How do I find the subset of genes in an ontology group that identified in a GSEA analysis or a Fisher’s Exact test that are included in my experimental data list?

To find the overlap between the members of a group and the proteins in an experimental data set, do the following:

1.       Right click on the group and select “Copy contents”.  This will copy the entities in the group to the clipboard. 

2.       Next, open a new pathway and select Edit > Paste.  The entities from the clipboard are now displayed in a Pathway View.

3.       In the Experiment View, select the proteins of interest. 

4.       The proteins selected in the experiment view are now selected (blue edge) in the Pathway View.

Note:  You can then delete the proteins that are not selected in the Pathway View by:  Select >Invert Selection, then Edit > Remove.