Running SCORPION with only 10 motif-backed TFs

[arjunp22-lgtm]

I am using SCORPION for Plasmodium vivax single-cell data, but I only have Position Weight Matrices (PWMs) for 10 transcription factors. As a result I can build the trasncription factor - target gene motif score pairs for only 10 transcription factors.

​Since the paper mentions SCORPION can quantify the activity of unprioritized TFs, I have a question : Can the algorithm effectively infer the regulatory links for the remaining TFs using only co-expression and PPI data?
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[dosorio]

Hi @arjunp22-lgtm, if you have the pairs of TF - Target for the Plasmodium vivax, you can use them, and SCORPION will assign the weights of the relationships based on the coexpression and PPI network. If you only have 10 PWMs and run a scan of the promoters, you will only get a 10 tfs x targets genes GRN.