KB005490: To compare two entity lists of different technologies - GeneSpring GX. 

You could compare the entity lists of different technologies present in a project by using a ‘Venn Diagram’. If you have gene lists in different projects,  add the experiment that you are interested into the current project by following the steps below:
GeneSpring GX10 Menu Bar -> Project ->Add Experiment
Now you will see the two experiments in a project.
To perform Venn diagram, both the experiments should be open, then launch venn diagram (GeneSpring GX10 Menu Bar -> View -> Venn Diagram). Choose the desired 2 gene lists which you want to compare. By default it would show you a Venn diagram with 3 circles, you could restrict it to 2 circles (i.e. your 2 gene lists) by right clicking on the Venn diagram -> Properties. Here,  “Choose Entity Lists” Select Entity List with just “EL1 and EL2” and click OK. This would restrict the view to just the 2 gene lists.
To create an entity list, highlight the region of interest in the Venn Diagram view and select the fourth icon in this window ‘Create Entity List’. The entity list created would get saved under “All Entities” in the active experiment.