reactome-database

Pathway enrichment analysis on a gene list is performed by submitting identifiers to the Reactome Analysis Service to obtain enriched pathways, result tokens, and browser URLs. It supports overrepresentation and expression analyses.

Reactome pathway analysis accepts gene identifiers in multiple formats, including UniProt, gene symbols, Ensembl, and Entrez. The service processes these supported IDs and returns structured JSON results.

The Reactome Content Service retrieves pathway data by querying its REST API to fetch pathway information, participating entities, and pathway structures, returning the results in a structured JSON format.

You can query Reactome REST APIs using Python through the reactome2py package, which wraps API calls for easier scripting. It requires the requests library to handle interactions with the Content and Analysis Services.

The best way to programmatically map genes to biological pathways is using the Reactome Analysis Service API. It processes submitted gene lists to perform overrepresentation analysis and returns structured JSON mapping genes to pathways.

Yes, you need the requests library installed as a dependency to run reactome2py and execute pathway analysis. It handles the HTTP requests required to communicate with the Reactome REST APIs.