(I) Volcano plot of NEF-induced changes to BHEL cell transcription. NEF-expressing or control CD4OT-II cells were co-cultured with BHEL cells in the presence of HEL-OVA for 4h before isolation of BHEL cells and transcriptome analysis by microarray. Shown are mRNAs with log2fold change against -log10 p-value. Out of around 20,000 genes investigated, 564 genes were induced and 977 genes were suppressed by NEF (see Dataset EV1), with 187 genes induced and 407 suppressed by NEF in a statistically significant manner. 