In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of “omics” data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks. In this chapter, we demonstrate a workflow to integrate gas chromatography coupled to mass spectrometry (GC-MS)-based metabolomics data of tomato fruit pericarp (flesh) tissue, at five developmental stages, with a genome-scale reconstruction of tomato metabolism. This method allows for the extraction of context-specific networks reflecting changing activities of metabolic pathways throughout fruit development and maturation.
CITATION STYLE
Töpfer, N., Seaver, S. M. D., & Aharoni, A. (2018). Integration of plant metabolomics data with metabolic networks: Progresses and challenges. In Methods in Molecular Biology (Vol. 1778, pp. 297–310). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7819-9_21
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