There could be two reasons for this result:

GeneSpring applies Homologene translation (for genes) for matching experiment entities with pathway entities when the selected pathway organism is different from the experiment organism.

You can create a Venn Diagram to illustrate common pathways. Select Pathway List from the Venn Diagram icon drop-down list   in the main toolbar, or select View > Venn Diagram > Pathway List from the main menu.

You can export a pathway list table in three different formats: Image, HTML, Text. Right-click the pathway list table at the top left of the Pathway View and select the desired option from the Export As submenu. Please note that exporting the table as an Image, or HTML only exports the visible pathway list panel area, while exporting it as a Text file exports the contents of the pathway list panel as a table.

The result of an MOA workflow is an MOA experiment, which is saved in open project. An MOA experiment contains the input entity lists that you selected during the MOA workflow and an object referred to as Pathway List. A Pathway List resulting from an MOA workflow contains all the pathways (that were previously imported into GeneSpring) of the selected pathway type and organism that were chosen in Step 1 of 4 of the MOA workflow.

Yes, you can custom save selected pathways in Step 3 of 4 of the Multi-Omic Analysis workflow. The selected pathways are saved as a pathway list in a new MOA experiment, which is saved in the same project as the two input experiments.

For running the Multi-Omic Analysis workflow you require:

• The two selected experiments present in the same project
• Pathways and/or Literature Derived Networks for the chosen pathway organism
• BridgeDb databases for metabolites and all the relevant organisms
• Annotations for the entities in the experiment
• Interaction Databases for all the relevant organisms, if you want to include non-GPML pathways in the analysis

A maximum of two experiments can be selected for Multi-Omic Analysis.