Dataset Information

Smallbone2013 - Human metabolism global reconstruction (recon 2.1x)

ABSTRACT: Smallbone2013 - Human metabolism global reconstruction (recon 2.1x) Recon 2.1x. This model is described in the article: Striking a balance with Recon 2.1 Kieran Smallbone Molecular Networks (q-bio.MN) Abstract: Recon 2 is a highly curated reconstruction of the human metabolic network. Whilst the network is state of the art, it has shortcomings, including the presence of unbalanced reactions involving generic metabolites. By replacing these generic molecules with each of their specific instances, we can ensure full elemental balancing, in turn allowing constraint-based analyses to be performed. The resultant model, called Recon 2.1, is an order of magnitude larger than the original. This model is hosted on BioModels Database and identified by: MODEL1311110001 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Kieran Smallbone

PROVIDER: MODEL1311110001 | BioModels | 2005-01-01

REPOSITORIES: BioModels

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			Action	DRS
	MODEL1311110001?filename=MODEL1311110001-biopax2.owl	Owl
	MODEL1311110001?filename=MODEL1311110001-biopax3.owl	Owl
	MODEL1311110001?filename=MODEL1311110001.m	Other
	MODEL1311110001?filename=MODEL1311110001.pdf	Pdf
	MODEL1311110001?filename=MODEL1311110001.png	Other

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Publications

Metabolism of vitamin D3 by cytochromes P450.

Sakaki Toshiyuki T Kagawa Norio N Yamamoto Keiko K Inouye Kuniyo K

Frontiers in bioscience : a journal and virtual library 20050101

The vitamin D3 25-hydroxylase (CYP27A1), 25-hydroxyvitamin D3 1alpha-hydroxylase (CYP27B1) and 1alpha,25-dihydroxyvitamin D3 24-hydroxylase (CYP24A1) are members of the cytochrome P450 superfamily, and key enzymes of vitamin D3 metabolism. Using the heterologous expression in E. coli, enzymatic properties of the P450s were recently investigated in detail. Upon analyses of the metabolites of vitamin D3 by the reconstituted system, CYP27A1 surprisingly produced at least seven forms of minor metabo ...[more]

PMID: 15574355

Publication: 1/2787

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Project description:Thiele2013 - Human metabolism global reconstruction (Recon 2) Community-driven global reconstruction of human metabolism (version 2.02). This model is described in the article: A community-driven global reconstruction of human metabolism. Thiele I, et al. Nature Biotechnology Abstract: Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ~2x more reactions and ~1.7x more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/. This model is hosted on BioModels Database and identified by: MODEL1109130000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:IntroductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.ObjectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.MethodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.ResultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.ConclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001).

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