A global approach to analysis and interpretation of metabolic data for plant natural product discovery

Natural Product Reports

Volumn 30, Issue 4, 2013, Pages 565-583

  Hur, Manhoi ^a   Campbell, Alexis Ann ^a   Almeida De Macedo, Marcia ^a   Li, Ling ^a   Ransom, Nick ^a   Jose, Adarsh ^a   Crispin, Matt ^a   Nikolau, Basil J ^a   Wurtele, Eve Syrkin ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PRODUCT;

ARABIDOPSIS; CHEMISTRY; DRUG DEVELOPMENT; FACTUAL DATABASE; GENETICS; MEDICINAL PLANT; METABOLISM; METABOLOMICS; REVIEW;

ARABIDOPSIS; BIOLOGICAL AGENTS; DATABASES, FACTUAL; DRUG DISCOVERY; METABOLOMICS; PLANTS, MEDICINAL;

EID: 84874977344     PISSN: 02650568     EISSN: 14604752     Source Type: Journal    
DOI: 10.1039/c3np20111b     Document Type: Review

References (118)

1. R. J. Bino et al. Trends Plant Sci. 2004 9 418 425
2. D. J. Oliver B. Nikolau E. S. Wurtele Metab. Eng. 2002 4 98 106
3. W. Weckwerth O. Fiehn Curr. Opin. Biotechnol. 2002 13 156 160
4. A. Ounaroon et al. Plant J. 2003 36 808 819
5. J. M. Gennity P. K. Stumpf Arch. Biochem. Biophys. 1985 239 444 454
6. M. Bafor et al. Biochem. J. 1991 280 507 514
7. M. Lee et al. Science 1998 280 915 918
8. M. Bafor et al. Arch. Biochem. Biophys. 1993 303 145 151
9. E. B. Cahoon et al. J. Biol. Chem. 2001 276 2637 2643
10. J. M. Dyer et al. Plant Physiol. 2002 130 2027 2038
11. P. Sperling et al. Eur. J. Biochem. 2000 267 3801 3811
12. T. Cakir et al. Mol. Syst. Biol. 2006 2 50
13. D. B. Murray M. Beckmann H. Kitano Proc. Natl. Acad. Sci. U. S. A. 2007 104 2241 2246
14. M. T. Kresnowati et al. Mol. Syst. Biol. 2006 2 49
15. M. A. Smith et al. Biochem. J. 1992 287 141 144
16. N. Amiour et al. J. Exp. Bot. 2012 63 5017 5033
17. T. T. Dang P. J. Facchini Plant Physiol. 2012 159 618 631
18. A. Jauhiainen et al. Biostatistics 2012 13 748 761
19. S. Osorio et al. Plant Physiol. 2012 159 1713 1729
20. S. P. Singh et al. Curr. Opin. Plant Biol. 2005 8 197 203
21. Y. Gibon et al. GenomeBiology 2006 7 R76
22. P. Broun et al. Science 1998 282 1315 1317
23. H. Jenkins et al. Nat. Biotechnol. 2004 22 1601 1606
24. P. Bais et al. Plant Physiol. 2010 152 1807 1816
25. S. M. Quanbeck et al. Front. Plant Sci. 2012 3 15
26. C. R. Raetz et al. J. Lipid Res. 2009 50 S103 S108
27. D. W. J. James et al. Plant Cell 1995 7 309 319
28. C. S. Oh et al. J. Biol. Chem. 1997 272 17376 17384
29. M. N. Ngaki et al. Nature 2012 485 530 533
30. F. Matsuda et al. Plant Physiol. 2010 152 566 578
31. H. Goda et al. Plant J. 2008 55 526 542
32. E. S. Wurtele et al. Metabolites 2012 2 1031 1059
33. M. C. Crispin and E. S. Wurtele, in Biotechnology for Medicinal Plants, ed., S. Chandra, H. Lata, and, A. Varma, Springer Berlin Heidelberg, 2013, ch. 17, pp. 395-411
34. L. A. Giddings et al. J. Biol. Chem. 2011 286 16751 16757
35. Y. S. Yeo et al. J. Biol. Chem. 2013 288 5 3163 3173
36. S. Takahashi et al. Biotechnol. Bioeng. 2007 97 170 181
