Could we get all genes in a pathway listed in cellchat@netP$pathways?

[Chrisdoan9]

Hi all,

When we run cellchat, cellchat@netP$pathways will list all signaling detected in the dataset. If we interested in a signaling, could we get all the genes related to this signal? As I understand, a pathway should include many genes.

all_pathways <- CellChatDB$interaction
all_pathways[all_pathways$pathway_name == "abc", ]

will give more information (ligand, receptor) of abc signal but not give us all the genes related to this signal. Thank you so much!

[sqjin]

@Chrisdoan9 netAnalysis_contribution, extractEnrichedLR. Try these two functions. Please check our full tutorial.

[Chrisdoan9]

Hi @sqjin, I tried the two functions above. It gave me list of ligand receptor genes, but not genes name involve in a pathway. I read figure 2 of the cellchat paper and a pathway such as TGFb, so I understand pathway in this case only has two kind genes: ligand gene and receptor gene. But not many gene such as pathway COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP: AFP, ALS2, AMD1, ARHGAP29, ASNS, BCL2L14, etc.

[dkzhang777]

Hi, were you able to make progress on this as I'm also curious about downstream genes to pathways?

[Chrisdoan9]

I think genes in this case are ligands and receptors genes only, not genes in a typical pathway as I replied above.