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Open Access Research article

A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress

Fiona Achcar12, Jean-Michel Camadro2 and Denis Mestivier1*

Author Affiliations

1 Modelling in Integrative Biology, Institut Jacques Monod - UMR7592 - CNRS - Univ. Paris-Diderot, Paris, France

2 Mitochondria, Metals and Oxidative Stress, Institut Jacques Monod - UMR7592 - CNRS - Univ. Paris-Diderot, Paris, France

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BMC Systems Biology 2011, 5:51  doi:10.1186/1752-0509-5-51

Published: 13 April 2011

Additional files

Additional file 1:

The WT model as used for the simulations. The WT model as used for the simulations. Lines beginning with "%"are comments. Each reaction of the model is followed by its weight (separated by a tab spacing). Elements with name beginning with "#"are constant elements. The cellular location of an element is separated from the element name by "::". Reactions may take four main forms: 1) A + C = > B + C (A gives B using C) 2) A = [C] = > B (different formalism for the same reaction) 3) A = > (A is degraded) 4) A < = > B (reversible reaction).

Format: TXT Size: 63KB Download file

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Additional file 2:

Sensitivity analysis of the outputs of the model (PoP at steady state) when the weights of the reactions are modified.

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This file can be viewed with: Adobe Acrobat Reader

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Additional file 3:

PoP of elements in simulated mutants versus phenotypes manually curated by SGD in the corresponding mutants. The spreadsheet le is composed of 6 sheets (one for each type of phenotype). Each sheet contains the simulated PoP on the left and the SGD phenotypes on the right panel (as they appeared in the original file). One phenotype can be represented by multiple lines when multiple articles reproduced it. ND = no difference between the WT and the mutant were observed. Red cells mean that the differences observed in the in silico mutant is not in agreement with the experimental observations. Yellow cells mean that the differences observed in the in silico mutant is not in agreement with the experimental observations as referenced by SGD but that a more recent publication is in agreement with our simulations (the happened once, see text for more details). Columns in the "SGD Reference" section: - Reference (SGD REF Required, PMID optional) -PMID: #### SGD REF: #### (separated by pipe)(one reference per row) - Experiment Type (Mandatory) -The method used to detect and analyze the phenotype - Mutant Type (Mandatory) -Description of the impact of the mutation on activity of the gene product - Allele (Optional) -Allele name and description, if applicable - Strain Background (Optional) -Genetic background in which the phenotype was analyzed - Phenotype (Mandatory) -The feature observed and the direction of change relative to wild type - Chemical (Optional) -Any chemicals relevant to the phenotype - Condition (Optional) -Condition under which the phenotype was observed - Details (Optional) -Details about the phenotype - Reporter (Optional) -The protein(s) or RNA(s) used in an experiment to track a process

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This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

List of the elements of the model that are always "ON" during the simulations.

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Additional file 5:

The WT model implementing the first hypothesis. The WT model implementing the first hypothesis explored in "Results/Exploration of alternative hypothesis: an example of a use of the model".

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Additional file 6:

Clustering presented in Figure 6. cdt file (readable using Java TreeView or a spreadsheet program) of the clustering presented in Figure 6.

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