PIP-seq uncovers protein-bound sequence motifs that co-occur in groups of functionally related transcripts. (A) MDS analysis of RBP-bound motif co-occurrence in human mRNAs. The motifs used for this study were identified by a MEME-based analysis of PPS sequences. Sequences for all of the motifs used in this analysis can be found in Additional file 10. Colors indicate cluster membership as defined by k-means clustering (k = 5). (B) The most significantly enriched biological processes (and corresponding P value) for target transcripts, where the specified clusters of motifs identified in (A) are co-bound. MDS, multidimensional scaling; PIP-seq, protein interaction profile sequencing; PPS, protein-protected site; RBP, RNA-binding protein.