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MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

Genome-scale metabolic network reconstructions are considered a key step in quantifying the genotype-phenotype relationship. We present a novel gap-filling approach, MetabolIc Reconstruction via functionAl GEnomics (MIRAGE), which identifies missing network reactions by integrating metabolic flux an...

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Detalles Bibliográficos
Autores principales: Vitkin, Edward, Shlomi, Tomer
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053740/
https://www.ncbi.nlm.nih.gov/pubmed/23194418
http://dx.doi.org/10.1186/gb-2012-13-11-r111
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author Vitkin, Edward
Shlomi, Tomer
author_facet Vitkin, Edward
Shlomi, Tomer
author_sort Vitkin, Edward
collection PubMed
description Genome-scale metabolic network reconstructions are considered a key step in quantifying the genotype-phenotype relationship. We present a novel gap-filling approach, MetabolIc Reconstruction via functionAl GEnomics (MIRAGE), which identifies missing network reactions by integrating metabolic flux analysis and functional genomics data. MIRAGE's performance is demonstrated on the reconstruction of metabolic network models of E. coli and Synechocystis sp. and validated via existing networks for these species. Then, it is applied to reconstruct genome-scale metabolic network models for 36 sequenced cyanobacteria amenable for constraint-based modeling analysis and specifically for metabolic engineering. The reconstructed network models are supplied via standard SBML files.
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spelling pubmed-40537402014-06-13 MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Vitkin, Edward Shlomi, Tomer Genome Biol Method Genome-scale metabolic network reconstructions are considered a key step in quantifying the genotype-phenotype relationship. We present a novel gap-filling approach, MetabolIc Reconstruction via functionAl GEnomics (MIRAGE), which identifies missing network reactions by integrating metabolic flux analysis and functional genomics data. MIRAGE's performance is demonstrated on the reconstruction of metabolic network models of E. coli and Synechocystis sp. and validated via existing networks for these species. Then, it is applied to reconstruct genome-scale metabolic network models for 36 sequenced cyanobacteria amenable for constraint-based modeling analysis and specifically for metabolic engineering. The reconstructed network models are supplied via standard SBML files. BioMed Central 2012 2012-11-29 /pmc/articles/PMC4053740/ /pubmed/23194418 http://dx.doi.org/10.1186/gb-2012-13-11-r111 Text en Copyright © 2013 Vitkin and Shlomi; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Vitkin, Edward
Shlomi, Tomer
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
title MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
title_full MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
title_fullStr MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
title_full_unstemmed MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
title_short MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
title_sort mirage: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053740/
https://www.ncbi.nlm.nih.gov/pubmed/23194418
http://dx.doi.org/10.1186/gb-2012-13-11-r111
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