Display options
Cite
Naithani S, Partipilo CM, Raja R, et al. FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. Front Plant Sci. 2016;7:242doi: 10.3389/fpls.2016.00242.
Naithani, S., Partipilo, C. M., Raja, R., Elser, J. L., & Jaiswal, P. (2016). FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. Frontiers in plant science, 7242. https://doi.org/10.3389/fpls.2016.00242
Naithani, Sushma, et al. "FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca." Frontiers in plant science vol. 7 (2016): 242. doi: https://doi.org/10.3389/fpls.2016.00242
Naithani S, Partipilo CM, Raja R, Elser JL, Jaiswal P. FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. Front Plant Sci. 2016 Mar 04;7:242. doi: 10.3389/fpls.2016.00242. eCollection 2016. PMID: 26973684; PMCID: PMC4777718.
Copy Download .nbib Format: NLM
Share it on

Front Plant Sci. 2016 Mar 04;7:242. doi: 10.3389/fpls.2016.00242. eCollection 2016.

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca.

Frontiers in plant science

Sushma Naithani, Christina M Partipilo, Rajani Raja, Justin L Elser, Pankaj Jaiswal

Affiliations

  1. Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA.

PMID: 26973684 PMCID: PMC4777718 DOI: 10.3389/fpls.2016.00242

Abstract

FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition of new pathways, enzymes, reactions, compounds, and small molecules in the database. To date, FragariaCyc comprises 66 super-pathways, 488 unique pathways, 2348 metabolic reactions, 3507 enzymes, and 2134 compounds. In addition to searching and browsing FragariaCyc, researchers can compare pathways across various plant metabolic networks and analyze their data using Omics Viewer tool. We view FragariaCyc as a resource for the community of researchers working with strawberry and related fruit crops. It can help understanding the regulation of overall metabolism of strawberry plant during development and in response to diseases and abiotic stresses. FragariaCyc is available online at http://pathways.cgrb.oregonstate.edu.

Keywords: Fragaria vesca; FragariaCyc; gene-expression analysis; metabolic network; plant pathway database; strawberry

