Reactome GSEA Service

The Reactome GSEA service performs GSEA enrichment analysis on an expression dataset against the Reactome Pathways Gene Set.

This is a REST service with the analyse POST` method. The request body is a list consisting of [symbol, value] records, where:

• symbol is the gene symbol

• value is the rank value, e.g. fold change or p-value

Optional query parameters include the following:

• nperms: number of permutations

• dataSetSizeMin: minimum gene set size

• dataSetSizeMax: maximum gene set size

The procedure and parameters are described in the GSEA User Guide Running Analyses topic.

Installation

1. Clone this Git repository.

2. Install Maven.

3. Build the .war file:

    mvn clean package -U
   

4. Copy the .war file to tomcat:

    cp target/GseaService.war $TOMCAT_HOME/webapps
   

   where $TOMCAT_HOME is the tomcat deployment location.

5. Alternatively, the REST service can be started locally in an embedded server with the Maven tomcat7:run goal:

    mvn tomcat7:run