How to do a over/under expression simulation
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 definin! 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.