Fig. 4: HERGAST enable fine-scale tumor microenvironment mapping in colorectal cancer. | Nature Communications

Fig. 4: HERGAST enable fine-scale tumor microenvironment mapping in colorectal cancer.

From: Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST

Fig. 4

a Spatial clustering results of different methods in Visium HD human colorectal cancer slice. These same results are observed across 10 repeated experiments. b A zoomed-in view of a tumor area with hematoxylin and eosin (H&E) stained image (top left panel), HERGAST result (top right panel), PCA result (bottom left panel), and STAGATE(DIC) result (bottom right panel). c Left: dot plot of the highly expressed genes in HERGAST’s unique cluster indicated as box c in Fig. 3a. Right top: spatial expression of the combined metagene. Right bottom: corresponding significantly enriched biological pathways determined with the Metascape web tool. d Zoom-in view of six example of the spatial cluster of phagocytes uniquely identified by HERGAST (indicated as dash line boxes d in Fig. 3a) and the corresponding H&E image. e SPP1 spatial expression plot. f Separate display of the corresponding spatial cluster of HERGAST. g Separate display of the spatial cluster of PCA containing the corresponding area.

Back to article page