Fig. 3

B7-H4 regulates breast cancer cell EMT and stemness genes. A Cell morphology was investigated in SKBR3-KO and -WT cells. Scale bar = 50 μm. B The identification of over- and under-represented gene groups and enriched pathways based on differentially expressed genes in SKBR3-KO and SKBR3-WT cells was performed by the GSEA analysis. C The differentially expressed genes of enriched biological functions compared to WT and SKBR3-KO cells were analyzed by Gene Ontology (GO). D Venn diagram shows the overlapping genes associated with EMT and cell stemness in SKBR3-KO, MCF7-OE and MDA-MB-231-OE cell lines. E–G RNA-seq results show the mRNA expression levels of EMT, cell stemness and self-renewal genes significantly altered in (E) SKBR3-KO, (F) MDA-MB-231-OE and (G) MCF7-OE cells versus respective control cells (Log 2 scale). The unit used to establish the fold change in RNA-seq analysis is TPM