Fig. 6

Concordance of Saluki predictions and functional data from massively parallel reporter assays. a Effect of mutation on RNA stability, as measured by an MPRA [87], for tiles along the CXCL2 3′ UTR separated by 8-nt intervals. Also shown are variant effect predictions from Saluki (smoothed along a local 8-nt window) for the same region, and vertebrate base conservation as measured by PhyloP [90]. Predicted AREs are boxed in red, and novel elements detected by the MPRA are boxed in orange. b Saturation mutagenesis of a segment of the CXCL2 3′ UTR, boxed in purple in part a. Shown are the observed variant effects (top) and Saluki’s predicted variant effects (bottom). The reference sequence is shown for each, in which the nucleotide height is scaled according to the mean observed or predicted effect for that position. c Scatter plot of the observed and predicted variant effects shown in panel b. d Scatter plot of the observed and predicted 3′ UTR effects for each of 3000 conserved 3′ UTRs profiled by fastUTR [87]. e Scatter plot of the observed and predicted variant effects, as measured in Beas2B cells [88]. Also indicated are the Pearson (r) and Spearman (rho) correlation values for panels c–e