The phenotype of each individual is modeled as the gene expression pattern at time . It is represented by a state vector  in this model.
whose element  denotes the expression state of gene i at time t.  In the original Wagner model,
where 1 represents the gene is expressed while -1 implies the gene is not expressed.  The expression pattern can only be ON or OFF.  The continuous expression pattern between -1 (or 0) and 1 is also implemented in some other variants.