reactome-database

Gene enrichment analysis identifies affected biological pathways by submitting gene or protein lists to the Reactome Analysis Service for over-representation computation. This helps interpret RNA-seq differentially expressed gene lists by highlighting significantly enriched pathways.

Query biological pathways by stable IDs or keywords via the Reactome Content Service REST API to retrieve detailed pathway and reaction information. You can search for specific terms like apoptosis in humans and retrieve participating entities and molecules.

Reactome pathway analysis is the process of querying a biological pathway database to retrieve reaction details and perform gene list enrichment. You need it for systems biology research to identify significantly enriched pathways from gene lists, such as those from RNA-seq experiments.

Accessing the Reactome REST API requires the requests dependency to query the Content Service and Analysis Service. Ensure the requests package is installed in your environment to retrieve pathway data and compute enrichment results.

Yes, you can retrieve participating entities and molecules for a specific biological pathway by querying the Reactome database with a stable ID. The Content Service returns detailed information about the molecules involved in the queried pathway.

Using REST API queries for Reactome pathway data limits you to the endpoints provided by the Content Service and Analysis Service. Over-representation analysis results depend on the accuracy of the submitted gene lists and the pathway database's current coverage.