Pathway Enrichment Analysis with Reactome


This recipe provides an outline of how to perform pathway enrichment analysis on the reactome website using a list of genes or protein Ids in GenomeSpace.  Given a list of gene ideintifers, the goal is to query the reactome database for pathways whose components include the proteins in the supplied list.  Enriched pathways are then displayed with the specified proteins highlighted, and the diagrams can be saved back to GenomeSpace. 


  • A list of genes or protein identifiers (see examples below) 

Input Formats:

A list of NCBI/Entrez gene ids:


A list of UniProt ids:


Tab-delimited expression data:

#Probeset 10h_control 10h 14h 18h 24h
200000_s_at 9.381569 9.710802 9.874874 9.934639 9.495911
200002_at 12.555275 12.511045 12.564419 12.538642 12.439174
200003_s_at 12.401259 12.054083 12.275169 12.206342 12.015476

For more information about input data, see


Recipe Details

1. Drag your gene list file onto the Reactome OR click the icon and select Launch on File, then select your gene list file

You will be sent to the Reactome website.

2. When the analysis is complete, click on one of the top-level pathways, at the left hand side of the screen.

This will take you to the Reactome pathway browser.

3. Navigate the pathway hierarchy by clicking on the  symbol on the left side of the pathway labels.

The pathway diagrams are colorized according to the number of enriched proteins.

4. Once you have selected your pathway, click the  icon and select Save Diagram to GenomeSpace.

A window will pop up with a GenomeSpace dialog.

5. Select a location to save the file to in your GenomeSpace data store.  Click Submit to save the file, then Close.

 6. Return to the GenomeSpace website.  Your pathway diagram file should now be there, after refreshing the page.

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