Comments (1)
Hi @csennis
If I understand you correctly, I see two possible reasons for the similarities you find:
- Your set of potential ligands (based on expressed genes) is very similar because you used a rather loose cutoff (as default) and/or the two populations are similar
- if you would have taken the DE genes between the two populations as 'gene set of interest', this gene set of interest would be the same for both analyses, resulting in similar top predicted upstream ligands. If you did this, I would recommend to look at only upregulated genes in one population and predict potential upstream ligands for this subset.
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