Flux-dependent graphs for metabolic networks
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of metabolic fluxes via edges that represent the flow of metab...
| Huvudupphovsmän: | , , , , |
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| Materialtyp: | Journal article |
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Springer Nature
2018
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| _version_ | 1826280800196231168 |
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| author | Beguerisse-Díaz, M Bosque, G Oyarzún, D Picó, J Barahona, M |
| author_facet | Beguerisse-Díaz, M Bosque, G Oyarzún, D Picó, J Barahona, M |
| author_sort | Beguerisse-Díaz, M |
| collection | OXFORD |
| description | Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of metabolic fluxes via edges that represent the flow of metabolites from source to target reactions. The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed through constraint-based approaches such as Flux Balance Analysis. We illustrate our approach on the central carbon metabolism of Escherichia coli and on a metabolic model of human hepatocytes. The flux-dependent graphs under various environmental conditions and genetic perturbations exhibit systemic changes in their topological and community structure, which capture the re-routing of metabolic fluxes and the varying importance of specific reactions and pathways. By integrating constraint-based models and tools from network science, our framework allows the study of context-specific metabolic responses at a system level beyond standard pathway descriptions. |
| first_indexed | 2024-03-07T00:19:09Z |
| format | Journal article |
| id | oxford-uuid:7bec3f3b-61d9-41f3-8acf-6f33731b7b27 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T00:19:09Z |
| publishDate | 2018 |
| publisher | Springer Nature |
| record_format | dspace |
| spelling | oxford-uuid:7bec3f3b-61d9-41f3-8acf-6f33731b7b272022-03-26T20:53:48ZFlux-dependent graphs for metabolic networksJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:7bec3f3b-61d9-41f3-8acf-6f33731b7b27Symplectic Elements at OxfordSpringer Nature2018Beguerisse-Díaz, MBosque, GOyarzún, DPicó, JBarahona, MCells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of metabolic fluxes via edges that represent the flow of metabolites from source to target reactions. The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed through constraint-based approaches such as Flux Balance Analysis. We illustrate our approach on the central carbon metabolism of Escherichia coli and on a metabolic model of human hepatocytes. The flux-dependent graphs under various environmental conditions and genetic perturbations exhibit systemic changes in their topological and community structure, which capture the re-routing of metabolic fluxes and the varying importance of specific reactions and pathways. By integrating constraint-based models and tools from network science, our framework allows the study of context-specific metabolic responses at a system level beyond standard pathway descriptions. |
| spellingShingle | Beguerisse-Díaz, M Bosque, G Oyarzún, D Picó, J Barahona, M Flux-dependent graphs for metabolic networks |
| title | Flux-dependent graphs for metabolic networks |
| title_full | Flux-dependent graphs for metabolic networks |
| title_fullStr | Flux-dependent graphs for metabolic networks |
| title_full_unstemmed | Flux-dependent graphs for metabolic networks |
| title_short | Flux-dependent graphs for metabolic networks |
| title_sort | flux dependent graphs for metabolic networks |
| work_keys_str_mv | AT beguerissediazm fluxdependentgraphsformetabolicnetworks AT bosqueg fluxdependentgraphsformetabolicnetworks AT oyarzund fluxdependentgraphsformetabolicnetworks AT picoj fluxdependentgraphsformetabolicnetworks AT barahonam fluxdependentgraphsformetabolicnetworks |