Using only the transcription network structure information, a probabilistic model was developed that computes the probabilities with which a pair of genes responds simultaneously (SR) or differentially (DR) to a random network perturbation. Study of yeast’s transcription regulatory network in association with gene expression profiles shows that SR and DR probabilities are significantly associated with the distribution of strong co-expression. It is 100 fold more probable to observe co-expression when P(SR)»0.5 for a random perturbation of 3 transcription factors (TFs), allowing for perturbation spread until a depth of 3 connections in the regulatory network. The model also predicts that positive co-expression enhancement is related with the proportion of common TFs (number of TFs that regulate both genes in a pair divided by the total number of TFs that regulate at least one gene in the pair), and not to the absolute number. The relationship between the model derived probabilities and other graph-theoretic measures used to analyse biological networks is discussed.