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Fig. 3 | Genome Biology

Fig. 3

From: Refining colorectal cancer classification and clinical stratification through a single-cell atlas

Fig. 3

Fibroblast clusters in colon and colorectal tumors. A t-SNE of fibroblasts colored by Normal, CAF-S1 and CAF-S4 subtypes. B Dot plots showing the variable expression of fibroblast specific marker genes across CAF-S1 and CAF-S4. C Integration analysis of five CAFs subtypes from a breast cancer (BC) cohort to validate the existence of specific CAF subtypes in the CRC samples. D IHC representative images of CAF-S1 (FAP+, PDGFR-ß+) and CAF-S4 (RGS5+, MCAM+) in CRC sections from five independent patients. Asterisk (*) indicates tumor cells and arrows (>) indicate CAFs. Annotated by a board-certified GI pathologist. All images are × 20 magnification. High-resolution images are available on GitHub as source data [43]. E Boxplots show the distribution of cell types in two CRC bulk expression datasets, within tumors based on CMS status. The whiskers depict the 1.5 x IQR. The P-values for pairwise t-tests comparisons (with Benjamini-Hochberg correction) of cell abundance across CMS are shown in the figure. Note “NS”: P > 0.05, *P </=0.05, **P </=0.01, ***P </=0.001, ****P </=0.0001

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