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Transcriptome analysis of zebrafish yquem/urod mutant

ABSTRACT: Zebeafish yquem harbors a mutation in the gene encoding uroporphyrinogen decarboxylase (UROD), the fifth enzyme in heme biosynthesis, and was established as a vertebrate model for human hepatoerythropoietic porphyria (HEP). In an effort to investigate the unknown aspects of UROD deficiency pathogenesis, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in yquem/urod (-/-) and wild type control zebrafish larvae. Keywords: zebrafish, Danio rerio, wild-type yquem, urod, porphyria

ORGANISM(S): Danio rerio

PROVIDER: GSE8651 | GEO | 2007/08/03

SECONDARY ACCESSION(S): PRJNA101843

REPOSITORIES: GEO

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Project description:Bekaert2012 - Reconstruction of D.rerio Metabolic Network Danio rerio metabolic model accounting for subcellular compartmentalisation (ZebraGEM) This SBML representation of the D. rerio (zebrafish) metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org ). This model is described in the article: Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation. Bekaert M. PLoS One. 2012;7(11):e49903. Abstract: Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture. This model is hosted on BioModels Database and identified by: MODEL1204120000 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID: 20587024 . 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>http://creativecommons.org/publicdomain/zero/1.0/] for more information.

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Transcriptome analysis of zebrafish yquem/urod mutant

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