search

saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
160 stars 28 forks source link

Source of interaction #136

Open hemadelon opened 6 months ago

hemadelon commented 6 months ago

Hi there,

I'm consequently getting the interaction IL6 - FCGR3B out of my data. I am not aware of Fc-receptors being able to bind cytokines, though the target cell does have a lot of IL6R expression (which doesnt come up). I'm just wondering if there could possibly be an error in annotation of the interaction.

Is there anyway in which I can see which underlying algorithm (CellPhoneDB, Connectome, Cellchat etc.) generated the interaction so I can approach the developers?

Thank you!

dbdimitrov commented 6 months ago

Hi @hemadelon,

I traced the interaction and it's original source is Cellinker: http://www.rna-society.org/cellinker/mysql_php/more.php?id=LR00955&species=Homo%20sapiens

If you think that it's erroneous, I'm planning to update the PK of liana soon, and I can make sure that it's removed in subsequent releases.

hemadelon commented 6 months ago

Hey @dbdimitrov

Thanks for getting back at me. I looked at the source paper, and it does look like it picked it up in their analyses, although it's not been validated. I am not including it in my final figures, because it is quite an odd pairing, so I guess it's not erroneous perse!

Thank you

dbdimitrov commented 6 months ago

Hi @hemadelon,

Thanks a lot for the feedback. I will make sure we exclude this interaction in subsequent versions. And I will also double check other interactions coming from this reference.

Daniel