Frequently Asked Questions
A maximum of two experiments can be selected 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
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.
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.
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.
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.
GeneSpring applies Homologene translation (for genes) for matching experiment entities with pathway entities when the selected pathway organism is different from the experiment organism.
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.