References

  1. Nelson D: Plant cytochrome P450s from moss to poplar.

    Phytochem Rev 2006, 5:193-204. Publisher Full Text OpenURL

  2. Schuler M, Duan H, Bilgin M, Ali S: Arabidopsis cytochrome P450s through the looking glass: a window on plant biochemistry.

    Phytochem Rev 2006, 5:205-237. Publisher Full Text OpenURL

  3. Werck-Reichhart D: Cytochromes P450. [http:/ / www.bioone.org/ perlserv/ ?request=get-document&issn=1543-812 0&volume=2&issue=1&page=1]

    In The Arabidopsis book Edited by: Somerville C and Meyerowitz E. Rockville MD, American Society of Plant Biologists, Rockville, MD; 2002. OpenURL

  4. Schuler MA, Werck-Reichhart D: Functional genomics of P450s.

    Annu Rev Plant Biol 2003, 54:629-667. PubMed Abstract | Publisher Full Text OpenURL

  5. Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S: Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot.

    Plant Physiol 2004, 135:756-772. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  6. Aoki K, Ogata Y, Shibata D: Approaches for extracting practical information from gene co-expression networks in plant biology.

    Plant Cell Physiol 2007, 48:381-390. PubMed Abstract | Publisher Full Text OpenURL

  7. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles--database and tools update.

    Nucleic Acids Res 2007, 35:D760-D765. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  8. Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A: ArrayExpress--a public database of microarray experiments and gene expression profiles.

    Nucleic Acids Res 2007, 35:D747-D750. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  9. Toufighi K, Brady SM, Austin R, Ly E, Provart NJ: The Botany Array Resource: e-northerns, expression angling, and promoter analyses.

    Plant J 2005, 43:153-163. PubMed Abstract | Publisher Full Text OpenURL

  10. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W: GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.

    Plant Physiol 2004, 136:2621-2632. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  11. Paquette SM, Bak S, Feyereisen R: Intron-exon organization and phylogeny in a large superfamily, the paralogous cytochrome P450 genes of Arabidopsis thaliana.

    DNA Cell Biol 2000, 19:307-317. PubMed Abstract | Publisher Full Text OpenURL

  12. Katagiri F: A global view of defense gene expression regulation--a highly interconnected signaling network.

    Curr Opin Plant Biol 2004, 7:506-511. PubMed Abstract | Publisher Full Text OpenURL

  13. Tao Y, Xie Z, Chen W, Glazebrook J, Chang HS, Han B, Zhu T, Zou G, Katagiri F: Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae.

    Plant Cell 2003, 15:317-330. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  14. Schuhegger R, Nafisi M, Mansourova M, Petersen BL, Olsen CE, Svatos A, Halkier BA, Glawischnig E: CYP71B15 (PAD3) catalyzes the final step in camalexin biosynthesis.

    Plant Physiol 2006, 141:1248-1254. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  15. Zhou N, Tootle TL, Glazebrook J: Arabidopsis PAD3, a gene required for camalexin biosynthesis, encodes a putative cytochrome P450 monooxygenase.

    Plant Cell 1999, 11:2419-2428. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  16. Nafisi M, Goregaoker S, Botanga CJ, Glawischnig E, Olsen CE, Halkier BA, Glazebrook J: Arabidopsis cytochrome P450 monooxygenase 71A13 catalyzes the conversion of indole-3-acetaldoxime in camalexin synthesis.

    Plant Cell 2007, 19:2039-2052. PubMed Abstract | Publisher Full Text OpenURL

  17. Godiard L, Sauviac L, Dalbin N, Liaubet L, Callard D, Czernic P, Marco Y: CYP76C2, an Arabidopsis thaliana cytochrome P450 gene expressed during hypersensitive and developmental cell death.

    FEBS Lett 1998, 438:245-249. PubMed Abstract | Publisher Full Text OpenURL

  18. Morikawa T, Mizutani M, Aoki N, Watanabe B, Saga H, Saito S, Oikawa A, Suzuki H, Sakurai N, Shibata D, Wadano A, Sakata K, Ohta D: Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato.

