Extended Data Fig. 5: JPLE reconstructs RNA-binding specificities for thousands of eukaryotic RBPs.

a, The number of RBPs identified in each of 690 eukaryotes split across major eukaryotic clades. Boxes span the interquartile range (IQR) with the center line marking the median. Whiskers span from minimum to maximum value within IQR*3/2 from box boundaries. Outliers are displayed as dots. b, Precision-recall curves for RNA-binding profile reconstructions generated by amino acid sequence identity (AA SID) and JPLE. Precision (y-axis) is the mean rolling Pearson correlation coefficient (PCC) for reconstructions at least as confident as the threshold (top axes). The selection size for the rolling average window is 25 reconstructions. AA SID confidence is percent amino acid identity, JPLE confidence is the minimum e-dist. Grey and green dashed lines indicate the confidence at which the rolling mean PCC first hits 0.70 (red dashed line). Standard error is shown in the shaded area around each line. c, The fraction of measured and reconstructed specificities for RRM- and KH-domain-containing RBPs for 49 representative species. The proportion of reconstructed specificities that were identified by AA SID, JPLE, or both are indicated. The clade to which the species belongs is indicated below the x-axis. d, Scatterplot displays the percentage of specificities for RRM- and KH-domain-containing RBPs that were reconstructed by JPLE (with an e-dist cutoff of 0.127) compared to a 40% AA SID for 49 representative species (listed in panel c). e, The fraction of measured and reconstructed RBP specificities for major eukaryotic clades and all eukaryotes contained in EuPRI and on CisBP-RNA. This plot includes measured and reconstructed RBPs that do not contain RRM- or KH-domain-containing RBPs.