Pathway Studio Enterprise offers a software solution that is fully scalable from a single user to multiple-users located at single or multiple sites. Pathway Studio Enterprise offers server-side applications in addition to the client-side applications that Pathway Studio Desktop offers. Server applications take advantage of server architecture to offer more computationally intense algorithms. In addition the Enterprise edition offers access to MedScan Enterprise, which is MedScan without limitations on the number of abstracts that can be scanned in a single query.

The Enterprise edition comes with a Web Client that accesses the database server and server applications. The Web Client can be used for analysis from any PC in your organization, providing simplicity in data browsing.

Pathway Studio Enterprise offers methods in addition to measurement of Differential Expression for the analysis of microarray gene expression data. Pathway Studio Enterprise offers several unique advantages to Gene Set Enrichment Analysis (GSEA) among them being an ability to build custom ontologies as well as edit and enhance existing public ontologies. This can be done both by creating new groups unavailable in public classifications as well as adding or curating proteins in the groups.  MedScan can also be used to mine the literature to create custom pathways and pathway components that can be included in the GSEA analysis.