Weighted correlation network analysis (WGCNA) applied to the tomato fruit metabolome

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  DiLeo, Matthew V ^a,b,c   Strahan, Gary D ^c   den Bakker, Meghan ^a,b   Hoekenga, Owen A ^a,b  

^a United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

^b ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

^c EASTERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; FRUIT RIPENING; GENE EXPRESSION PROFILING; GENE MUTATION; GENE REGULATORY NETWORK; GENETIC TRAIT; GENETIC VARIABILITY; METABOLITE; METABOLOME; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PHENOTYPIC VARIATION; PLANT GENETICS; STATISTICAL ANALYSIS; SYSTEMS BIOLOGY; TOMATO; TRANSGENIC PLANT; WEIGHTED GENE CORRELATION NETWORK ANALYSIS; METABOLISM; PRINCIPAL COMPONENT ANALYSIS;

LYCOPERSICON ESCULENTUM;

LYCOPERSICON ESCULENTUM; METABOLOME; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PRINCIPAL COMPONENT ANALYSIS;

EID: 80054843453     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026683     Document Type: Article

References (56)

1. Bader DA, (2004) Computational Biology and High-Performance Computing. Communications of the ACM 47: 34-41.
2. Maltsev N, (2006) Computing and the "Age of Biology". CTWatch Quarterly 2.
3. Barenco M, Brewer D, Papouli E, Tomescu D, Callard R, et al. (2009) Dissection of a complex transcriptional response using genome-wide transcriptional modelling. Molecular Systems Biology 5: 327.
4. Aoki K, Ogata Y, Shibata D, (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant & Cell Physiology 48: 381-390.
5. Horvath S, Dong J, (2008) Geometric Interpretation of Gene Coexpression Network Analysis. PLoS Computational Biology 4: e1000117.
6. Langfelder P, Horvath S, (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 559.
7. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, et al. (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proceedings of the National Academy of Sciences (USA) 101: 10205-10210.
8. Fait A, Hanhineva K, Beleggia R, Dai N, Rogachev I, et al. (2008) Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development. Plant Physiology 148: 730-750.
9. Zhang B, Horvath S, (2005) A general framework for weighted gene co-expression network analysis. Statistical Applications in Genetics and Molecular Biology 4.
10. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. 11 Accessed from http://www.r-project.org/verified 10/5/.
11. Dettmer K, Aronov PA, Hammock BD, (2007) Mass spectrometry-based metabolomics. Mass Spectrometry Reviews 26: 51-78.
12. Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, et al. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9: 418-425.
13. Carrari F, Fernie AR, (2006) Metabolic regulation underlying tomato fruit development. Journal of Experimental Botany 57: 1883-1897.
14. Dunn WB, (2008) Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes. Physical Biology.
15. Champy MF, Selloum M, Piard L, Zeitler V, Caradec C, et al. (2004) Mouse functional genomics requires standardization of mouse handling and housing conditions. Mammalian Genome 15: 768-783.
16. Fiehn O, (2002) Metabolomics - the link between genotypes and phenotypes. Plant Molecular Biology 48: 155-171.
17. Harborne JB, Baxter H, (1999) The Handbook of Natural Flavonoids volume 2 Chichester Wiley.
18. Andersen ØM, Markham KR, eds. (2006) Flavonoids: Chemistry, Biochemistry and Applications. Boca Raton, FL CRC Press. pp. 1237 P.
19. USDA-ARS, (2007) Database for the Flavonoid Content of selected foods, release 2.1.
20. Giovannoni JJ, (2004) Genetic Regulation of Fruit Development and Ripening. Plant Cell 16: S170-180.
21. Goff SA, Klee HJ, (2006) Plant Volatile Compounds: Sensory Cues for Health and Nutritional Value? Science 311: 815-819.
22. Moco S, Capanoglu E, Tikunov Y, Bino RJ, Boyacioglu D, et al. (2007) Tissue specialization at the metabolite level is perceived during the development of tomato fruit. Journal of Experimental Botany 58: 4131-4146.
23. Bertin N, Causse M, Brunel B, Tricon D, Genard M, (2009) Identification of growth processes involved in QTLs for tomato fruit size and composition. Journal of Experimental Botany 60: 237-248.
24. Mathieu S, Cin VD, Fei Z, Li H, Bliss P, et al. (2009) Flavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. Journal of Experimental Botany 60: 325-337.
25. Slimestad R, Verheul M, (2009) Review of flavonoids and other phenolics from fruits of different tomato Lycopersicon esculentum Mill. cultivars. Journal of the Science of Food and Agriculture 89: 1255-1270.
26. Davies JN, Kempton RJ, (1975) Changes in the individual sugars of tomato fruit during ripening. Journal of the Science of Food and Agriculture 26: 1103-1110.
