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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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Question on calculation of interaction probability #287

Open lucyu2668 opened 3 years ago

lucyu2668 commented 3 years ago

Hi! Thanks for your innovation, still I have a question on the calculation of interaction probability, as an unexplainable phenomena for me.

I am doing a case-control analysis currently, and found an interesting pathway-VISFATIN.

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The blue bar here represents the flow in case group, and I further found the sender and receiver as shown below:

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The weird phenomena is that when I checked the DGE of the sender cell group, though the NAMPT expression percentage was higher in case group, the ave.log2FC was below 0. I took this to be that the expression strength was higher in control group.

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As demonstrated in your paper Inference of intercellular communications part, communication probability was identified by DGE, which was not inconsistent with my analysis.

Is my understanding about your tool correct? And how to explain this phenomena? In such case, is this pathway reliable and worth further experiment?

Looking forward to your answer~

sqjin commented 3 years ago

@lucyu2668 The DEG analysis in the initial step of CellChat is identifying the altered signaling genes across different cell types instead of conditions. You can check the tutorial on Part III: Identify the upgulated and down-regulated signaling ligand-receptor pairs. Before further experiment, it will be necessary to examine the expression patterns.