OptFlux allows the simulation of mutants including over/under expression of genes or reactions.
The user interface for these operations is similar to the ones for reaction and gene deletions.
The main difference, in this case, lies in the need of defining a value for relative expression for each gene or reaction selected. In this case, values over 1 represent overexpression, i.e. the value of the flux (in reaction simulation), or of the gene expression in gene simulation), are constrained to values greater than the wild type by the defined factor. In the case this value is less than 1, an under expression is defined, i.e the flux/expression value is constrained to be smaller than the wild type.
It should be mentioned that knockouts are represented by the value 0, while the value 1 represents no changes in the flux/expression value.
By accessing the "Under-Over" Expression option in the OptFlux menu or by right clicking a Project or Model it's possible to select Under-Over expression simulation for genes and reactions.
Like stated above the user interface for both operations are similar.
For the "Gene" option, the selection of genes and specification of expression values for those particular genes is possible.
The "Reaction" option will allow the user to under/over express the reactions directly
From here on the same principles of the other simulation methods are applied:
Choose the Project to do the simulation.
2.Select Genes/Reactions to under/over express
Choose the gene/reactions to under/over express and specify the expression value for them.
3.Objective Function Configuration
In the objective function section, you have select a reaction (typically the biomass/ growth reaction, selected by default) to maximize or minimize the corresponding flux.
4.Select the simulation method
Select one of the multiple simulation methods available.
4.Select Environmental Conditions
If you have created environmental conditions you can select them to be used as constraints in the optimization. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.
And that's all!! You can press OK and the results will be loaded into the clipboard.