Q7. How does GeneSpring enable MOA from experiments and pathways with different organisms?

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

Q6. I have two pathway lists. How can I find the pathways that are common to both lists?

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.

Q5. How can I export the pathway list table in an open pathway list from GeneSpring?

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.

Q4. What is the result of an MOA workflow?

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.

Q3. Can I save only the pathways of my interest in the Multi-Omic Analysis 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.

Q2. What are the pre-requisites for Multi-Omic Analysis?

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


Q1. How many experiments can be used for a Multi-Omic Analysis?

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

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