    Plant Cell 2006, 18:1008-1022. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  19. Chehab EW, Perea JV, Gopalan B, Theg S, Dehesh K: Oxylipin pathway in Rice and Arabidopsis.

    J Integr Plant Biol 2007, 49:43-51. Publisher Full Text OpenURL

  20. Duan H, Schuler MA: Differential expression and evolution of the Arabidopsis CYP86A subfamily.

    Plant Physiol 2005, 137:1067-1081. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  21. Xiao F, Goodwin SM, Xiao Y, Sun Z, Baker D, Tang X, Jenks MA, Zhou JM: Arabidopsis CYP86A2 represses Pseudomonas syringae type III genes and is required for cuticle development.

    EMBO J 2004, 23:2903-2913. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  22. Glawischnig E: The role of cytochrome P450 enzymes in the biosynthesis of camalexin.

    Biochem Soc Trans 2006, 34:1206-1208. PubMed Abstract | Publisher Full Text OpenURL

  23. Mikkelsen MD, Petersen BL, Glawischnig E, Jensen AB, Andreasson E, Halkier BA: Modulation of CYP79 genes and glucosinolate profiles in Arabidopsis by defense signaling pathways.

    Plant Physiol 2003, 131:298-308. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  24. Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL: Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3.

    Genes Dev 2002, 16:3100-3112. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  25. Turk EM, Fujioka S, Seto H, Shimada Y, Takatsuto S, Yoshida S, Denzel MA, Torres QI, Neff MM: CYP72B1 inactivates brassinosteroid hormones: an intersection between photomorphogenesis and plant steroid signal transduction.

    Plant Physiol 2003, 133:1643-1653. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  26. Turk EM, Fujioka S, Seto H, Shimada Y, Takatsuto S, Yoshida S, Wang H, Torres QI, Ward JM, Murthy G, Zhang J, Walker JC, Neff MM: BAS1 and SOB7 act redundantly to modulate Arabidopsis photomorphogenesis via unique brassinosteroid inactivation mechanisms.

    Plant J 2005, 42:23-34. PubMed Abstract | Publisher Full Text OpenURL

  27. Takei K, Yamaya T, Sakakibara H: Arabidopsis CYP735A1 and CYP735A2 encode cytokinin hydroxylases that catalyze the biosynthesis of trans-zeatin.

    J Biol Chem 2004, 279:41866-41872. PubMed Abstract | Publisher Full Text OpenURL

  28. Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA: Cytochrome P450 CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime, a precursor of indole glucosinolates and indole-3-acetic acid.

    J Biol Chem 2000, 275:33712-33717. PubMed Abstract | Publisher Full Text OpenURL

  29. William DA, Su Y, Smith MR, Lu M, Baldwin DA, Wagner D: Genomic identification of direct target genes of LEAFY.

    Proc Natl Acad Sci U S A 2004, 101:1775-1780. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  30. Ehlting J, Mattheus N, Aeschliman DS, Li E, Hamberger B, Cullis IF, Zhuang J, Kaneda M, Mansfield SD, Samuels L, Ritland K, Ellis BE, Bohlmann J, Douglas CJ: Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation.

    Plant J 2005, 42:618-640. PubMed Abstract | Publisher Full Text OpenURL

  31. Aubourg S, Lecharny A, Bohlmann J: Genomic analysis of the terpenoid synthase ( AtTPS) gene family of Arabidopsis thaliana.

    Mol Genet Genomics 2002, 267:730-745. PubMed Abstract | Publisher Full Text OpenURL

  32. Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG: An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.

    Phytochemistry 2003, 64:1097-1112. PubMed Abstract | Publisher Full Text OpenURL

  33. Kliebenstein DJ, Kroymann J, Mitchell-Olds T: The glucosinolate-myrosinase system in an ecological and evolutionary context.

