Fig. 5: SOTIP applications on two spatial proteomics datasets.
From: SOTIP is a versatile method for microenvironment modeling with spatial omics data
a–c Schematic diagram to show how SOTIP works spatial proteomics datasets. Illustration of tumor-immune interplay (a), Voronoi diagram used to visualize spatial domains (b), and molecular polarization to tissue boundary (c). a Tumor and immune cells have complex interplay around the tumor-immune boundary. b Voronoi diagram (as implemented in https://stackoverflow.com/questions/20515554/colorize-voronoi-diagram/20678647#20678647%203.18.2019) is a visualization method for spatial omics data29. c Molecular polarization is a phenomenon that some molecules exhibit gradient changes perpendicular to tissue boundaries. d Ground truth of tumor-immune boundary from the original paper of CRC samples. Top panel: point 16. Bottom panel: point 23. Edited from original paper. Scale bar: 100 μm. e Voronoi diagram of SpaGCN-detected (left column), and SOTIP-detected (right column) spatial domains for point 16 (top row) and point 23 (bottom row). f Comparison of SpaGCN-detected and SOTIP-detected spatial domains to find polarized proteins to/away tumor region, in CRC point 16 (top row) and CRC point 23 (bottom row). Left column: The power plots show the proportion of true positives (y axis) detected by different methods at a range of FDRs (x axis) for point 16 (top row) and point 23 (bottom row). Right column: The overlay of three representative polarized proteins found by SOTIP-detected SDM in point 16 (top row) and point 23 (bottom row). Scale bar: 100 μm. g Ground truth of tumor-immune boundary from the original paper of TNBC samples. Top panel: patient 4. Bottom panel: patient 9. Edited from original paper. Scale bar: 100 μm. h Voronoi diagram of SpaGCN-detected (left column), and SOTIP-detected (right column) spatial domains for patient 4 (top row) and patient 9 (bottom row). i Similar with (f) but on TNBC patient 4 (top row) and patient 9 (bottom row). In d, e, g, h, all white arrows point to tumor regions. Scale bar: 100um. Source data are provided as a Source Data file. The experiment results in (d, f, g, i) were similar with three independent repeats.
