Figure 4

RUNX1, ZNF238, and miR-206 function through common mechanisms. (A) 3-way Venn diagram representing the overlap between significantly regulated (fold-change >2, FDR <0.05, overlap considers only changes in same direction) gene targets in RD cells differentiated either through RUNX1, ZNF238, or miR-206 expression relative to GFP-infected controls. The table indicates the breakdown of upregulated versus down-regulated genes for each portion of the Venn diagram. (B) Scatter plots showing pairwise comparisons of gene expression. All values are plotted as the log₂ of the fold-change relative to GFP-infected controls, as indicated along the x- and y-axes. Correlation is listed for each comparison in the matrix. (C) (upper panel) Bar graph demonstrating that the majority of the 95 genes listed as being ‘uniquely’ regulated by miR-206 in 4A are also regulated by RUNX1 and/or ZNF238, but at lower levels of expression change. FDR was kept constant (<0.05) in this analysis, and to be included as a ‘shared’ target, the change had to occur in the same direction (either up- or down-regulated) in RUNX1 and/or ZNF238 as in miR-206. (bottom panel) Analysis as in the top panel for genes in the ZNF238 unique and ZNF238:miR-206 intersection groups relative to RUNX1 changes. (D) RT-PCR for select gene targets from Additional file 9: Table S4. TIMM17b serves as the internal control.