The Gene Tree is drawn to the left of the Heat Map display and shows the clustering of genes as calculated by the selected clustering method.
Sorting of the gene display is determined by the Clustering Method. In general, similar genes appear closer together, and the level of similarity is expressed both by color and by the tree on the left. In some cases, the similarity metric and/or the structure of the tree force ArrayStar to make more arbitrary placement decisions. This happens, for example, at the edges of groups which cannot be placed near other similar genes, or between genes in a k-Means clustering group. In such cases, ArrayStar attempts to follow the ordering of the input files.
There are two modes in the Heat Map Gene Tree:
•While in selection mode, click on a node in the tree to select that sub-tree of genes.
•While in zoom-in mode, click on a node in the tree to zoom-in so that only the sub-tree you clicked on is displayed.
When a node in the Gene Tree is selected, you can use the left and right arrow keys on your keyboard to navigate through the tree. The left arrow key moves from the currently selected node to its parent node. The right arrow key moves from the currently selected node to the previously selected node.
The Gene Tree can also identify the sub-tree that includes all of the genes you have currently selected on the Heat Map. With your genes of interest selected on the Heat Map, press the left arrow key on your keyboard. The parent node containing all of the currently selected genes will be identified, and the entire sub-tree will be selected.
Beneath the Gene Tree is a splitter tool that allows you to select tree nodes based on their distance metrics, as computed during clustering:
Click and drag the white triangle above the scale to select the tree nodes you desire.
Or use the left and right arrows on either side of the value to increase or decrease the distance value. Doing so will increase or decrease the value enough so that at least one node is either added or removed from the current selection.
All of the nodes in the tree with a distance less than or equal to the value specified will be selected.
Note: Splitting the gene tree creates a new global gene selection within your project.
Once you change your selection in the Heat Map, you can restore the previous split tree selection by clicking directly on the distance value.
After splitting the gene tree, you may click on the link Show a Line Graph Thumbnails view of this clustering result in the Info Pane of the Heat Map to view the groups into which the tree was split.