PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

Table 1 Summary of motif matches in the different PAR-CLIP datasets

	Number of motif matches	Total nucleotides	Signal-to-noise	Number of interaction sites with motif/Total number of interaction sites
Argonaute (top 20 expressed miRNAs)
PARalyzer	3,933	207,334	2.68	3,041/11,353
Hafner et al. (CCRs)	4,106	301,227	1.92	3,090/6,796
Background (3' UTRs)	131,741	18,602,068	-	-
PUM2
PARalyzer	1,262	127,168	60.28	1,344/6,990
Hafner et al.	1,371	200,228	41.59	1,290/5,668
Background	113,478	689,309,457	-	-
QKI
PARalyzer	3,001	155,237	19.19	2,771/5,361
Hafner et al.	2,593	127,201	20.24	2,079/3,903
Background	694,229	689,309,457	-	-
IGF2BP1
PARalyzer	31,507	1,718,152	1.35	24,758/55,831
Hafner et al.	51,429	3,739,750	1.01	32,303/59,784
Background	9,343,410	689,309,457	-	-

The Argonaute results are specific to only the 3' UTR region and contain only non-redundant seed matches. Summary of the motif matches for Pumilio2 (PUM2), Quaking (QKI), and Insulin-like growth factor 2 binding protein 1 (IGF2BP1) were generated from the analysis of the full transcript of all genes, including 5' UTRs, 3' UTRs, introns and coding regions. The Hafner et al. [7] crosslink-centered regions (CCRs) are those provided in their manuscript.

ISSN: 1474-760X