Probability of downregulation and seed class distributions derived from mirSVR score analysis. (a) Empirical probabilities of microRNA-mediated downregulation for different mirSVR scores. Using mirSVR prediction scores on the Linsley et al. data, we compute the empirical probability that a gene's Z-transformed log expression change is below a (a = -0.1, -0.5, -1.0, -1.5), conditioned that its (sigmoid-transformed) mirSVR score is less than a threshold S (x-axis). Points on the plot represent mirSVR score cutoffs S and their corresponding probability P(y ≤ a|x ≤ S). The black curve represents the fraction of predictions with scores equal to or less than the cutoff scores. For example, 10% of predicted targets have a score of ≤ -0.8 and their expected probability of observing a log expression change of ≤ -0.5 is approximately 40%. (b) The proportion of the four seed classes: 8-mers, 7m8, 7A1 and 6-mer in equal-size mirSVR score bins. The canonical sites from Linsley et al. were divided into equal size bins and the proportion of the four seed classes is shown by color. As expected the score distribution correlates with seed type hierarchy (for example, 8-mers have generally more negative mirSVR scores than 7m8 sites). However, inspection of the top 30% predicted target sites (mirSVR score ≤ -0.1) highlights the broad overlapping distributions of the four seed types, suggesting that the classification of target sites to seed classes is inadequate to represent their relative efficiency.
Betel et al. Genome Biology 2010 11:R90 doi:10.1186/gb-2010-11-8-r90