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Fig. 3 | Genome Biology

Fig. 3

From: Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP

Fig. 3

Influence of size-matched input controls on motif discovery. a The graph shows recall for 57 eCLIP datasets for which orthogonal RBNS or RNAcompete data was available. The datasets were processed with PEKA, using either Clippy peaks or eCLIP narrowPeaks from merged replicates, downloaded from the ENCODE consortium [4, 5]. The datasets are sorted into three groups: (1) datasets where higher recall was achieved with Clippy peaks, (2) datasets with no change in recall between groups, and (3) datasets where higher recall was achieved with narrowPeaks. Within each group, datasets are ordered by decreasing recall values. Heatmaps on the right show mean nucleotide composition across the top 50 k-mers as ranked by in vitro method, by PEKA using Clippy or PEKA using narrowPeaks. b Boxplots show differences in mean nt composition of top 50 k-mers as ranked by PEKA using Clippy or narrowPeaks, for 215 eCLIP datasets, which had sufficient tXn coverage in narrowPeaks for PEKA analysis. c Number of tXn detected by PEKA in the “protein-coding gene” region when using Clippy vs narrowPeaks (paired t-test, p < 0.0001) for 57 eCLIP datasets shown in panel a)

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