reactome-database

Gene enrichment analysis is performed by submitting a list of differentially expressed genes to the Reactome Analysis service for overrepresentation analysis. This identifies significantly enriched biological pathways and maps genes to specific molecular interactions within those pathways.

Querying biological pathways and molecular interactions is best handled through the Reactome REST API using the reactome2py Python package. This provides programmatic access to the Content service for data retrieval and the Analysis service for computational systems biology studies.

Yes, you can retrieve specific disease pathways and molecular entities using Python. The skill queries the Reactome REST API Content service to extract data on specific reactions, pathway information, and molecular entities relevant to disease research.

Yes, this pathway analysis approach supports expression analysis for systems biology studies. The Reactome Analysis service handles both overrepresentation and expression analysis on gene lists, enabling comprehensive computational analysis of biological pathway relationships.

Yes, you need the reactome2py package along with the requests library to access Reactome database content. These dependencies provide the programmatic interface required to query the REST API and retrieve pathway analysis data.

The limitations of using the Reactome REST API for pathway analysis include dependency on external service availability and the scope of the Reactome database itself. Data retrieval and computational analysis are constrained by the current Content and Analysis service endpoints.