37. R. Tautenhahn Anal. Chem. 2012 84 5035 5039
38. N. Lewis, et al., MedPlTranscriptome, http://uic.edu/pharmacy/ MedPlTranscriptome/database.html
39. A. J. Carroll M. R. Badger A. Harvey Millar BMC Bioinformatics 2010 11 376
40. M. Scholz O. Fiehn Pacific Symp. Biocomp. 2007 12 169 180
41. K. Skogerson et al. BMC Bioinformatics 2011 12 321
42. B. Clark, NoSQL: If only it was that easy, http://bjclark.me/2009/08/04/ nosql-if-only-it-was-that-easy/
43. A. J. M. Lith, Master Thesis, Chalmers University of Technology, Sweden, 2010, http://www.bibsonomy.org/bibtex/2601013440b9ba0f3617c705820fc95ac/ nosebrain?layout=din1505, http://publications.lib.chalmers.se/records/fulltext/ 123839.pdf
44. P. Sadalage and M. Fowler, NoSQL Distilled: A Brief Guide to the Emerging World of Polyglot Persistence, 1st edn, 2012
45. S. Kumar, What is a Key/Value store database?, http://dba.stackexchange. com/questions/607/what-is-a-key-value-store-database
46. C. G. Renzo Angles, Survey of graph database models, http://dl.acm.org/ citation.cfm?id=1322433
47. K. Chodorow, E. Horowitz and D. Merriman, mongoDB website, http://www.mongodb.org/
48. M. Kennedy, MongoDB vs. SQL Server 2008 Performance Showdown, http://blog.michaelckennedy.net/2010/04/29/mongodb-vs-sql-server-2008- performance-showdown/
49. M. Kennedy, The NoSQL Movement, LINQ, and MongoDB-Oh My!, http://blog.michaelckennedy.net/2010/04/22/the-nosql-movement-linq-and-mongodb- oh-my/
50. G. Parmigiani, et al., The Analysis of Gene Expression Data, Springer, New York, 2003
51. B. M. Bolstad et al. Bioinformatics 2003 19 185 193
52. K. A. Veselkov et al. Anal. Chem. 2011 83 5864 5872
53. A. Lommen Anal. Chem. 2009 81 3079 3086
54. A. Lommen H. J. Kools Metabolomics 2012 8 719 726
55. M. Katajamaa J. Miettinen M. Oresic Bioinformatics 2006 22 634 636
56. C. A. Smith et al. Anal. Chem. 2006 78 779 787
57. P. Shannon et al. Genome Res. 2003 13 2498 2504
58. M. Lawrence, et al., Chromatoplots, https://github.com/tengfei/ chromatoplots/
59. C. G. Healey J. T. Enns IEEE Trans. Visualization Comput. Graphics 1999 5 145 167
60. P. Vickers J. Faith N. Rossiter IEEE Trans. Vis. Comput. Graph. 2012
61. B. D. Hertogh et al. BMC Bioinformatics 2010 11 17
62. E. J. Perkins et al. BMC Bioinformatics 2006 7 S22
63. M.-Y. Brusniak et al. BMC Bioinformatics 2008 9 542
64. X. Cui G. A. Churchill GenomeBiology 2003 4 210
65. A. G. Marshall R. P. Rodgers Proc. Natl. Acad. Sci. U. S. A. 2008 105 18090 18095
66. M. Hur et al. Energy Fuels 2010 24 5524 5532
67. M. Krzywinski et al. Genome Res. 2009 19 1639 1645
68. M. Krzywinski, et al., IsMAGE MAPS-INTRODUCTION AND CLICKABLE IDEOGRAMS, http://circos.ca/documentation/tutorials/image-maps/
69. M. Krzywinski et al. Briefings Bioinf. 2012 13 627 644
70. A. H. Group, Hadoop project, http://hadoop.apache.org/
71. D. Smith, R and Hadoop: Step-by-step tutorials, http://blog. revolutionanalytics.com/2012/03/r-and-hadoop-step-by-step-tutorials.html
