For the two gene-gene relationship networks YkR and YkP, Bayesian inference of the parameters of the p1-model for an undirected network was applied. We used WinBUGS for scripting this inference and our scripts were inspired by Adams et al. [30]. We used 6000 MCMC iterations for parameter estimation with the first 5000 as ‘burn-in’. All the parameters in the p1-model appeared to converge rapidly during the burn-in iterations (data not shown). With the above settings, we estimated the posterior probabilities of each edge (gene-gene relationship) Pr(Yij1=1) in the two networks YkR and YkP. For each edge, the proportion of the 1000 sampled networks containing the edge was considered as the posterior probability of that edge being present in the network.