27. Roessner-Tunali U, Hegemann B, Lytovchenko A, Carrari F, Bruedigam C, et al. (2003) Metabolic Profiling of Transgenic Tomato Plants Overexpressing Hexokinase Reveals That the Influence of Hexose Phosphorylation Diminishes during Fruit Development. Plant Physiology 133: 84-99.
28. Alba R, Payton P, Fei Z, McQuinn R, Debbie P, et al. (2005) Transcriptome and Selected Metabolite Analyses Reveal Multiple Points of Ethylene Control during Tomato Fruit Development. Plant Cell 17: 2954-2965.
29. Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor M-I, et al. (2006) Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior. Plant Physiology 142: 1380-1396.
30. Mounet F, Moing A, Garcia V, Petit J, Maucourt M, et al. (2009) Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development. Plant Physiology 149: 1505-1528.
31. Adams-Phillips L, Barry C, Giovannoni J, (2004) Signal transduction systems regulating fruit ripening. Trends in Plant Science 9: 331-338.
32. Lincoln JE, Fischer RL, (1988) Regulation of Gene Expression by Ethylene in Wild-Type and rin Tomato (Lycopersicon esculentum) Fruit. Plant Physiology 88: 370-374.
33. Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, et al. (2002) A MADS-Box Gene Necessary for Fruit Ripening at the Tomato Ripening-Inhibitor (Rin) Locus. Science 296: 343-346.
34. Bai Y, Lindhout P, (2007) Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future? Annals of Botany 100: 1085-1094.
35. Hoekenga OA, (2008) Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. Journal of Biomolecular Technology 19: 159-166.
36. Gardner R, (2006) Mountain Crest hybrid tomato and its parent, NC 1rinEC. HortScience 41: 261-262.
37. Schripsema J, (2010) Application of NMR in plant metabolomics: techniques, problems and prospects. Phytochemical Analysis 21: 14-21.
38. Ringner M, (2008) What is principal component analysis? Nature Biotechnology 26: 303-304.
39. Jolliffe I, (2004) Principal Component Analysis. New York Springer-Verlag.
40. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, et al. (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. Journal of Biological Chemistry 280: 25590-25595.
41. Kim JK, Bamba T, Harada K, Fukusaki E, Kobayashi A, (2007) Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment. Journal of Experimental Botany 58: 415-424.
42. Sawada Y, Akiyama K, Sakata A, Kuwahara A, Otsuki H, et al. (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant & Cell Physiology 50: 37-47.
43. Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, et al. (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biology 8: 339-345.
44. Dong J, Horvath S, (2007) Understanding network concepts in modules. BMC Systems Biology 1: 24.
45. Jeong H, Mason SP, Barabasi AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
46. Samal A, Singh S, Giri V, Krishna S, Raghuram N, et al. (2006) Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics 7: 118.
47. Kohl M, Wiese S, Warscheid B, (2011) Cytoscape: software for visualization and analysis of biological networks. Methods in Molecular Biology 696: 291-303.
48. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, et al. (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiology 153: 1479-1491.
49. Aten J, Fuller T, Lusis A, Horvath S, (2008) Using genetic markers to orient the edges in quantitative trait networks: The NEO software. BMC Systems Biology 2: 34.
50. Doebley JF, Gaut BS, Smith BD, (2006) The molecular genetics of crop domestication. Cell 127: 1309-1321.
51. De Vos RCH, Moco S, Lommen A, Keurentjes JJB, Bino RJ, et al. (2007) Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nature Protocols 2: 778-791.
52. Goddard T, Kneller D, (2008) SPARKY 3. Computer program. San Francisco: University of California. 11 Accessed from http://www.cgl.ucsf.edu/home/sparky/ verified 10/5/.
53. Le Gall G, Colquhoun I, Davis A, Collins G, Verhoeyen M, (2003) Metabolite profiling of tomato (Lycopersicon esculentum) using 1H NMR spectroscopy as a tool to detect potential unintended effects following a genetic modification. Journal of Agricultural and Food Chemistry 51: 2447-2456.
54. Sobolev AP, Segre AL, Lamanna R, (2003) Proton high-field NMR study of tomato juice. Magnetic Resonance in Chemistry 41: 237-245.
55. Tiziani S, Schwartz SJ, Vodovotz Y, (2006) Profiling of carotenoids in tomato juice by one- and two-dimensional NMR. Journal of Agricultural and Food Chemistry 54: 6094-6100.
56. Neelam A, Cassol T, Mehta RA, Abdul-Baki AA, Sobolev AP, et al. (2008) A field-grown transgenic tomato line expressing higher levels of polyamines reveals legume cover crop mulch-specific perturbations in fruit phenotype at the levels of metabolite profiles, gene expression, and agronomic characteristics. Journal of Experimental Botany 59: 2337-2346.