Interpretation on Ligand Activity in Receptor Value

[VivianQM]

Hi,

Thank you for this great package. I have a quick question on how to interpret the value indicating ligand activity in receptors. Here we have a few pairs that are upregulated at 0hr timepoint.

However, when looking at the ligand activity.

We actually see a down-regulatory ligand activity at 0hrs and up-regulatory activity at 12hrs. Why is that the case and how to interpret the result in this situation?

Thank you so much.

[browaeysrobin]

Hi @VivianQM

down-regulatory ligand activity at 0hrs means: predicted target genes of the shown LR pairs are enriched among the genes downregulated at 0hrs (in your case probably: downregulated at 0hrs vs 4 and 12h). In your case that can mean: LR pairs higher expressed at 0hrs could lead to suppression of their target genes at 0hrs (hence the occurence of these genes in the set of downregulated genes at 0hr). Whether this is really due to suppression is not something we can say based on scRNA-seq data alone. It is also possible that other LR pairs, upregulated at 4/12h induce expression of target genes that overlap with the target genes of the LR pairs you show here.

Because the contrasts are linked to each other: genes upregulated in one condition will by definition be considered as downregulated in the other conditions etc.

We also recommend to rather look at the scaled activities than the regular ligand activities .