Extracting functionally accurate context-specific models of Atlantic salmon metabolism
Constraint-based models (CBMs) are used to study metabolic network structure and function in organisms ranging from microbes to multicellular eukaryotes. Published CBMs are usually generic rather than context-specific, meaning that they do not capture differences in reaction activities, which, in tu...
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ftpubmed:oai:pubmedcentral.nih.gov:10224981 2023-06-18T03:39:51+02:00 Extracting functionally accurate context-specific models of Atlantic salmon metabolism Molversmyr, Håvard Øyås, Ove Rotnes, Filip Vik, Jon Olav 2023-05-27 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10224981/ http://www.ncbi.nlm.nih.gov/pubmed/37244928 https://doi.org/10.1038/s41540-023-00280-x en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10224981/ http://www.ncbi.nlm.nih.gov/pubmed/37244928 http://dx.doi.org/10.1038/s41540-023-00280-x © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . NPJ Syst Biol Appl Article Text 2023 ftpubmed https://doi.org/10.1038/s41540-023-00280-x 2023-06-04T01:13:19Z Constraint-based models (CBMs) are used to study metabolic network structure and function in organisms ranging from microbes to multicellular eukaryotes. Published CBMs are usually generic rather than context-specific, meaning that they do not capture differences in reaction activities, which, in turn, determine metabolic capabilities, between cell types, tissues, environments, or other conditions. Only a subset of a CBM’s metabolic reactions and capabilities are likely to be active in any given context, and several methods have therefore been developed to extract context-specific models from generic CBMs through integration of omics data. We tested the ability of six model extraction methods (MEMs) to create functionally accurate context-specific models of Atlantic salmon using a generic CBM (SALARECON) and liver transcriptomics data from contexts differing in water salinity (life stage) and dietary lipids. Three MEMs (iMAT, INIT, and GIMME) outperformed the others in terms of functional accuracy, which we defined as the extracted models’ ability to perform context-specific metabolic tasks inferred directly from the data, and one MEM (GIMME) was faster than the others. Context-specific versions of SALARECON consistently outperformed the generic version, showing that context-specific modeling better captures salmon metabolism. Thus, we demonstrate that results from human studies also hold for a non-mammalian animal and major livestock species. Text Atlantic salmon PubMed Central (PMC) npj Systems Biology and Applications 9 1 |
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Article Molversmyr, Håvard Øyås, Ove Rotnes, Filip Vik, Jon Olav Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
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Article |
description |
Constraint-based models (CBMs) are used to study metabolic network structure and function in organisms ranging from microbes to multicellular eukaryotes. Published CBMs are usually generic rather than context-specific, meaning that they do not capture differences in reaction activities, which, in turn, determine metabolic capabilities, between cell types, tissues, environments, or other conditions. Only a subset of a CBM’s metabolic reactions and capabilities are likely to be active in any given context, and several methods have therefore been developed to extract context-specific models from generic CBMs through integration of omics data. We tested the ability of six model extraction methods (MEMs) to create functionally accurate context-specific models of Atlantic salmon using a generic CBM (SALARECON) and liver transcriptomics data from contexts differing in water salinity (life stage) and dietary lipids. Three MEMs (iMAT, INIT, and GIMME) outperformed the others in terms of functional accuracy, which we defined as the extracted models’ ability to perform context-specific metabolic tasks inferred directly from the data, and one MEM (GIMME) was faster than the others. Context-specific versions of SALARECON consistently outperformed the generic version, showing that context-specific modeling better captures salmon metabolism. Thus, we demonstrate that results from human studies also hold for a non-mammalian animal and major livestock species. |
format |
Text |
author |
Molversmyr, Håvard Øyås, Ove Rotnes, Filip Vik, Jon Olav |
author_facet |
Molversmyr, Håvard Øyås, Ove Rotnes, Filip Vik, Jon Olav |
author_sort |
Molversmyr, Håvard |
title |
Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
title_short |
Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
title_full |
Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
title_fullStr |
Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
title_full_unstemmed |
Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
title_sort |
extracting functionally accurate context-specific models of atlantic salmon metabolism |
publisher |
Nature Publishing Group UK |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10224981/ http://www.ncbi.nlm.nih.gov/pubmed/37244928 https://doi.org/10.1038/s41540-023-00280-x |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
NPJ Syst Biol Appl |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10224981/ http://www.ncbi.nlm.nih.gov/pubmed/37244928 http://dx.doi.org/10.1038/s41540-023-00280-x |
op_rights |
© The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
op_doi |
https://doi.org/10.1038/s41540-023-00280-x |
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npj Systems Biology and Applications |
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