Frequently Asked Questions
In order to perform pathway analysis on any of your entity lists or selected entities in GeneSpring 12.0 you require:
- A license for the Pathway Architect module (please contact GeneSpring technical support at informatics_support [at] agilent [dot] com for more details)
- Generic and organism specific interaction databases for analysis with non-GPML pathways (available to download for a number of organisms in GeneSpring from Tools > Annotations > Update Pathway Interactions)
- Metabolite and organism specific BridgeDb databases (available to download for supported organisms in GeneSpring from Tools > Annotations > Update BridgeDb)
- And most importantly pathways. GeneSpring supports pathways from the WikiPathways portal, which you can download directly in GeneSpring from Tools > Import Pathways from WikiPathways. You can also download pathways from BioCyc directly in GeneSpring from Tools > Import Pathways from BioCyc. In addition you can import pathways in the GPML, BioPAX (Level 2 and 3), and Text format.
If you downloaded any Interaction Databases in a previous version of GeneSpring, we recommend that you update them. All the Interaction Databases have been updated to include more entities and relations along with updated annotations for existing entities and relations. Obsolete entities and relations were removed. From GeneSpring 12.0 onwards, Interaction Databases are updated on a regular basis to remain up-to-date with scientific findings published through PubMed. Once such an update becomes available you will be notified the next time you start GeneSpring.
Existing pathways will not be affected during the update. Once the Interaction Databases are updated, the Update Pathways dialog will allow you to update your existing pathways by removing obsolete entities or relations and updating entities in case the name was changed.
If you are planning to use non-GPML pathways, you should have enough disk space for downloading the Interaction Databases. You can check the amount of disk space required from Annotations > Update Pathway Interactions > From Agilent Server. The amount of disk space required will be approximately three times mentioned in the update window. For example, around 7 GB of space will be required for the Human Interaction Database.
From GeneSpring 12.0 onwards, BridgeDb databases are used to match pathway entities with entities in the experiment when a direct match based on the same annotation is not possible. The BridgeDb algorithm allows GeneSpring to map entities if only differing annotations (e.g. Entrez Gene ID, Unigene ID) are available.
In the absence of a BridgeDb database for your organism, please contact technical support at informatics_support [at] agilent [dot] com.