From the home page, click the “Analysis Tools” button, and then select “Analyse gene list” (preselected on the analysis page).

Submit your list of differentially expressed genes, or try one of the sample data sets.

The leftmost column of the uploaded data set must have gene names or other gene/protein identifiers. The remainder of the data set consists of as many columns with numerical values as necessary. Columns may have headers, or not.

Click “Continue” and then “Analyse”,  maintaining the options in the second window (‘Project to human’, ‘Include interactors’) at their default values.

Reactome will perform a standard gene set enrichment analysis, based only on the gene list. In the results overview, pathways will be greyed out if they are not significantly enriched. If a pathway is enriched, its colour will be determined as follows:

The top end of the colour map is the highest value of all submitted numerical values. The bottom end of the colour map is the lowest of all submitted numerical values, across all columns.

The colour of a pathway is based on the average expression value for all genes which are in the submitted dataset and in the pathway. In the initial view, this average is based on the first column. If the data set has more than one column, users can cycle through the subsequent columns with the “Play” button at the bottom of the pathway window.

In the pathways overview (either the "Fireworks" or the "Reacfoam" view, selectable in the top left area of the main window), the user can double click (long click in Reacfoam to select a pathway and zoom in to the detailed molecular map view. In this view, proteins are coloured according to the user-provided values, and again the user can cycle through multiple columns with the "Play" controls.