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Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of netwo...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753198/ https://www.ncbi.nlm.nih.gov/pubmed/33384856 http://dx.doi.org/10.1016/j.csbj.2020.11.050 |
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author | Desmet, Sandrien Brouckaert, Marlies Boerjan, Wout Morreel, Kris |
author_facet | Desmet, Sandrien Brouckaert, Marlies Boerjan, Wout Morreel, Kris |
author_sort | Desmet, Sandrien |
collection | PubMed |
description | Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed. |
format | Online Article Text |
id | pubmed-7753198 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-77531982020-12-30 Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks Desmet, Sandrien Brouckaert, Marlies Boerjan, Wout Morreel, Kris Comput Struct Biotechnol J Review Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed. Research Network of Computational and Structural Biotechnology 2020-12-03 /pmc/articles/PMC7753198/ /pubmed/33384856 http://dx.doi.org/10.1016/j.csbj.2020.11.050 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Review Desmet, Sandrien Brouckaert, Marlies Boerjan, Wout Morreel, Kris Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks |
title | Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks |
title_full | Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks |
title_fullStr | Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks |
title_full_unstemmed | Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks |
title_short | Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks |
title_sort | seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753198/ https://www.ncbi.nlm.nih.gov/pubmed/33384856 http://dx.doi.org/10.1016/j.csbj.2020.11.050 |
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