ReviewFrontiers in plant science2020
Using Gene Expression to Study Specialized Metabolism-A Practical Guide.
Review in Frontiers in plant science, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- Genome-wide analysis of the R2R3-MYB family reveals potential regulators of lignin and tricin metabolism in the model grass Setaria viridis.Molecular genetics and genomics : MGG · 2026Article
- Metabolic engineering of narrow-leafed lupin for the production of enantiomerically pure (-)-sparteine.Plant biotechnology journal · 2025Article
- Combining Short- and Long-Read Transcriptomes for Targeted Enzyme Discovery.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Evolution of plant metabolism: the state-of-the-art.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Plant sesquiterpene lactones.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Medicinal plant genomics.BMC genomics · 2023Article
- Article
- Transcriptomic and metabolomic characterization of antibacterial activity ofFrontiers in plant science · 2023Article
- Article
- Flavonoids - flowers, fruit, forage and the future.Journal of the Royal Society of New Zealand · 2023Review
- Exploiting plant transcriptomic databases: Resources, tools, and approaches.Plant communications · 2022Review
- Identification of Gene Biomarkers for Tigilanol Tiglate Content inMolecules (Basel, Switzerland) · 2022Article
- PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum.Plant & cell physiology · 2022Article
- Unlocking plant metabolic diversity: A (pan)-genomic view.Plant communications · 2022Review
- Non-target molecular network and putative genes of flavonoid biosynthesis inFrontiers in plant science · 2022Article
- Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches.Frontiers in physiology · 2022Review
- A Metabolomics and Transcriptomics Resource for Identifying Candidate Genes in the Biosynthesis of Specialised Metabolites in Populus tremula.Physiologia plantarumArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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