Genomic location of PARalyzer generated interaction sites for four RNA-binding proteins. Locations of interaction sites that contained at least two T = > C conversions were compared to transcript sequences as annotated in ENSEMBL (release 57) . The different repeat region classes were identified by RepeatMasker . The following repeat types were collected for this analysis: low complexity repeat family (low complexity), long interspersed nuclear elements (LINE), short interspersed nuclear elements (SINE), DNA transposons (DNA), RNA repeat families (RNA), satellite repeat family (Satellite), rolling circle (RC), unknown repeat family (Unknown), long terminal repeats (LTR) and other repeats (Other).
Corcoran et al. Genome Biology 2011 12:R79 doi:10.1186/gb-2011-12-8-r79