The ARE stability motif is overrepresented in genes up-regulated after miRNA transfection. (A) UAUUUAU overrepresentation in up-regulated 3′ UTRs after transfection of two different miRNAs in HeLa cells. The plot shows the UAUUUAU running sum (left to right) of word overrepresentation scores in the ranked list of 3′ UTRs (black line) and running sums from 500 random permutations of the UAUUUAU word scores (red lines, see Methods). miR-128 is included as it has the strongest UAUUUAU correlation (FDR < 1 × 10−7) among the 11 different miRNA transfections in HeLa cells, while miR-133a transfection has the weakest correlation (P < 0.03, FDR < 0.11). (B) The gene set defined by UAUUUAU overrepresentation at the 0.05 level comprised 448 genes expressed in HeLa cells, and this gene set was significantly up-regulated in the 11 HeLa experiments (P < 2.5 × 10−60, Kolmogorov-Smirnov [KS] one-tailed test, standardized expression changes pooled for all 11 experiments). (C) For each of the seven time points following miR-124 transfection in HepG2 cells, the plot shows the significance level (−log10 P-value, Kolmogorov-Smirnov one-tailed test) for down-regulation of miR-124 targets relative to all expressed genes (blue line) and the UAUUUAU word correlation Z-score in up-regulated genes (red line, numbers correspond to the rank of the correlation score, N = 21 504 words).
