There could be two reasons for this result:
GeneSpring could neither find direct matches (same annotation available for both experiment entities and pathway entities) nor indirect matches using the BridgeDb algorithm to map differing annotations.
- To inspect available entities in your experiment, right-click the input entity list in the Experiment Navigator and select Inspect List. The Entity List Inspector that opens contains an additional column for each available annotation.
To inspect annotations for the pathway entities, right-click the pathway list in the Experiment Navigator and select Inspect Pathway List. Double-click the row corresponding to the pathway of interest in the Pathways spreadsheet to open a Pathway Inspector. Available annotations are listed in separate columns.
There are no matching entities between the input entity list and the pathways.
- To see if there are any matching entities with an open pathway for this experiment, look at the corresponding Heatmap table. If that table contains data for any of the listed pathway entities then at least one of the entity lists in your experiment has matching entities with this pathway.
- To see if another entity list in your experiment has matching entities with an open pathway, simply click on that entity list in the Experiment Navigator. Matching entities will appear highlighted by a light blue border in the Pathway Viewer. Or, to visualize matching entities more prominently, you can select a different entity list using the Choose another Entity List icon from the Pathway View Toolbar. Any matching entities between the open pathway and the new entity list will appear colored in yellow by default. However, the resulting changes from changing the entity list is not reflected in the pathway list panel and is not saved when closing the Pathway View for this pathway list.