Figure 3. Correspondence between computational target predictions and observed protein changes.

Analogous results were observed using the transfection data sets (Supplementary Fig. 8). a, Performance of programs that consider site conservation. Plotted is the average protein derepression (± standard error) of genes with ≥1 conserved or non-conserved 7-8mer 3′-UTR site (grey) and of genes predicted to be miR-223 targets. The number of quantified proteins in each set is in parenthesis. b, Recognition of an adenosine (A) opposite the first nucleotide of the miRNA. The cumulative plot of protein changes after miR-181 transfection compares proteins from messages with no seed-matched 3′-UTR site to those from messages with the indicated single 3′-UTR site. c, Relationship between the scores of predicted targets and protein derepression. Predictions corresponding to quantified proteins were divided into three equal-size bins according to the scores proposed to indicate the quality of the prediction or degree of repression. Statistically significant differences between the bottom and top third are indicated (asterisk, P < 0.01, Mann-Whitney U-test). d, Response of the top 29 predictions of each algorithm, plotted as in a. e, Performance of programs that do not consider site conservation, displayed as in a and c. Also shown is the response of quantified proteins from messages with only non-conserved 7-8mer 3′-UTR sites, binned by total context score.