The model and its variants have a number of simplifying assumptions.  Three of them are listing below.
#The organisms are modeled as gene regulatory networks.  The models assume that gene expression is regulated exclusively at the transcriptional level;
#The product of a gene can regulate the expression of (be a regulator of) that source gene or other genes.  The models assume that a gene can only produce one active transcriptional regulator;
#The effects of one regulator are independent of effects of other regulators on the same target gene.