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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2012
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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. |
format | Online Article Text |
id | pubmed-4053740 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT vitkinedward mirageafunctionalgenomicsbasedapproachformetabolicnetworkmodelreconstructionanditsapplicationtocyanobacterianetworks AT shlomitomer mirageafunctionalgenomicsbasedapproachformetabolicnetworkmodelreconstructionanditsapplicationtocyanobacterianetworks |