Fig. 1

Performance in predicting in vitro binding on the InVitro dataset. For each RBP, all methods were trained and tested on the InVitro dataset. Performance was measured by PCC of the predicted and real RNAcompete probe intensities. a Scatter plot shows our KNN (with optimal K) predicted PWMs perform better than or as well as 1NN predicted PWMs in all RBPs in terms of the PCCs of predicted and true probe intensities. p-value is calculated by paired t-test. b Scatter plot shows our KNN predicted PWMs also outperform the left-out original PWMs derived by Ray et al. [5]. c Box plot of PCCs for different methods including KNN, 1NN [5], DeepBind [10], RCK [17], and KNN-RCK. The vertical dashed line separates boxes for methods requiring only the target RBP’s homologous binding information for training to the left, and methods requiring the target RBP’s explicit binding data for training to the right. In each box, the dashed green line denotes the mean, and the brown line denotes the median