Extended Data Fig. 3: Enrichment of in vitro motifs in eCLIP peaks for different RNA types and comparison with in vivo eCLIP-derived motifs.

a, b, The average enrichment (geometric mean) of the top ten RBNS 5mers for a given RBP in the peaks of an eCLIP experiment compared to shuffled eCLIP peaks, among all RBPs predominantly bound to 3′ UTR + CDS (a) or introns (b) by eCLIP. RBPs arranged by RBNS motif similarity along the y-axis, with corresponding RBPs between RBNS and eCLIP boxed along the diagonals. c, RBP order and RBNS and eCLIP motifs as in Fig. 3a. Right, ratio of the percentage of eCLIP peaks attributable to the top ten RBNS 5mers for each RBP compared to the percentage of eCLIP peaks attributable to the same ten 5mers, averaged over all other eCLIP experiments in the same RNA type class (from a and b). For 18 out of 21 RBPs, the RBNS motifs explain more (R > 1) of the corresponding eCLIP peaks than eCLIP peaks of proteins binding similar transcript regions (SRSF9 and RBM22, shown in grey, were excluded because there were insufficient numbers of RBPs in their type class to perform this analysis). d, The proportion of the top ten RBNS 5mers that fall within an eCLIP peak, separated by transcript region. RBPs arranged from top to bottom according to the proportion that fall within an eCLIP peak over all transcript regions (all motif occurrences in expressed transcripts). e, Top motifs derived from all eCLIP peaks as well as eCLIP peaks within intronic, CDS, and 3′UTR regions. Motifs were derived only if there were at least 5,000 peaks or 5% of total peaks in that region, averaged over the 2 eCLIP replicates. Blue boxes indicate that eCLIP was not performed in that cell line. Filled circles indicate significant overlap (P < 0.05 by one-sided hypergeometric test) between RBNS and eCLIP motifs. f, The top eCLIP motifs that do not match RBNS for the corresponding RBP (if any). The eCLIP motif was considered as matching RBNS if any of its constituent 5mers were among the RBNS Z ≥ 3 5mers (always using at least 10 RBNS 5mers if there were fewer than 10 with Z ≥ 3). Blue boxes indicate that eCLIP was not performed in that cell line. Below right, percentage of eCLIP experiments aggregated over all RBPs or cell types in each category of agreement with RBNS. Horizontal line indicates a significant difference in the proportion of a particular eCLIP–RBNS agreement category between eCLIP analysis of all peaks versus eCLIP analysis of intron, CDS, or 3′UTR peaks (P < 0.05 by one-sided Fisher’s exact test).