Fig. 3

NOVA displays MN-specific binding patterns. a, b Pairwise comparison of intronic and exonic relative NOVA peak heights in MNs and WSC using the method illustrated in Additional file 2:Figure S3. Relative NOVA peak heights in introns or exons are calculated as following: 100 × Number of MN or WSC CLIP reads in a JP/Number of MN or WSC CLIP reads in all intronic or exonic JPs in the corresponding gene. NOVA peaks disproportionally over- or under-represented in MN (FDR ≤ 0.1, fold change ≥ 2) are shown in green and purple, respectively. The numbers of differential peaks and total peaks with sufficient coverage for the analysis are shown in the boxes. c, d UCSC genome browser images illustrating disproportionally different intronic (c) an exonic (d) NOVA binding sites in MNs. The YCAY track demarcates clusters of NOVA binding motifs. The WSC and MN CLIP tracks are pooled HITS-CLIP results, normalized for the displayed regions so that the highest unchanged peaks in WSC and MN share the same height. Significantly different NOVA binding sites between MNs and WSC are marked by arrowheads with FDR values indicated. UCSC gene annotation and transcript direction are shown at the bottom of each panel. e, f Positional enrichment of YYYY and U-rich tetramers and phastcons scores around intronic (e) and 3′ UTR (f) NOVA peaks over-represented in MNs, respectively. YYYY and U-rich tetramer enrichment is calculated from motif frequencies at each base position relative to over-represented (blue or red) or all (black) MN CLIP peaks in introns or 3′ UTRs, normalized by their expected frequencies based on random base distribution. Phastcons scores are plotted with solid dots denoting the mean phastcons values at a given base position, and lighter lines denoting 95% confidence intervals. Dark gray and brown represent phastcons scores around all and over-represented intronic/3′ UTR NOVA peaks, respectively. Motif enrichment scales are on the left and phastcons score scales are on the right. Light gray boxes highlight regions 100 nt around NOVA peaks