Fig. 3. Loss of SOX4 is associated with an increase in mammary differentiation.

A GO-term analysis of all differentially expressed genes. GO-terms are visualized by REVIGO to summarize similar GO-terms [44]. B GO-term analysis of 635 significantly upregulated genes in SOX4^KO organoids. C GO-term analysis of 304 significantly downregulated genes in SOX4^KO organoids. D GSEA comparing genes differentially expressed in SOX4^KO organoids to gene sets specific for fetal mammary stem cells, adult mammary basal cells, adult mammary luminal progenitors and adult mammary luminal mature cells (derived from [26]). E Confocal images of immunostaining for luminal marker K8 (green) and basal marker K14 (red) on organoids in vitro. F Quantification of proportion of organoids that exhibits predominantly K14 staining. Data is represented as average ± SD. ANOVA using Dunnett test for multiple comparisons was used to calculate p-values (n.s. = non-significant, *p < 0.05, **p < 0.01). Scale bar is 100 µm. G Confocal images of immunostaining for luminal marker K8 (magenta) and basal marker K14 (yellow) and DAPI (Cyan) on paraffin sections of lung metastases. Scale bar is 100 µm. H Quantification of K14-positive cells as a proportion the K8-positive cells, which make up all tumor cells. Data is represented as average ± SD. ANOVA using Dunnett test for multiple comparisons was used to calculate p-values (*p < 0.05, **p < 0.01).