How to display all ligand receptor from cellchat database v2?

[Chrisdoan9]

Hi @sqjin

I installed cellchat v2.1.2 but when I want to see which ligands and receptors are in a pathway of interested, seem I got result from database v1. The last column of all_pathways is version CellChatDB v1.

 CellChatDB <- CellChatDB.human
all_pathways <- CellChatDB$interaction
all_pathways[all_pathways$pathway_name == "ABC", ] 

plotGeneExpression(cellchat, signaling = "ABC", enriched.only = T)

The plot from plotGeneExpression() have ligand receptor genes that don't have in all_pathays.

Thank you so much!

[sqjin]

@Chrisdoan9 It is possible that the last column of all_pathways is version CellChatDB v1, which means that this signaling is not updated in CellChatDB v2.
For the question that "plotGeneExpression() have ligand receptor genes that don't have in all_pathays.", if there are multiple subunits for ligands or receptors, then you will see this result.

[Chrisdoan9]

Hi @sqjin. Thank you for your reply! So that mean the ligand receptor genes that don't have in all_pathways actually exist. Just because the CellChatDB v2 doesn't update, right? I googled the subunit and I think it exists.

[sqjin]

@Chrisdoan9 Yes, CellChatDB v2 labels the L-R pairs that are only newly added in the recent release.

[Chrisdoan9]

Thank you! Just try to find evidence that this ligand-receptor actually exist for biologist. Because I showed the result of cellchatDB v1, so the biologist was not convinced.