Fig. 3: Multi-dimensional analysis of spatially-informed sub-populations.

a Annotation of the six cortical layers alongside the adjacent white matter within two human middle temporal gyrus (MTG) brain samples (ST01101 and ST01103). b Detection of spatial domains by RESEPT. c Visualization using MAPLE to elucidate shared or unique spatial domains identified across the two Spatial Transcriptomics samples (ST01101 and ST01103). d Alluvial diagrams showcasing the progression of cells: originating from individual samples, aggregating into joint subpopulations, and culminating in layer annotations. e A heatmap depicting genes specific to the MAPLE-derived clusters for both AD and Control samples. f Heatmap representing the top 10 upregulated and top 10 downregulated genes distinguishing AD from Control within Cluster 1. g Gene Set Enrichment Analysis (GSEA) of DEGs from (F) plotted against REACTOME pathways. The bar plot shows the top 10 upregulated and downregulated pathways, accompanied by normalized enrichment scores. h Spatial feature plots highlighting the variance in gene expression of PLP1 and UCHL1 from Cluster 1, segregated by AD and Control samples. i Violin plots showcasing the activity of two selected TFs between AD and Control, with associated p-values calculated from a two-sided Wilcoxon rank-sum test. Each box showcases the minimum, first quartile, median, third quartile, and maximum ARI results of a tool performed on different data subsets (Control group: n = 232, and AD group: n = 1412). Dots represent spatial spots. Source data are provided as a Source Data file.