Help to understand how signals grouped base on similar functionality

[Chrisdoan9]

Hi all,

I read the vignette but still don't get how signal A grouped with signal B base on the similar functionality. Would you please have a explanation? I really appreciate it.
netVisual_embedding()

[sqjin]

@Chrisdoan9 High degree of functional similarity indicates major senders and receivers are similar, and it can be interpreted as the two signaling pathways or two ligand-receptor pairs exhibit similar and/or redundant roles. To examine this result, you can visualize the inferred networks using circle plot.

[Chrisdoan9]

@sqjin Thank you for your response! I mean for example, MIF and ANNEXIN are grouped based on which criteria? How the tool group these signal together? We use gene expression data for cellchat. So how from gene expression can know two signals have similar biological function? I see most of the signaling pathway use genes name but some are not gene name like COMPLEMENT. Also pathway in this case mean 2 genes: ligand gene and receptor gene, right? Or we can get more genes involve in a signal result? We have major senders/dominant senders, so do we have minor senders? Minor senders are not important in this case? Happy to help with your current work so you have little time to help me understand the tool better!

[sqjin]

@sqjin These appeared names are signaling pathway names instead of gene names. Here the similar functions are inferred based on the structure of the inferred communication networks. We compute the network similarity of two signaling pathways. The rationale is that when the major senders and receivers of two signaling pathways are the same, we consider they have similar biological functons.

[Chrisdoan9]

Hi @sqjin. The reason I confused between pathway in cellchat with gene name is because a pathway name usually have a long name such as KEGG_VIBRIO_CHOLERAE_INFECTION. I choose a pathway name from MSigDB. So for example pathway 1 has sender A and receiver B. C, D in the middle. Pathway 2 has sender A and receiver B. E, F in the middle. So pathway 1 and 2 has similar biological function, right? Would you please give an example of major senders? So what is minor senders? I am sorry because these terms are new to me.