Fig. 3: Spatial resolution of the high-risk signature. | npj Precision Oncology

Fig. 3: Spatial resolution of the high-risk signature.

From: A spatial transcriptomic signature of 26 genes resolved at single-cell resolution characterizes high-risk gastric cancer precursors

Fig. 3: Spatial resolution of the high-risk signature.

a An example of the expression profile of DMBT1 upon a Visium slide annotated by a pathologist for areas of normal glandular architecture (base and pit) and metaplasia. DMBT1 is shown as an example of a spatially resolved gene mapping to pathologist-annotated metaplasia, whereas SLC30A10 is shown as an example of a gene not mapping to metaplasia and, thus, discarded form the spatially-resolved signature. b Heatmap depicting 36 differentially expressed genes from spatial pseudobulk analysis that overlapped with bulk RNA-seq signature from GAPS (FDR-adjusted P value ≤ 0.05; analysis performed using limma-voom). c Scatter plot showing log2 fold-change of 36 upregulated genes from the spatial cohort (X-axis) and log2 fold-change from TCGA. Twenty-six genes overexpressed in both analyses are shown in red. d Spatial mapping of the refined 26-gene signature onto Visium spots. e Comparison of 26-gene signature between metaplastic foci vs normal stomach base or pit (Kruskal-Wallis and Dunn test FDR-adjusted p < 0.001). Note: each Visium spot is 55 µm in diameter, with 100 µm distance between the center of adjacent spots.

Back to article page