KNApSAcK family databases: Integrated metabolite-plant species databases for multifaceted plant research

Plant and Cell Physiology

Volumn 53, Issue 2, 2012, Pages

  Afendi, Farit Mochamad ^a,b   Okada, Taketo ^c   Yamazaki, Mami ^d   Hirai Morita, Aki ^a   Nakamura, Yukiko ^a   Nakamura, Kensuke ^a   Ikeda, Shun ^a   Takahashi, Hiroki ^a   Altaf Ul Amin, Md ^a   Darusman, Latifah K ^b   Saito, Kazuki ^d,e   Kanaya, Shigehiko ^a,e  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b BOGOR AGRICULTURAL UNIVERSITY   (Indonesia)

^c TOKUSHIMA BUNRI UNIVERSITY   (Japan)

^d CHIBA UNIVERSITY   (Japan)

^e RIKEN Center for Sustainable Resource Science   (Japan)

Author keywords

Database; Degree distribution; KNApSAcK family; Metabolomics; Scale free; Species metabolite relationship

Indexed keywords

ARTICLE; BIOLOGY; FACTUAL DATABASE; GEOGRAPHY; INDONESIA; INTERNET; JAPAN; MEDICINAL PLANT; METABOLISM; METABOLOMICS; METHODOLOGY; ORIENTAL MEDICINE; SEARCH ENGINE;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GEOGRAPHY; INDONESIA; INTERNET; JAPAN; MEDICINE, EAST ASIAN TRADITIONAL; METABOLOMICS; PLANTS, MEDICINAL; SEARCH ENGINE;

EID: 84857226999     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcr165     Document Type: Article

References (35)

