Next, we selected genes for linkage analysis: from each cluster select the top N = 28 enriched genes (based on pre-calculated enrichment score), perform initial clustering using linkage (Euclidean distance, Ward in MATLAB), and cut the tree based on distance criterion 50. This clustering aimed to capture the coarse structure of the hierarchy. For each of the resulting clusters, we calculated the enrichment score as the mean over the cluster divided by the total sum and selected the 1.5N top genes. These were added to the previously selected genes.
