Deletion¶
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deleteModelGenes
(model, geneList, downRegFraction)[source]¶ Deletes one or more genes and constrain the reactions affected to zero and appends ‘_deleted’ to the gene(s)
Usage
[model, hasEffect, constrRxnNames, deletedGenes] = deleteModelGenes(model, geneList, downRegFraction)Input
- model – COBRA model with the appropriate constrains for a particular condition
Optional inputs
- geneList – List of genes to be deleted (Default = all genes in model)
- downRegFraction – Fraction of the original bounds that the reactions corresponding to downregulated genes will be assigned (Default = 0 corresponding to a full deletion)
Outputs
- model – COBRA model with the selected genes deleted
- hasEffect – True if the gene deletion has an effect on the model
- constrRxnNames – Reactions that are associated to the genes in geneList
- deletedGenes – The list of genes removed from the model.
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doubleGeneDeletion
(model, method, geneList1, geneList2, printLevel)[source]¶ Performs double gene deletion analysis using FBA, MOMA or linear MOMA
Usage
[grRatioDble, grRateKO, grRateWT] = doubleGeneDeletion(model, method, geneList1, geneList2, printLevel)Input
- model – COBRA model structure
Optional inputs
- method – Either ‘FBA’ (default), ‘MOMA’ or ‘lMOMA’
- geneList1 – List of query genes to be deleted (default = all genes)
- geneList2 – List of target genes to be deleted (default = geneList1)
- printLevel – Level of verbose output (default = 0)
Outputs
- grRatioDble – Computed growth rate ratio between double deletion strain and wild type
- grRateKO – Double deletion strain growth rates (1/h)
- grRateWT – Wild type growth rate (1/h)
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singleGeneDeletion
(model, method, geneList, verbFlag, uniqueGene)[source]¶ Performs single gene deletion analysis using FBA, MOMA or linearMOMA
Usage
[grRatio, grRateKO, grRateWT, hasEffect, delRxns, fluxSolution] = singleGeneDeletion(model, method, geneList, verbFlag)Input
- model – COBRA model structure including gene-reaction associations
Optional inputs
- method – Either ‘FBA’, ‘MOMA’ or ‘lMOMA’ (Default = ‘FBA’)
- geneList – List of genes to be deleted (default = all genes)
- verbFlag – Verbose output (Default false)
- uniqueGene – Run unique gene deletion (default = 0).
Outputs
- grRatio – Computed growth rate ratio between deletion strain and wild type
- grRateKO – Deletion strain growth rates (1/h)
- grRateWT – Wild type growth rate (1/h)
- hasEffect – Does a gene deletion affect anything (i.e. are any reactions removed from the model)
- delRxns – List of deleted reactions for each gene KO
- fluxSolution – FBA/MOMA/lMOMA fluxes for KO strains
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singleRxnDeletion
(model, method, rxnList, verbFlag)[source]¶ Performs single reaction deletion analysis using FBA, MOMA or linearMOMA
Usage
[grRatio, grRateKO, grRateWT, hasEffect, delRxn, fluxSolution] = singleRxnDeletion(model, method, rxnList, verbFlag)Input
- model – COBRA model structure including reaction names
Optional inputs
- method – Either ‘FBA’, ‘MOMA’, or ‘lMOMA’ (Default = ‘FBA’)
- rxnList – List of reactions to be deleted (Default = all reactions)
- verbFlag – Verbose output (Default = false)
Outputs
- grRatio – Computed growth rate ratio between deletion strain and wild type
- grRateKO – Deletion strain growth rates (1/h)
- grRateWT – Wild type growth rate (1/h)
- hasEffect – Does a reaction deletion affect anything
- delRxn – Deleted reaction
- fluxSolution – FBA/MOMA/lMOMA fluxes for KO strains