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saezlab / OmnipathR

R client for the OmniPath web service
https://r.omnipathdb.org/
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How to get information about downstream target genes of ligands and receptors in cell interactions? #77

Open qijt123 opened 1 year ago

qijt123 commented 1 year ago

Hi,

Thank you very much for your Omnipath database.

Now I have some information about ligands and receptors, but I want to know what are the transcription factors and target genes downstream of these receptors?

In addition to this, I would also like to get information on whether the binding of ligands and receptors has an activating or inhibiting effect on these downstream genes.

Thanks.

deeenes commented 1 year ago

Hi,

Apologies for the late reply! There is a resource of cytokine induced transcriptional signatures, called CytoSig. The predictive power is much lower than in case of TF or pathway activities. I'm sure alternative methods exist or are in development. I recommend to read the papers and docs of LIANA and ask my colleague @dbdimitrov who is expert on these methods.

dbdimitrov commented 1 year ago

OmniPath's PPI network can be used to find downstream TFs in a sign-coherent way, see fig 4 here: https://www.biorxiv.org/content/10.1101/2023.08.19.553863v1