(E-G) Effects of NEF expression in CD4OT-II cells on gene expression in BHEL cells. After 24h of B-T co-culture, BHEL cells were separated from CD4OT-II using magnetic beads before RNA isolation for microarray analysis. The top 235 deregulated genes (see Dataset EV2) were grouped into genes that were highly induced (E), moderately induced (F) or repressed (G) by Ag stimulation in control cells and the effects of NEF WT or NEF ∆12-39 displayed as heat maps. Heat map values are plotted as average Log2 FC (n=3 biological repeats) relative to unstimulated BHEL. Red and green represents higher and lower expression, respectively. 