Can I submit a list of differentially expressed genes, as log2 fold change values, coming from two different conditions to have a quantitative representation of pathways involvement? If yes, how can I prepare and submit my file?

For this, please use the Reactome Gene Set Analysis tool, accessed through the "Analyze Gene Expression" button after "Analysis" is selected from the home page. The detailed analysis approaches underlying this feature are described here .

The Reactome GSA tool is an enhancement of GSEA and can take your original expression data directly, perform differential expression analysis and then highlight pathways according scores.

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