Gene Set Enrichment and Pathway Analysis

Galter Health Sciences Library has canceled its license for GeneGO MetaCore, so what can researchers use in its place?

We have a few free options to suggest for the primary functions that MetaCore served: gene set enrichment analysis and pathway/network building.

There is no single free option that has as many features as licensed pathway analysis products such as MetaCore, Ingenuity IPA, etc. This is the reason why licensed tools are so costly: they combine two computationally intensive tasks into a single package, and content is reviewed and curated by subject experts.

Users can find a free tool that serves their needs in most cases, or may need to combine the functionality of a couple of different tools. Some of these tools are simple, web-hosted interfaces, while others require download of the software to the user's computer to run the package.

This is not meant to be an exhaustive list of pathway or enrichment tools. It is merely a sampling of free options to help users perform pathway and biological network analysis on their genes of interest.

The pages in this guide are divided into categories:

• Resources for gene set enrichment analysis
• Pathway databases - for exploring known, curated biological pathways
• Pathway and network visualization resources - for visualizing your list of genes/objects in the context of known biological pathways, or creating custom networks built from your list
• All-in-one resources - for combining enrichment, pathway, and network visualizations