Fig. 3
From: Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
Evaluation of RBPNet on iCLIP and miCLIP data. As in contrast to mESC, no control signal is used for m6a peak calling on HEK data, we consequently used RBPNet target and total track predictions for auROC and AP computation for mESC and HEK, respectively. A RBPNet PCC performance on hold-out samples of miCLIP experiments in HEK293 and mESC cell lines. B, C ROC performance of RBPNet whole-transcript predictions with respect to crosslink and non-crosslink positions called by PureCLIP for HEK293 and mESC cell lines, respectively. D AP performance on HEK293 and mESC in across transcripts for different PureCLIP crosslink site frequency quartiles. E, F Example RBPNet-HEK293 miCLIP predictions on ENSG00000142937.11 and ENSG00000161016.15. Notably, both predicted signal shape and observed miCLIP signal occurs predominantly in CDS and UTR regions. G Test set PCC performance on iCLIP experiments for PTBP1 and TDP43. H Predicted RBPNet signal shape for SCARNA2 (ENSG00000278249.1)