Extracting functionally accurate context-specific models of Atlantic salmon metabolism
Abstract 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, whi...
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ftdoajarticles:oai:doaj.org/article:32855d39937b479c8e68371796922405 2023-06-18T03:39:52+02:00 Extracting functionally accurate context-specific models of Atlantic salmon metabolism Håvard Molversmyr Ove Øyås Filip Rotnes Jon Olav Vik 2023-05-01T00:00:00Z https://doi.org/10.1038/s41540-023-00280-x https://doaj.org/article/32855d39937b479c8e68371796922405 EN eng Nature Portfolio https://doi.org/10.1038/s41540-023-00280-x https://doaj.org/toc/2056-7189 doi:10.1038/s41540-023-00280-x 2056-7189 https://doaj.org/article/32855d39937b479c8e68371796922405 npj Systems Biology and Applications, Vol 9, Iss 1, Pp 1-10 (2023) Biology (General) QH301-705.5 article 2023 ftdoajarticles https://doi.org/10.1038/s41540-023-00280-x 2023-06-04T00:40:30Z Abstract 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. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles npj Systems Biology and Applications 9 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Biology (General) QH301-705.5 |
spellingShingle |
Biology (General) QH301-705.5 Håvard Molversmyr Ove Øyås Filip Rotnes Jon Olav Vik Extracting functionally accurate context-specific models of Atlantic salmon metabolism |
topic_facet |
Biology (General) QH301-705.5 |
description |
Abstract 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 |
Article in Journal/Newspaper |
author |
Håvard Molversmyr Ove Øyås Filip Rotnes Jon Olav Vik |
author_facet |
Håvard Molversmyr Ove Øyås Filip Rotnes Jon Olav Vik |
author_sort |
Håvard Molversmyr |
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 Portfolio |
publishDate |
2023 |
url |
https://doi.org/10.1038/s41540-023-00280-x https://doaj.org/article/32855d39937b479c8e68371796922405 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
npj Systems Biology and Applications, Vol 9, Iss 1, Pp 1-10 (2023) |
op_relation |
https://doi.org/10.1038/s41540-023-00280-x https://doaj.org/toc/2056-7189 doi:10.1038/s41540-023-00280-x 2056-7189 https://doaj.org/article/32855d39937b479c8e68371796922405 |
op_doi |
https://doi.org/10.1038/s41540-023-00280-x |
container_title |
npj Systems Biology and Applications |
container_volume |
9 |
container_issue |
1 |
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1769004646581403648 |