Fig. 7: Regulon activity analysis.

a The binary active heatmap illustrates the activity status of 32 regulons in the SC-spot clusters, as calculated by SECNIC. Black indicates an active status, while white represents an inactive status for the corresponding regulon in that particular ST-spot cluster. b The heatmap illustrates the average AUC score of the 32 regulons in the SC region. The AUC score measures each regulon’s activity level based on its associated geneset. c Spatial AUC scores of selected representative regulons in SC are shown in the upper panel. The lower panel depicts a t-SNE plot displaying the AUC scores of these representative regulons across each cell. d A heatmap displays the expression levels of regulons’ TFs and their target genes across ST-spots, revealing regional-specific distribution patterns. e UMAP and spatial plots depicting the expression patterns of Hoxb9 and Penk. The plots indicate that the two genes exhibit similar patterns. f Left panel (Penk Promoter): the diagram displays the transcription start site (TSS) location and five HOXB9 binding sites. Right Panel (Luciferase Assay): a luciferase assay was performed in HEK-293 cells to evaluate the promoter activity of Penk (−1500 to 0 base pairs) compared to a control vector called pGL3-basic. The effect of HOXB9 overexpression (OE-HOXB9) on Penk promoter activity was compared to a control condition of GFP overexpression (OE-GFP). Values are shown as mean (bar) ± SD (error bar). N = 4, ****P < 0.0001, Student’s t test. g The spatial AUC scores of the Mafb-16g regulon. h The ridge plot (right panel) represents the activity of the Mafb-16g regulon across the sham and SNL ST-spot clusters. i The heatmap illustrates the weighted mean expression of TF Mafb and its target genes from the Mafb-16g regulon across each cell subpopulation identified by snRNA-seq. Microglia exhibit the most prominent expression of these genes.