search

ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
304 stars 52 forks source link

Directionality of interactions #187

Open Pedramto89 opened 1 month ago

Pedramto89 commented 1 month ago

Hi there

As you mentioned in the tutorial, the interactions are not symmetric. So, I am wondering how we can infer the directionality of the interactions.

Best

cakirb commented 1 month ago

Hi @Pedramto89,

The directionality of the interactions can be found from the "interaction_input" of CellPhoneDB database. You can access it from https://www.cellphonedb.org/, and search by the partners of interactions

Please let us know if this doesn't help.

Best, Batu

luzgaral commented 2 weeks ago

Hi @Pedramto89

Note that directionality and symmetry are different concepts here.

By symmetry we mean that the interaction ligand-cellA <---> receptor-cellB is different to ligand-cellB <---> receptor-cellA and will get different expression values. See the Interpreting the outputs from the Documentation here.

Regarding directionality, from CellphoneDB v5.0.0 all interactions in the database have been reorganised so that partnerA is the ligand/sender while partner B is the receptor/receiver. Note some interactions are not directional (for example those involving extracellular matrix proteins).

Hope this helps,

Luz