Gene expression analysis upon SOX11 overexpression in DG75-ER-SOX11 BL cell line. (A) Western blot experiment showing the levels of ER-SOX11 protein in DG75 ER-SOX11 BL cell line. DG75-ER was used as SOX11-negative control cell line, and tubulin as loading control. (B) Immunofluorescence experiments showing the nuclear localization of the SOX11 protein in DG75 ER-SOX11 cells, induced (+) or not induced (−) with 4-OHT for 24 hours. DG75 ER cell line was used as SOX11⁻ control. DAPI (4′,6-diamidino-2-phenylindole) marks the cellular nucleus, and a merge of the 2 immunofluorescences images (DAPI and SOX11) was done. (C) Heat map illustrating the scaled expression (Z score) of 1694 DEGs (866 upregulated and 828 downregulated genes; supplemental Table 7) in DG75 ER-SOX11 compared with DG75 ER cell lines induced with 4-OHT for 8 and 24 hours, obtained by RNA-seq. Genes with an adjusted P value <.1 and absolute log₂-transformed fold change of >0.65 were considered. (D) Volcano plot showing genes differentially expressed, obtained by RNA-seq, upon SOX11 overexpression in DG75 ER-SOX11 compared with DG75 ER BL cell lines treated with 4-OHT. The graph shows on the y-axis –log₁₀(P value) and on the x-axis the log₂-transformed fold change. Genes upregulated and downregulated in DG75 ER-SOX11 vs DG75 ER with an adjusted P value <.1 and log₂-transformed fold change of >0.65 or less than −0.65 are colored in red and blue, respectively, and genes with an adjusted P value <.00005 and absolute log₂-transformed fold change of >3 are labeled with their gene symbol. (E-F) Panther pathway enrichment analysis using DEGs (E) upregulated and (F) downregulated between DG75 ER-SOX11 and DG75 ER after 4-OHT treatment. Number of genes, fold enrichment, and –log₁₀(P value) for each pathway are shown. Only pathways with a P value <.05 were considered.