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Gene Set Enrichment and Pathway Analysis

Differences between pathway tools and network tools

For the purposes of this guide, the term "pathway visualization tools" (or "pathway tools") is used for tools that can be used to visualize data for canonical or curated biological pathways from biological pathway databases or resources, while "network visualization tools" is a term used for creating custom networks from biological data (or any network data). Networks may be created using canonical pathways to inform their connections, but a network can be created from any set of data with connections between objects, while pathways describe already established or known biological systems interactions.

In some cases, there is some overlap between pathway visualization sites and sites listed in the gene set enrichment page of this guide. For example, Reactome is both a pathway visualization site browsing pathways or for a list of user-supplied genes, but it does also allow for upload of experimental data results (with more than one sample per file) for enrichment analysis.

Pathway Visualization Tools

Network Visualization Tools