Working with Sets of Spots

In the terminology of the TIGR Multiple Experiment Viewer (MeV), a cluster can be any set of expression profiles or samples (gel images). You can create new clusters by choosing Store Cluster in many displays of analysis results.

Storing a cluster of expression profiles: In a clustering display, select a branch of the dendrogram by clicking inside it. The corresponding expression profiles will be selected. Now right-click and select Store Cluster. The new cluster will be shown in the Cluster Manager under Gene Clusters. In a hierachical clustering, you can select a whole branch of the dendrogram by clicking inside it.

Storing a sample cluster: In a hierarchical clustering, click on a part of the dendrogram for samples (column dendrogram), maybe you want to select a set of replicate gel images. Note how columns are selected in the heatmap display. Now right-click and select Store Cluster. A dialog opens that lets you define a name, comment and color of the cluster. Click the OK button. The new sample cluster should now be visible in the Cluster Manager. By default, the color of the cluster will now be shown on top of the heatmap column, and in other displays such as PCA (for samples).

In the Cluster Manager you can change any attribute, e.g. cluster colors, or whether the color should be used in displays. Note that clusters may overlap, but only one cluster's color will be used in displays.

Cluster A	Cluster B
Intersection of A and B	Union of A and B	XOR of A and B

When you have multiple clusters you can create new clusters that are combinations of selected ones:

• Intersection: The new cluster contains only expression profiles that are present in each of the selected clusters. This extracts the overlap of two or more clusters.
• Union: The new cluster contains all expression profiles that were present in any of the selected clusters. This merges clusters.
• XOR: The new cluster contains only expression profiles that are found exclusively in one of the selected clusters. This extracts spots that are specific to either one of the clusters.

In the Cluster Manager, select the clusters you want to combine. Right click, then select the operation you want to perform from the Cluster Operations submenu.

Statistical Analysis is Integrated with Image Analysis

When you select one or more spots in a heatmap display, the selection will be immediately visible in other parts of Delta2D, such as the dual view, or the gel image regions view. You can extend the selection to a range of rows by holding down the Shift-key while clicking on the end of the range. You can add or remove a single row by holding down the Control key while clicking on it.

If you have organized spots of interest in the Cluster Manager, you can use these directly in Delta2D. Just right click on a cluster and choose Select in Delta2D this will select the expression profiles in the cluster throughout all parts of Delta2D.

Getting a spot album of relevant spots

Using Delta2D's Spot Album Report it is easy to show snapshots of the statistically significant spots you have found. All you have to do is mark these spots in the Delta2D project.

Part of a spot album for differentially expressed spots.

Make sure you have selected the spots of interest. Switch to the Statistics tab of the Quantitation Table and choose Mark > Unmark all spots to unmark all spots that you might have marked previously. Then choose Mark > Mark selected spots. Then switch to the Project Manager and choose Reports > Spot Album. Note that the spot album may by quite large, as there is one image for each spot on each image. You can restrict the album to a single group by clicking on the "hide others " link in the group caption.