Deletion

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 deletedGenes

  • deletedGenes – The list of genes removed from the model.

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)

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

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