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. When you complete the MOA workflow, the Pathway List opens in the GeneSpring Desktop in the Pathway View.
The Pathway View consists of:
- the Pathway View Toolbar – this toolbar contains additional icons to the main menu that are specific to the functionality of the Pathway View, for example changing an interpretation or entity list.
- the Pathway List Panel -a table illustrating the number of matching entities with the chosen entity lists and associated p-values (not available for Metabolomics experiments). You can select the pathway you would like to visualize in the Pathway Viewer here.
- the Pathway Viewer – the selected pathway (from the pathway list panel) is displayed in this area; experimental data associated with the matching entities is displayed here in the form of Heatstrips.
- the Filter Panel – using this panel you can filter the list of pathways in the pathway list panel by the number of matches with the chosen entity lists and associated p-values.
- the Heatmap – this table lists all the pathway entities and the experimental data for matching entities with the selected pathway in a Heatmap fashion. There is a separate table for each of the two input experiments.
Use the Filter Panel options to identify significant pathways for the chosen entity lists.