Deletion

deleteModelGenes(model, geneList, downRegFraction)

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)

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)

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)

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