Fig. 4

The effect of UNC5A knockdown on basal and estradiol (E2)-regulated gene expression in MCF7 and T-47D cells. a Venn diagram showing the number of differentially expressed genes in UNC5A knockdown MCF7 and T-47D cells compared with sh-Control cells with and without 3 h E2 treatment. b UNC5A knockdown MCF7 but not T-47D cells express higher levels of APOBEC3B (**p < 0.01 and ***p < 0.001). c Signaling pathways affected by UNC5A knockdown under vehicle and E2-treated conditions. The number of genes in each of the networks is shown and name of the genes in each network and fold changes in expression are presented in Additional files 7 and 6, respectively. UNC5A affected mainly basal gene expression in T-47D cells. The gene set ‘E2 regulation unique in sh-UNC5A MCF7 cells’ corresponds to those genes whose magnitude of E2-regulated expression differed from sh-Control cells, although these genes may be E2-regulated in both cell types. The gene set ‘E2 regulation exclusively in sh-UNC5A MCF7 cells’ corresponds to those genes whose expression was E2-regulated only in sh-UNC5A cells. d Heatmap of genes uniquely upregulated or downregulated by E2 in sh-UNC5A MCF7 cells. E2 did not affect their expression in sh-Control MCF-7 cells. e The effect of UNC5A knockdown on basal and E2-inducible expression of TFF1 and GREB1. TFF1 and GREB1 expression was measured by qRT-PCR in vehicle, 3-h, and 6-h E2-treated cells. GREB1 expression in 3-h and 6-h E2 treated sh-UNC5A cells was modestly but significantly higher compared with E2-treated sh-Control cells (indicated by *)