When you right-click on a cluster in the main graph, you can show the cluster in the Closest Clusters window. It will appear on the left side of the window (Part A in the following figure). The clusters on the right (Part B) are the ones closest to the cluster in Part A, sorted by distance between average profiles.

   In the example in the following figure, the selected cluster is the cluster with ID 1. Its nearest neighbor (the cluster with average profile most similar to that of ID1) is the cluster of ID 6, the second-nearest is the cluster of ID 2. You can change the selected cluster by directly clicking on the C control. You can also scan all the closest neighbors by using the D control.

Closest cluster window 1

    The selected cluster is displayed using gray profiles (Part A), while its average is drawn with a thick light cyan line (E). The profiles in the closest clusters are displayed in blue with their average colored in yellow (F and G). For facility of comparison, the average of the selected cluster is displayed in light cyan on all graphs (E), which shows in a very clear way the differences between the selected cluster and the other clusters.

     The distance of the average profile of a cluster to the selected one is displayed in blue on the top of each graph. In the Figure 1 the distance between the cluster with ID 1 and the cluster with the ID 6 is 0.110, and the distance between cluster with ID 1 and cluster with ID 2 is 0.252.
The controls in the bottom left part of the window (H) are used to set how many clusters should be displayed.

    You can click on a profile to compare its distance to each group, as illustrated in the following figure.

Closest cluster window 2

    The selected profile is displayed in green in its own cluster, and is displayed in red in the other graphs. The distance between the selected profile and the average of the cluster is displayed in green or red depending on the fact that the profile is or is not in the cluster.

    In this example, the selected gene is "cfos2". The distance between the profile of "cfos2" and the average profile of its cluster (ID1) is 0.086, while the distance between the gene's profile and the average profile of cluster with ID 6 is 0.185.

    This view is very useful for assessing the differences between clusters on the basis of the profiles of the genes in each of them.