References

  1. Am J Clin Nutr. 2001 Oct;74(4):418-25 - PubMed
  2. Plant Biotechnol J. 2013 Apr;11(3):269-78 - PubMed
  3. BMC Genomics. 2015 Jan 27;16:29 - PubMed
  4. Front Plant Sci. 2013 Jun 14;4:198 - PubMed
  5. Plant J. 2004 Mar;37(6):914-39 - PubMed
  6. J Exp Bot. 2006;57(10 ):2445-53 - PubMed
  7. PLoS One. 2015 Dec 16;10(12):e0144960 - PubMed
  8. Ann Oncol. 2005 Nov;16(11):1841-4 - PubMed
  9. Nucleic Acids Res. 2016 Jan 4;44(D1):D590-4 - PubMed
  10. Front Plant Sci. 2013 Apr 17;4:79 - PubMed
  11. J Exp Bot. 2016 Feb;67(3):619-31 - PubMed
  12. J Exp Bot. 2012 Aug;63(13):4741-50 - PubMed
  13. Nutr J. 2004 May 12;3:5 - PubMed
  14. PLoS One. 2014 Feb 11;9(2):e88446 - PubMed
  15. Methods Mol Biol. 2016;1374:71-87 - PubMed
  16. Food Chem. 2014 Dec 1;164:272-7 - PubMed
  17. Nat Genet. 2011 Feb;43(2):109-16 - PubMed
  18. Molecules. 2014 Jul 17;19(7):10370-85 - PubMed
  19. J Agric Food Chem. 2011 Dec 14;59(23 ):12569-77 - PubMed
  20. Plant Physiol Biochem. 2014 Sep;82:289-98 - PubMed
  21. J Agric Food Chem. 1999 Feb;47(2):655-8 - PubMed
  22. J Exp Bot. 2002 Oct;53(377):2073-87 - PubMed
  23. Bioinformatics. 2007 Jun 1;23(11):1418-23 - PubMed
  24. J Exp Bot. 2009;60(6):1579-88 - PubMed
  25. Plant Methods. 2009 Oct 31;5:15 - PubMed
  26. J Agric Food Chem. 2005 Mar 23;53(6):2341-3 - PubMed
  27. BMC Plant Biol. 2013 Dec 23;13:223 - PubMed
  28. Genetics. 2008 May;179(1):157-66 - PubMed
  29. Plant Signal Behav. 2011 Dec;6(12):1950-3 - PubMed
  30. BMC Genomics. 2014 Apr 17;15:217 - PubMed
  31. Nucleic Acids Res. 2000 Jan 1;28(1):56-9 - PubMed
  32. PLoS One. 2007 Dec 19;2(12):e1326 - PubMed
  33. Plant Cell. 2013 Jun;25(6):1960-78 - PubMed
  34. Am J Bot. 2014 Oct;101(10):1711-25 - PubMed
  35. J Exp Bot. 2013 Nov;64(14):4421-39 - PubMed
  36. J Proteomics. 2009 May 2;72(4):586-607 - PubMed
  37. Plant Physiol. 2003 Jun;132(2):453-60 - PubMed
  38. Methods Mol Biol. 2007;406:179-212 - PubMed
  39. Plant Physiol. 2010 Aug;153(4):1479-91 - PubMed
  40. Curr Opin Plant Biol. 2012 Apr;15(2):177-84 - PubMed
  41. Plant Physiol Biochem. 2013 Sep;70:433-44 - PubMed
  42. Nucleic Acids Res. 2016 Jan 4;44(D1):D1133-40 - PubMed
  43. J Proteome Res. 2007 Aug;6(8):3011-20 - PubMed
  44. Ann Agric Environ Med. 2014;21(2):339-43 - PubMed
  45. BMC Bioinformatics. 2008 Sep 19;9:386 - PubMed
  46. J Sci Food Agric. 2014 Mar 15;94(4):752-9 - PubMed
  47. Nature. 2014 Jun 19;510(7505):356-62 - PubMed
  48. Nucleic Acids Res. 2014 Jan;42(Database issue):D459-71 - PubMed
  49. Plant Physiol. 2015 Sep;169(1):594-610 - PubMed
  50. Mol Phylogenet Evol. 2009 Jun;51(3):515-30 - PubMed
  51. Genet Mol Res. 2015 Dec 07;14(4):16113-25 - PubMed
  52. BMC Genomics. 2010 Sep 17;11:503 - PubMed
  53. Rice (N Y). 2013 May 29;6(1):15 - PubMed
  54. Food Funct. 2015 May;6(5):1386-98 - PubMed
  55. Bioinformatics. 2002;18 Suppl 1:S225-32 - PubMed
  56. Plant Physiol. 2003 Jun;132(2):530-43 - PubMed
  57. Plant Physiol. 2006 Mar;140(3):1047-58 - PubMed
  58. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5 - PubMed
  59. Mol Nutr Food Res. 2005 Feb;49(2):159-74 - PubMed
  60. New Phytol. 2011 Jul;191(2):376-90 - PubMed
  61. Phytochemistry. 2012 May;77:99-109 - PubMed
  62. Plant J. 2002 Sep;31(6):755-65 - PubMed
  63. Food Chem. 2014 Jul 15;155:298-303 - PubMed
  64. BMC Evol Biol. 2011 Jan 12;11:9 - PubMed
  65. Front Plant Sci. 2014 Dec 09;5:644 - PubMed
  66. J Exp Bot. 2011 May;62(8):2855-73 - PubMed
  67. Front Plant Sci. 2015 Jun 12;6:444 - PubMed
  68. J Exp Bot. 2011 Jan;62(3):1103-18 - PubMed
  69. Plant Cell. 2004 Nov;16(11):3110-31 - PubMed
  70. New Phytol. 2015 Oct;208(2):482-96 - PubMed
  71. J Sci Food Agric. 2016 Jan 30;96(2):365-71 - PubMed
  72. Molecules. 2015 May 21;20(5):9326-43 - PubMed
  73. Sensors (Basel). 2013 Jun 20;13(6):7939-78 - PubMed
  74. Plant Physiol. 2011 Sep;157(1):188-99 - PubMed
  75. Plant Physiol. 2002 Jul;129(3):1019-31 - PubMed
  76. Plant Physiol. 2008 Oct;148(2):730-50 - PubMed
  77. Nature. 2007 Sep 27;449(7161):463-7 - PubMed

Publication Types