Fig. 3

A Ligands from the niche cell type are received by the index cell type, resulting in a change in downstream gene expression. We expect these downstream genes to be \((index,niche)\) genes. B Overview of niche-DE Ligand-Receptor pipeline: We aim to determine which ligand-receptor pairs are active between the ligand expressing niche cell type \(n\) and the receptor expressing index cell type \(i\). (1): Using the ligand-target potential matrix from niche-net, we extract the top \(K\) downstream genes for each ligand. (2): Using these downstream genes, we calculate a ligand activity score using the niche-DE T-statistic vector between index-niche pair \(\left(i,n\right)\) for the top \(K\) downstream genes. (3): Ligands with an activity score greater than a threshold value and their corresponding receptor(s) are screened for expression in the niche cell type. C Comparison of ligands inferred between the niche-DE-based pipeline and a permutation-based pipeline [29]. D Sensitivity of top 20 and top 50 ligands by ligand activity score vs spot size using slide-seq cerebellum data as the reference