Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome

作者: Matthew V. DiLeo , Gary D. Strahan , Meghan den Bakker , Owen A. Hoekenga

DOI: 10.1371/JOURNAL.PONE.0026683

关键词: Weighted correlation network analysisMultivariate statisticsComputational biologyMetabolomeMetabolic networkMetabolomicsNetwork analysisBiotechnologyBiological dataPrincipal component analysisBiology

摘要: … We suggest that this approachable network analysis tool would be extremely useful to biologists who are hoping to condense meaning from large, multidimensional and incompletely …

参考文章(52)
Oyvind M. Andersen, Kenneth R. Markham, FLAVONOIDS: Chemistry, Biochemistry and Applications ,(2018)
Michael Kohl, Sebastian Wiese, Bettina Warscheid, Cytoscape: software for visualization and analysis of biological networks. Methods of Molecular Biology. ,vol. 696, pp. 291- 303 ,(2011) , 10.1007/978-1-60761-987-1_18
Owen A Hoekenga, Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. Journal of biomolecular techniques. ,vol. 19, pp. 159- 166 ,(2008)
Oliver Fiehn, Metabolomics - the link between genotypes and phenotypes Plant Molecular Biology. ,vol. 48, pp. 155- 171 ,(2002) , 10.1023/A:1013713905833
M. Y. Hirai, M. Yano, D. B. Goodenowe, S. Kanaya, T. Kimura, M. Awazuhara, M. Arita, T. Fujiwara, K. Saito, Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana Proceedings of the National Academy of Sciences of the United States of America. ,vol. 101, pp. 10205- 10210 ,(2004) , 10.1073/PNAS.0403218101
Eisuke Chikayama, Takayuki Tohge, Kazuo Shinozaki, Masami Yokota Hirai, Yukihisa Shimada, Kazuki Saito, Tetsuya Sakurai, Kenji Akiyama, Jun Kikuchi, Hiroaki Yuasa, PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. in Silico Biology. ,vol. 8, pp. 339- 345 ,(2008)
R.G. Gardner, 'Mountain Crest' Hybrid Tomato and its Parent, NC 1 rinEC Hortscience. ,vol. 41, pp. 261- 262 ,(2006) , 10.21273/HORTSCI.41.1.261
Areejit Samal, Shalini Singh, Varun Giri, Sandeep Krishna, Nandula Raghuram, Sanjay Jain, None, Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics. ,vol. 7, pp. 118- 118 ,(2006) , 10.1186/1471-2105-7-118
Peter Langfelder, Steve Horvath, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. ,vol. 9, pp. 559- 559 ,(2008) , 10.1186/1471-2105-9-559
Fabien Mounet, Annick Moing, Virginie Garcia, Johann Petit, Michael Maucourt, Catherine Deborde, Stéphane Bernillon, Gwénaëlle Le Gall, Ian Colquhoun, Marianne Defernez, Jean-Luc Giraudel, Dominique Rolin, Christophe Rothan, Martine Lemaire-Chamley, 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. ,vol. 149, pp. 1505- 1528 ,(2009) , 10.1104/PP.108.133967