Interaction between two different organs

[Yuwang-art]

Hi Dr. Jin,

I have single cell data from two different organs, A and B, respectively. I intend to find the ligand-receptor interaction pairings between the two organs. Therefore, I have directly merged the data sets from organ A and organ B together. Is this OK? Or is there a better way?

Furthermore, I am only concerned with ligand-receptor pairs where the ligand is in A and the receptor is in B (or where the ligand is in B and the receptor is in A), not ligand-receptor pairs where both the ligand and the receptor are in A (or both are in B). Thus, if a ligand is highly expressed in all cell types in organ A but less so in organ B, and its corresponding receptor is highly expressed in all cell types in organ B but less so in organ A, will this gene always be selected as a significant ligand-receptor pair because of the difference in expression in the two organs?

Thanks!

[rojweber]

I have a similar question. I am interested in hormones which are produced distantly and not captured in the data set of local ligands. What is the best way to handle ligands that come from the blood stream? Would it be to produce a 'synthetic' cluster that represents the blood stream and just put a list of ligands in there? Examples would be things like insulin or thyroid hormone.