mischel PS, Horvath S, Nelson SF (2006) Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics 7: 40
4. Cutler S, McCourt P (2005) Dude, where's my phenotype? Dealing with redundancy in signaling networks. Plant Physiol 138: 558-559
5. Daniel WW (2004) Biostatistics: A Foundation for Analysis in the Health Sciences, Ed 8. Wiley, New York
6. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686
7. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
8. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, et al (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285-293
9. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80
10. Glawischnig E, Hansen BG, Olsen CE, Halkier BA (2004) Camalexin is synthesized from indole-3-acetaldoxime, a key branching point between primary and secondary metabolism in Arabidopsis. Proc Natl Acad Sci USA 101: 8245-8250
11. Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43: 205-227
12. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66
13. Gutierrez RA, Shasha DE, Coruzzi GM (2005) Systems biology for the virtual plant. Plant Physiol 138: 550-554
14. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261
15. Ihmels J, Bergmann S, Barkai N (2004a) Defining transcription modules using large-scale gene expression data. Bioinformatics 20: 1993-2003
16. Ihmels J, Levy R, Barkai N (2004b) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22: 86-92
17. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42
18. Larkin RM, Alonso JM, Ecker JR, Chory J (2003) GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 299: 902-906
19. Minorsky PV (2003) Frontiers of plant cell biology: signals and pathways, system-based approaches 22nd Symposium in Plant Biology (University of California-Riverside). Plant Physiol 132: 428-435
20. Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132: 453-460
21. Pavlidis P, Noble WS (2003) Matrix2png: a utility for visualizing matrix data. Bioinformatics 19: 295-296
22. Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102: 8633-8638
23. Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29: 153-159
24. Redman JC, Haas BJ, Tanimoto G, Town CD (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J 38: 545-561
25. Rodgers JL, Nicewander WA (1988) Thirteen ways to look at the correlation coefficient. Am Stat 42: 59-66
26. Schuhegger R, Nafisi M, Mansourova M, Petersen BL, Olsen CE, Svatos A, Halkier BA, Glawischnig E (2006) CYP71B15 (PADS) catalyzes the final step in camalexin biosynthesis. Plant Physiol 141: 1248-1254
27. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
28. Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255
29. Sweetlove LJ, Fernie AR (2005) Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. New Phytol 168: 9-24
30. Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, et al (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J 42: 218-235
31. Trivedi P, Edwards JW, Wang J, Gadbury GL, Srinivasasainagendra V, Zakharkin SO, Kim K, Mehta T, Brand JP, Patki A, et al (2005) HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data. BMC Bioinformatics 6: 86
32. Watts DJ, Strogatz SH (1998) Collective dynamics of "small- world" networks. Nature 393: 440-442
33. Wille A, Zimmermann P, Vranova E, Furholz A, Laule O, Bleuler S, Hennig L, Prelic A, von Rohr P, Thiele L, et al (2004) Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biol 5: R92
34. Winkel-Shirley B (2001) Flavonoid biosynthesis: a colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 126: 485-493
35. Zhou N, Tootle TL, Glazebrook J (1999) Arabidopsis PAD3, a gene required for camalexin biosynthesis, encodes a putative cytochrome P450 monooxygenase. Plant Cell 11: 2419-2428