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Title: Using gene expression to study specialized metabolism - a practical guide
Authors: Delli-Ponti, Riccardo
Shivhare, Devendra
Mutwil, Marek
Keywords: Science::Biological sciences
Issue Date: 2021
Source: Delli-Ponti, R., Shivhare, D. & Mutwil, M. (2021). Using gene expression to study specialized metabolism - a practical guide. Frontiers in Plant Science, 11.
Project: MOE2018-T2-2-053
Journal: Frontiers in Plant Science
Abstract: Plants produce a vast array of chemical compounds that we use as medicines and flavors, but these compounds' biosynthetic pathways are still poorly understood. This paucity precludes us from modifying, improving, and mass-producing these specialized metabolites in suitable bioreactors. Many of the specialized metabolites are expressed in a narrow range of organs, tissues, and cell types, suggesting a tight regulation of the responsible biosynthetic pathways. Fortunately, with unprecedented ease of generating gene expression data and with >200,000 publicly available RNA sequencing samples, we are now able to study the expression of genes from hundreds of plant species. This review demonstrates how gene expression can elucidate the biosynthetic pathways by mining organ-specific genes, gene expression clusters, and applying various types of co-expression analyses. To empower biologists to perform these analyses, we showcase these analyses using recently published, user-friendly tools. Finally, we analyze the performance of co-expression networks and show that they are a valuable addition to elucidating multiple the biosynthetic pathways of specialized metabolism.
ISSN: 1664-462X
DOI: 10.3389/fpls.2020.625035
Schools: School of Biological Sciences 
Rights: © 2021 Delli-Ponti, Shivhare and Mutwil. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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