Fig. 2

CAF^low resemble iCAFs and CAF^high resemble myCAFs. a Bar plots showing mean of transcript levels of the iCAF marker IL6 and myCAF marker ACTA2 in CAF^low and CAF^high. Asterisks (*) indicate adjusted p < 0.001. Error bars represent ± standard deviation (SD). b Heatmap representation and FPKM levels of differentially expressed iCAF and myCAF genes (≥ 5 FPKM, ≥ 1.5-fold change, adjusted p < 0.001) by RNA-Seq in CAF^low and CAF^high. GAPDH and ACTB are included as reference genes. Color key represents the logarithm (base 2) of the CAF^high/CAF^low ratio. c Signature scores for each CAF^low (upper) and CAF^high (lower) cell line visualized onto Unifold Manifold Approximation and Projection (UMAP) representations of stromal cell types reproduced from a published breast cancer single-cell RNA-Seq dataset [17]. The color keys indicate the signature scores. iCAF-like and myCAF-like in the UMAPs refer to the nomenclature used in [17], and the dotted line has been applied to visualize the approximate division of these two clusters. While the CAF^low has a representation within the iCAF-like and myCAF-like cluster, the CAF^high is represented primarily in the myCAF-like cluster. d Dot plots showing KEGG (upper) and Reactome (lower) pathways significantly enriched when comparing CAF^low and CAF^high signatures. Size key indicates the ratio of enriched genes to background genes (top key). Color key indicates the Benjamini–Hochberg-adjusted p-value (bottom key). Key terms in bold text