How to obtain cell-cell interaction list

Question

[miyeok]

Hi,

im doing Ligand-receptor interaction analysis with single cell data. I have two questions.

1) there are several ligand-receptor databases. How can i combine these databases and use that for LR interaction?

2) after cell-cell interaction analysis, how to obtain final results including the interacting cell types, ligands,receptors,potential targets in signal receiver cell type, etc?

any answer would be much appreciated.

Thank you

Answer 1

[shiyang_bio]

Hi miyeok, For your first question, the answer is yes. If I remember correctly, both cellphone DB and cellchat integrate several databases together when doing analysis. As for getting the final interacting celltypes/ligands/etc, different software has different criteria. For example, CellphoneDB provides a interaction P value for you to select the candidates.

Good luck

[miyeok]

Thank you so much!!

Answer 2

[fracarb8]

I often use LIANA, which is a framework that combines 7 methods and 16 different databases for ligand-receptor analysis. You can either run each method/resource indipendently or you can combine multiple into one final result.

[miyeok]

Thank you so much. i'll check :)