EGF treatment of HeLa cells induces extensive uncoupling between transcriptome and translatome gene expression variations. (A) Flowchart of differential expression analysis between transcriptome and translatome after EGF treatment and definition of uncoupling. Uncoupling qualifies genes classified as DEGs (differentially expressed genes) with significant variations only in the transcriptome (in cyan), only in the translatome (in yellow) and with opposite significant variations between transcriptome and translatome (in red). Coupling qualifies genes classified as differentially expressed (DEGs) by both transcriptome and translatome profile comparisons and with homodirectional changes (in green). (B) Western blots indicating the activation of the EGFR signaling pathway by the increase of known EGFR mediators and targets: phosphorylated Akt1, phosphorylated Elk1 and Myc. (C) Comparison between sucrose gradient profiles of HeLa cells without EGF (in black) and with EGF (in red). (D) Scatterplot of transcriptome and translatome log2 transformed fold changes, showing genes belonging to the coupling and uncoupling categories as defined in panel A. Spearman correlation between fold changes is also shown. (E) Barplot highlighting the uncoupling value between translatome and transcriptome DEGs. The number of DEGs and the corresponding percentages are displayed following the same colour scheme adopted in the rest of the figure (F-G) Scatterplot showing correlation between transcriptome (F) and translatome (G) log2 transformed fold changes derived from microarray hybridizations and quantitative RT-PCR on a set of twelve genes, displayed as black dots. Regression lines are drawn in grey.