Fig. 6: Cell–cell communication network of spatial proximity brain-related cell types in mouse embryo organogenesis.

a Schematic showing the number of significant L–R pair interactions between olfactory sensory neurons and olfactory epithelium cells by STcomm analysis (top). The bottom panel showing the spatial mapping (color intensity) and colocalization of olfactory sensory neurons and olfactory epithelium cells according to deconvoluted weights in section 4 (S4). b Dot plot showing significant L–R pairs between olfactory sensory neurons and olfactory epithelium cells via secreted signaling (left) and cell-cell contact (right) with p < 0.05. The dot color represents communication probability and the size indicates p-values which are computed from one-sided permutation test by Cellchat. c The spatial distribution of expression of L–R pairs of Wnt4 and Fzd3, and their co-expression in S4. The inlet shows the co-expression level of Wnt4 and Fzd3 in co-localized region of olfactory sensory neurons and olfactory epithelium. d The spatial distribution of expression of L–R pairs of Efna5 and Epha4, and their co-expression in S4. e Dot plot showing significant L–R pairs communication among spatial proximity brain-related cell types calculated by STcomm. The dot color and size indicate communication probability and p-values which are computed from the one-sided permutation test by Cellchat. f Schematic showing the number of significant L–R interactions between neuron progenitor cells and inhibitory interneurons. g Circos plots representing significant interaction of L–R pairs of Nrxn3 and Nlgn1 among spatial proximity brain-related cell types. h Spatial plots showing the spatial distribution (color intensity) and colocalization with spots of neuron progenitor cells and inhibitory interneurons according to deconvoluted weights in section 2 (S2). i Spatial distribution of expression and co-expression of L–R Nrxn3 and Nlgn1 in S2. j Nrxn3 and Nlgn1 spatial expression pattern examined by RNA-scope in brain tissue sections matched to S2 in (i) (n = 4). White dashed box showing the staining of Nrxn3 and Nlgn1 in spatial proximity cells. Blue, DAPI; green, Nrxn3; red, Nlgn1; yellow, co-location of Nrxn3 and Nlgn1. Source data are provided as a Source Data file.