Mutual information (MI) as a function of number of gene pairs swapped between clusters. At each permutation, two genes are chosen at random from each of two randomly chosen clusters (there are 30 clusters in all). The genes are swapped, and the MI (between cluster membership and attribute possession) is recomputed. For convenience, the MI is shown as a fraction of its initial value. It is clear that MI decreases monotonically as the genes are swapped, illustrating that it is a good gauge of the quality of the clusters. It does not fall to zero because even with random assignment of genes to clusters, it is likely that genes will coincidentally end up in the same cluster. (Clusters taken from Tavazoie et al. 1999.)