1. Adnyana, I.K. and Soemardji, A.A. (2007) Evaluation of Pharmacological Efficacy of Jamu Medicine Institute of Natural Medicine, University of Toyama, Toyama.
2. Albert, R., Jeong, H. and Barbási, A.-L. (1999) Internet: diameter of the world-wide web. Nature 401: 130-131.
3. Bairoch, A. (2000) The ENZYME database in 2000. Nucleic Acids Res. 28: 304-304.
4. Bike, S. and Peterson, C. (2001) Topological properties of citation and metabolic networks. Phys. Rev. E 64: 036106.
5. Bino, R.J., Hall, R.D., Fiehn, O., Kopka, J., Saito, K., Draper, J. et al. (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9: 418-425. (Pubitemid 39160937)
6. Beers, S.J. (2001) Jamu: The Ancient Indonesian Art of Healing. Periplus Editions Ltd., Vermont.
7. Chan, K. (2005) Chinese medicinal materials and their interface with Western medical concepts. J. Ethnopharmacol. 96: 1-18. (Pubitemid 39575027)
8. De Luca, V. and St Pierre, B. (2000) The cell and developmental biology of alkaloid biosynthesis. Trends Plant Sci. 5: 168-173. (Pubitemid 30192274)
9. Goto, S., Okuno, Y., Hattori, M., Nishioka, T. and Kanehisa, M. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30: 402-404. (Pubitemid 34679597)
10. Guillaume, J.-L. and Latapy, M. (2009) Bipartite graphs as models of complex networks. Physica A 371: 795-813. (Pubitemid 44397327)
11. Iwatsuki, K., Yamazaki, T., Boufford, D.E. and Ohba, H. (1995) Flora of Japan, Vol. 1 Pteridophyta and Gymnospermae, Kodansha Ltd., Tokyo.
12. Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N. and Barabasi, A.L. (2000) The large-scale organization of metabolic networks. Nature 407: 651-654.
13. Ji, H.-F., Li, X.-J. and Zhang, H.-Y. (2009) Natural products and drug discovery. EMBO Rep. 10: 194-199.
14. Kanehisa, M., Goto, S., Kawashima, S. and Nakaya, A. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res. 30: 42-46.
15. Macel, M., van Dam, N.M. and Keurentjes, J.B. (2010) Metabolomics: the chemistry between ecology and genetics. Mol. Ecol. Resources 10: 583-593.
16. Mitsuhashi, H., Okada, M., Nunome, S., Terabayashi, S., Miki, E., Fujita, T. et al. (1988) Illustrated Medicinal Plants of the World in Colour. Hokuryukan Co. Ltd., Tokyo.
17. Moco, S., Bino, R.J., De Vos, C.H. and Vervoort, J.V. (2007) Metabolomics technologies and metabolite identification. Trends Anal. Chem. 26: 855-866. (Pubitemid 47532208)
18. Ohkubo, J. (2005) Generation of complex bipartite graphs by using a preferential rewiring process. Phys. Rev. 72: 036120.1-10.
19. Okada, T., Afendi, F.M., Md., Altaf-Ul-Amin, Takahashi, H., Nakamura, K. and Kanaya, S. (2010) Metabolomics of medicinal plants: the importance of multivariate analysis of analytical chemistry data. Curr. Comput. Aided Drug Des. 6: 179-196.
20. Penso, G. (1980) WHO Inventory of Medicinal Plants Used in Different Countries. WHO, Geneva.
21. Pramono, S. (2007) Jamu in Indonesian Daily Life and Industry. Institution of Natural Medicine, University of Toyama, Toyama.
22. Qiu, J. (2007) Traditional medicine: a culture in the balance. Nature 448: 126-128. (Pubitemid 47067352)
23. Rzhetsky, A. and Gomez, S.M. (2001) Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 17: 988-996. (Pubitemid 33009257)
24. Saito, K. and Matsuda, F. (2010) Metabolomics for functional genomics, systems biology, and biotechnology. Annu. Rev. Plant. Biol. 61: 463-489.
25. Sangat, H.M., Zuhud, E.A.M. and Damayanti, E.K. (2000) Kamus Penyakit dan Tumbuhan Obat Indonesia [Etnofitomedika], Jakarta: Yayasan Obor Indonesia (in Javanese).
26. Sawada, Y., Akiyama, K., Sakata, A., Kuwahara, A., Otsuki, H., Sakurai, T. et al. (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol. 50: 37-47.
27. Schippmann, U., Leaman, D.J. and Cunningham, A.B. (2002) Impact of Cultivation and Gathering of Medicinal Plants on Biodiversity: Global Trends and Issues. Biodiversity and the Ecosystem Approach in Agriculture, Forestry and Fisheries Inter-Departmental Working Group on Biological Diversity for Food and Agriculture, Rome.
28. Scotland, R.W. and Wortley, A.H. (2003) How many species of seed plants are there? Taxon 52: 101-104. (Pubitemid 37065030)
29. Shyur, L.F. and Yang, N.S. (2008) Metabolomics for phytomedicine research and drug development. Curr. Opin. Chem. Biol. 12: 66-71.
30. Tohge, T. and Fernie, A. (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat. Protoc. 5: 1210-1227.
31. Verpoorte, R., Choi, Y.H. and Kim, H.K. (2005) Ethnopharmacology and systems biology: a perfect holistic match. J. Ethnopharmacol. 100: 53-56. (Pubitemid 41073521)
32. Watanabe, K., Matsuura, K., Gao, P., Hottenbacher, L., Tokunaga, H., Nishimura, K. et al. (2011) Traditional Japanese Kampo medicine: clinical research between modernity and traditional medicine-the state of research and methodological suggestions for the future. Evid. Based Complement. Alternat. Med. (in press).
33. Watts, D.J. and Strogatz, S.H. (1998) Collective dynamics of 'smallworld' networks. Nature 393: 440-442.
34. Wolf, Y.I., Karev, G. and Koonin, E.V. (2002) Scale-free networks in biology: new insights into the fundamentals of evolution? BioEssays 24: 105-109. (Pubitemid 34179287)
35. Wuchty, S. (2001) Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18: 1694-1702. (Pubitemid 32776920)