72. D. Smith, Data distillation with Hadoop and R, http://blog. revolutionanalytics.com/2012/06/data-distillation-with-hadoop-and-r.html, 2012
73. Neo4J project, http://neo4j.org/
74. C. W. Churchman, The systems approach, New York: Delacorte Press 1968
75. R. A. Irizarry et al. Biostatistics 2003 4 249 264
76. A. Mortazavi et al. Nat. Methods 2008 5 621 628
77. R. A. van den Berg et al. BMC Genomics 2006 8 142
78. T. Ji P. Liu D. Nettleton Stat. Appl. Genet. Mol. Biol. 2012 11 12
79. K. Wang et al. IEEE Trans. Inf. Technol. Biomed. 2009 13 848 853
80. B. Durbin D. M. Rocke Bioinformatics 2004 20 660 667
81. D. M. Rocke B. Durbin J. Comput. Biol. 2001 8 557 569
82. M. D. Robinson G. K. Smyth Bioinformatics 2007 23 2881 2887
83. M. D. Robinson G. K. Smyth Biostatistics 2008 9 321 332
84. L. M. McIntyre et al. BMC Genomics 2011 12 293
85. J. C. Marioni et al. Genome Res. 2008 18 1509 1517
86. M. Dehmer, et al., Applied statistics for network biology: methods in systems biology, Wiley-Blackwell, 2011
87. L. J. Heyer S. Kruglyak S. Yooseph Genome Res. 1999 9 1106 1115
88. D. Jiang C. Tang A. Zhang IEEE Trans. Knowl. Data Eng. 2004 16 1370 1386
89. Z. Dastani et al. PLoS Genet. 2012 8 e1002607
90. A. Fukushima et al. BMC Syst. Biol. 2011 5 1
91. R. Steuer et al. Biochem. Soc. Trans. 2003 31 1476 1478
92. M. Kanehisa et al. Nucleic Acids Res. 2010 38 D355 360
93. F. Carrari et al. Plant Physiol. 2006 142 1380 1396
94. P. H. Bradley et al. PLoS Comput. Biol. 2009 5 e1000270
95. G. W. Snedecor and W. G. Cochran, Statistical methods Iowa State University Press, Ames, IA, 1989
96. Y. Benjamini Y. Hochberg J. R. Stat. Soc. 1995 57 289 300
97. J. D. Storey R. Tibshirani Proc. Natl. Acad. Sci. U. S. A. 2003 100 9440 9445
98. J. D. Storey J. R. Stat. Soc., Ser. B: Stat. Methodol. 2002 64 479 498
99. H. K. Lee et al. Genome Res. 2004 14 1085 1094
100. E. Allen et al. BMC Syst. Biol. 2010 4 62
101. M. Kanehisa et al. Nucleic Acids Res. 2006 34 D354 357
102. E. V. Koonin Annu. Rev. Genet. 2005 39 309 338
103. M. Remm C. E. Storm E. L. Sonnhammer J. Mol. Biol. 2001 314 1041 1052
104. R. L. Tatusov E. V. Koonin D. J. Lipman Science 1997 278 631 637
105. B. J. Blacklock J. G. Jaworski Biochem. Biophys. Res. Commun. 2006 346 583 590
106. J. Joubes et al. Plant Mol. Biol. 2008 67 547 566
107. A. E. Leonard et al. Prog. Lipid Res. 2004 43 36 54
108. V. Denic J. S. Weissman Cell 2007 130 663 677
109. F. Beaudoin et al. J. Biol. Chem. 2002 277 11481 11488
110. D. B. Jump Methods Mol. Biol. 2009 579 375 389
111. D. A. Toke C. E. Martin J. Biol. Chem. 1996 271 18413 18422
112. X. Li et al. Mol. Plant 2009 2 138 151
113. T. M. Dunn et al. Ann. Bot. 2004 93 483 497
114. Y. Feng et al. Chem. Biodiversity 2012 9 868 887
115. L. Li et al. Plant J. 2009 58 485 498
116. L. Li et al. J. Exp. Bot. 2007 58 3323 3342
117. W. I. Mentzen E. S. Wurtele BMC Plant Biol. 2008 8 99
118. W. I. Mentzen et al. BMC Plant Biol. 2008 8 76