Fig. 3: STAMP deconvolutes CAFs from regular fibroblasts in SMI NSCLC data.
From: Interpretable spatially aware dimension reduction of spatial transcriptomics with STAMP
a, NSCLC sample data acquired using CosMx Spatial Molecular Imager (SMI) with the original cell type annotation. b, Gene module rankings (number) and scores (color) of marker genes for each topic. c, Spatial plots of topics annotated using their gene modules. d, Spatial co-occurrence of different cell types with respect to CAFs (Topic 13) as computed using Squidpy. CAFs are the closest to the tumor edge (Topic 9). e, Canonical pathway enrichment analysis obtained from ingenuity pathway analysis (IPA) of CAFs against the other fibroblast populations. Spot color reflects the IPA z-score enrichment of CAFs versus fibroblasts, with red indicating predicted pathway activation and blue indicating pathway repression. The x axis shows the level of significance via −log10 (adj. P). Adj. P values were calculated with the Fisher’s exact test (right tailed) followed by the Benjamini–Hochberg adjustment. NK, natural killer; cDC, conventional dendritic cell; mDC, myeloid dendritic cell; pDC, plasmacytoid dendritic cell.
