reactome-database

Pathway enrichment analysis on a gene expression list is performed by submitting identifiers to the Reactome AnalysisService to obtain statistically ranked pathways with p-values and FDR. You can run overrepresentation analysis from gene or protein identifier lists for immediate enrichment results.

Reactome pathway hierarchy exploration works by querying the ContentService API to retrieve pathway metadata, participating physical entities, and related molecular interaction information using stable IDs. This allows you to map genes or proteins directly to their corresponding curated human biological pathways.

You can submit a TSV expression matrix to the Reactome AnalysisService to identify relevant pathways and generate Pathway Browser URLs. The service processes the expression-based payload and returns an analysis token for result retrieval and sharing within its validity window.

You need the requests library to make REST calls to Reactome's ContentService and AnalysisService endpoints from Python scripts. This dependency is required to handle text/plain identifier payloads, submit TSV expression matrices, and retrieve data using the returned analysis tokens.

The limitation of using Reactome analysis tokens for pathway retrieval is that tokens are only valid for a specific time window. You must use the returned analysis tokens to fetch expression-based or enrichment results from the AnalysisService before their validity expires.