Fig. 3: scLRSomatoDev, an atlas to infer LRs involved in cortex wiring.

A Curated ligand–receptor database containing 8789 LR pairs compiled from 109 sources (LR_DB_2025). To increase biological relevance for our study, we generated a brain-focused subset (LR_DB_2025_Brain) by retaining only ligands and receptors expressed in our single-cell dataset, resulting in 5341 LR pairs. See Supplementary Data S1 and S2 for full listings. B Correlations between transcriptional landscapes of neurodevelopmental process-associated ligands in ITs and receptors in GABANs, suggesting a ligand–receptor code for neuronal adhesion and synaptogenesis that involves the cadherin family of adhesion molecules. (Left) bars show the mean correlation between IT ligand and GABAN receptor landscapes for random ligand–receptor (LR) pairs, ADAM metalloproteases, cadherins and Ig-like cell-adhesion molecules. (Right) bars show the mean correlation for LR pairs assigned to neurodevelopmental categories (brain-associated, migration, cell death, differentiation, cell adhesion and synaptogenesis). Data are presented as mean values, statistical significance was assessed by comparing each category to its respective reference group (Left: random non-LR gene pairs; Right: “Brain associated” category) using a two-sided z-test based on Fisher’s r-to-z transformation, with no adjustment for multiple comparisons. Exact P values were: cadherins vs random LR pairs, P = 0.00125; cell adhesion vs “ Brain associated ”, P = 2.215e-05; synaptogenesis vs “ Brain associated ”, P = 7.0357e-04. Asterisks indicate significance levels: P < 0.05 (*), P < 0.01 (**), P < 0.001 (***). C Simplified method for the inference of LR-mediated interactions. TF, transcription factor; TG, target gene; S_inter, score for intercellular communication; S_intra, score for intracellular signaling. See Figs. S13–14. D Heatmaps illustrating the number of inferred LR interactions that persist across at least two consecutive ages for all 729 cell-type pairs. From left to right and top to bottom: all possible interactions; interactions unique to a single cell-type pair, widely shared interactions (by >400 pairs) and very rare interactions (shared by <10 pairs). Associated source data are provided.