Background binding sites are present in many published PAR-CLIP libraries especially putatively weak binding RBPs. Previously published PAR-CLIP results from multiple studies were processed using PARalyzer and analyzed for sites that overlap with background and with each other. A) Genome browser window depicting overlapping sites in an exon of the XIST lncRNA from various PAR-CLIP studies. Red horizontal bars in the top panel indicate areas with read evidence in at least one of the three background libraries. Horizontal blue bars indicate reads from various PAR-CLIP studies, re-analyzed in this study, all with the same PARalyzer parameters. Black bars indicate PAR-CLIP studies not re-analyzed in this study but found in the doRiNA database. B) Bar graph depicting percent overlap of background sites with sites from 33 different PAR-CLIP experiments (see Additional file 1: Table S1 for info on RBP and study). Vertical red bars are from PAR-CLIPs of putative or “non-professional” RBPs, which are defined as previously unrecognized RBPs because they do not contain any known RNA recognition motifs or domains. Orange bars are PAR-CLIP experiments that produced very few reads, those containing roughly 10,000 or fewer reads (post-processing and mapping). Blue bars are all other PAR-CLIP experiments using established RBPs.
Friedersdorf and Keene Genome Biology 2014 15:R2 doi:10.1186/gb-2014-15-1-r2