    Curr Opin Plant Biol 2005, 8:264-271. PubMed Abstract | Publisher Full Text OpenURL

  34. Lange BM, Ghassemian M: Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps. [http:/ / www.sciencedirect.com/ science?_ob=ArticleURL&_udi=B6TH7-4 FC8V01-2&_user=113008&_coverDate=02 %2F01%2F2005&_rdoc=3&_fmt=summary&_ orig=browse&_srch=doc-info(%23toc%2 35275%232005%23999339995%23565818%2 3FLA%23display%23Volume)&_cdi=5275& _sort=d&_docanchor=&view=c&_ct=11&_ acct=C000008898&_version=1&_urlVers ion=0&_userid=113008&md5=0575077fc8 e852b4d3210b60d0aadf9b]

    Phytochemistry 2005, 66:413-451. PubMed Abstract | Publisher Full Text OpenURL

  35. Raes J, Rohde A, Christensen JH, Van de PY, Boerjan W: Genome-wide characterization of the lignification toolbox in Arabidopsis.

    Plant Physiol 2003, 133:1051-1071. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  36. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes HW: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.

    Nucleic Acids Res 2004, 32:5539-5545. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  37. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY: Functional annotation of the Arabidopsis genome using controlled vocabularies.

    Plant Physiol 2004, 135:745-755. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  38. Ehlting J, Hamberger B, Million-Rousseau R, Werck-Reichhart D: Cytochrome P450 in phenolic metabolism.

    Phytochem Rev 2006, 5:239-270. Publisher Full Text OpenURL

  39. Urban P, Mignotte C, Kazmaier M, Delorme F, Pompon D: Cloning, yeast expression, and characterization of the coupling of two distantly related Arabidopsis thaliana NADPH-cytochrome P450 reductases with P450 CYP73A5.

    J Biol Chem 1997, 272:19176-19186. PubMed Abstract | Publisher Full Text OpenURL

  40. Franke R, Humphreys JM, Hemm MR, Denault JW, Ruegger MO, Cusumano JC, Chapple C: The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism.

    Plant J 2002, 30:33-45. PubMed Abstract | Publisher Full Text OpenURL

  41. Schoch G, Goepfert S, Morant M, Hehn A, Meyer D, Ullmann P, Werck-Reichhart D: CYP98A3 from Arabidopsis thaliana is a 3'-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway.

    J Biol Chem 2001, 276:36566-36574. PubMed Abstract | Publisher Full Text OpenURL

  42. Kim J, DellaPenna D: Defining the primary route for lutein synthesis in plants: The role of Arabidopsis carotenoid b-ring hydroxylase CYP97A3.

    Proc Natl Acad Sci USA 2006, 103:3474-3479. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  43. Tian L, Musetti V, Kim J, Magallanes-Lundback M, DellaPenna D: The Arabidopsis LUT1 locus encodes a member of the cytochrome P450 family that is required for carotenoid e-ring hydroxylation activity.

    Proc Natl Acad Sci USA 2004, 101:402-407. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  44. Szekeres M, Nemeth K, Koncz-Kalman Z, Mathur J, Kauschmann A, Altmann T, Redei GP, Nagy F, Schell J, Koncz C: Brassinosteroids rescue the deficiency of CYP90, a cytochrome P450, controlling cell elongation and de-etiolation in Arabidopsis.

    Cell 1996, 85:171-182. PubMed Abstract | Publisher Full Text OpenURL

  45. Bancos S, Szatmari AM, Castle J, Kozma-Bognar L, Shibata K, Yokota T, Bishop GJ, Nagy F, Szekeres M: Diurnal regulation of the brassinosteroid-biosynthetic CPD gene in Arabidopsis.

    Plant Physiol 2006, 141:299-309. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  46. Gershenzon J, Dudareva N: The function of terpene natural products in the natural world.

    Nat Chem Biol 2007, 3:408-414. PubMed Abstract | Publisher Full Text OpenURL

  47. Lodeiro S, Xiong Q, Wilson WK, Kolesnikova MD, Onak CS, Matsuda SPT: An oxidosqualene cyclase makes numerous products by diverse mechanisms: A challenge to prevailing concepts of triterpene biosynthesis.

