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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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Questions about the LR-TF database #45

Open qijt123 opened 1 year ago

qijt123 commented 1 year ago

Thank you so much for developing the tool!

I would like to know if in the LR-TF database you collected, are all LR's effects on TF activated? Is it possible that LR's effect on TF is inhibitory?

Looking forward to your reply!

ShellyCoder commented 1 year ago

In cell biology, there are many situations where a ligand (often a signaling molecule, such as a hormone, growth factor, or neurotransmitter) binds to a specific receptor, triggering a series of biochemical reactions, and ultimately impacting the activity of downstream transcription factors.

Yes, you're absolutely correct, the impact of ligand-receptor binding on downstream transcription factors could be either activating or inhibiting. Therefore, we used the enrichment score of the transcription factor target gene sets in the samples, and this score is used in absolute value. Our hypothesis is that even if a transcription factor is inhibited, the downstream target genes should be significantly enriched (with the enrichment score being negative).

I hope my answer can address your question.

qijt123 commented 1 year ago

Thank you for your timely reply. I can understand your hypothesis, which is very reasonable.

I have another question: Is TF's influence on TG positive?

Looking forward to your reply!

ShellyCoder commented 1 year ago

The influence of a transcription factor (TF) on its target gene (TG) can be either positive or negative, depending on the specific interaction. The transcription factor Myc is a classic example of a transcription factor that has a positive influence on its target genes. Nearly half of the ~300 transcription factors (TFs) in Escherichia coli make use of negative feedback on their own expression, which was proved by Andreas et al. (PMID, 23673649).