GalterGuides: Gene Set Enrichment and Pathway Analysis: Pathway Databases

Pathway Database Resources

This is a sampling of some of the most-used pathway databases. It is not an exhaustive list, but rather a select list of the most comprehensive databases for biological pathways. Many of these databases have integrated visualization functionality that allows you to view your objects of interest in functionally connected pathways.

KEGG: Kyoto Encyclopedia of Genes and Genomes
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

The main entry point to KEGG is the KEGG2 link on this page, but you can access KEGG's many tools from the home page, as well.
Reactome
Reactome's web interface accepts both gene lists and experimental data uploads, and performs enrichment analyses of your uploaded objects, outputting a list and visual representation of canonical pathways represented in your list. It also has a desktop application for integration with Cytoscape, so you can create networks based on your interaction analyses.
PANTHER
The PANTHER database and PANTHER Pathway consists of over 177, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. The web-based service allows for upload of protein lists for pathway discovery, with many species to use for background.
IntAct
IntAct is a web-based service for discovery of molecular interactions among biological objects. In addition to biological pathway interactions in several species, IntAct has curated several interactome datasets for specific diseases.
PharmGKB
PharmGKB is an online pharmacogenomics knowledge base which has over 150 curated pathways and hundreds of drug annotations. It is specifically intended for discovery of drug interactions within biological pathways.
WikiPathways
For those who wish to share their own annotated pathways, or participate in community discussion and curation of pathways, WikiPathways provides a forum for upload, annotation, and discussion of user-supplied pathways.