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.