    J Am Chem Soc 2007, 129:11213-11222. PubMed Abstract | Publisher Full Text OpenURL

  48. Shibuya M, Hoshino M, Katsube Y, Hayashi H, Kushiro T, Ebizuka Y: Identification of beta-amyrin and sophoradiol 24-hydroxylase by expressed sequence tag mining and functional expression assay.

    FEBS J 2006, 273:948-959. PubMed Abstract | Publisher Full Text OpenURL

  49. Fazio GC, Xu R, Matsuda SP: Genome mining to identify new plant triterpenoids.

    J Am Chem Soc 2004, 126:5678-5679. PubMed Abstract | Publisher Full Text OpenURL

  50. Xiong Q, Wilson WK, Matsuda SP: An Arabidopsis oxidosqualene cyclase catalyzes iridal skeleton formation by Grob fragmentation.

    Angew Chem Int Ed Engl 2006, 45:1285-1288. PubMed Abstract | Publisher Full Text OpenURL

  51. Fujioka S, Li J, Choi YH, Seto H, Takatsuto S, Noguchi T, Watanabe T, Kuriyama H, Yokota T, Chory J, Sakurai A: The Arabidopsis deetiolated2 mutant is blocked early in brassinosteroid biosynthesis.

    Plant Cell 1997, 9:1951-1962. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  52. Sun TP, Kamiya Y: The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis.

    Plant Cell 1994, 6:1509-1518. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  53. Field B, Osbourn AE: Metabolic diversification - Independent assembly of operon-like gene clusters in plants.

    Science 2008, 320:543-7. PubMed Abstract | Publisher Full Text OpenURL

  54. Fang R, Houghton PJ, Luo C, Hylands PJ: Isolation and structure determination of triterpenes from Iris tectorum.

    Phytochemistry 2007, 68:1242-1247. PubMed Abstract | Publisher Full Text OpenURL

  55. Wasternack C: Jasmonates: An Update on Biosynthesis, Signal Transduction and Action in Plant Stress Response, Growth and Development.

    Ann Bot (Lond) 2007.PubMed Abstract | Publisher Full Text OpenURL

  56. Benveniste I, Saito T, Wang Y, Kandel S, Huang HW, Pinot F, Kahn RA, Salaun JP, Shimoji M: Evolutionary relationship and substrate specificity of Arabidopsis thaliana fatty acid omega-hydroxylase.

    Plant Sci 2006, 170:326-338. Publisher Full Text OpenURL

  57. Naur P, Petersen BL, Mikkelsen MD, Bak S, Rasmussen H, Olsen CE, Halkier BA: CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis.

    Plant Physiol 2003, 133:63-72. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  58. Olry A, Schneider-Belhaddad F, Heintz D, Werck-Reichhart D: A medium-throughput screening assay to determine catalytic activities of oxygen-consuming enzymes: a new tool for functional characterization of cytochrome P450 and other oxygenases.

    Plant J 2007, 51:331-340. PubMed Abstract | Publisher Full Text OpenURL

  59. Mao X, Cai T, Olyarchuk JG, Wei L: Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary.

    Bioinformatics 2005, 21:3787-3793. PubMed Abstract | Publisher Full Text OpenURL

  60. Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY: MetaCyc and AraCyc. Metabolic pathway databases for plant research.

    Plant Physiol 2005, 138:27-37. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  61. Beisson F, Koo AJ, Ruuska S, Schwender J, Pollard M, Thelen JJ, Paddock T, Salas JJ, Savage L, Milcamps A, Mhaske VB, Cho Y, Ohlrogge JB: Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database.

    Plant Physiol 2003, 132:681-697. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  62. Lange BM, Ghassemian M: Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism.

    Plant Mol Biol 2003, 51:925-948. PubMed Abstract | Publisher Full Text OpenURL

  63. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P: The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

    Nucl Acids Res 2003, 31:224-228. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  64. Team RDC: [http://www.R-project.org]

    R: A language and environment for statistical computing. Vienna, Austria, R Foundation for Statistical Computing; 2006. OpenURL