reactome-database

Pathway enrichment analysis identifies which Reactome pathways are overrepresented in your gene list. Use the Analysis Service via the helper script—pass your gene list (JSON or TSV format) to run overrepresentation analysis, which returns statistical significance scores and matched pathways with token-based result retrieval.

Yes. The Reactome2py Python client wraps the REST API to query the Content Service, retrieving pathway participation data and entity details for genes across species. Map genes by querying pathway membership or entity information endpoints directly.

The Skill accepts JSON and TSV formats for gene and expression datasets. Results are returned in JSON with token-based retrieval—tokens expire after seven days, so plan data export accordingly.

The Content Service supports cross-species pathway queries. Use the helper script or Python client to retrieve pathway info and gene-to-pathway mappings by species identifier, enabling comparative analysis across organisms.

Yes. The Analysis Service includes expression analysis functionality alongside overrepresentation analysis. Submit expression datasets with your gene list to correlate expression patterns with pathway participation.

Prepare a gene or protein list in JSON or TSV format. The Skill uses the requests library to communicate with Reactome REST endpoints, so internet access and valid gene identifiers are prerequisites; no additional bioinformatics tools are required.