Table 3.

Quantification of quadruplex forming motifs in genes targeted by FMRP

A	Genes with ≥1 WGGA QFM
Dataset	Genes	% of Total	Perm P-value
WGGA
Ascano-PAR	1206	18.1	<1 × 10−7
Ascano-RIP	281	30.5	<1 × 10−7
Brown	112	31.6	<1 × 10−7
Darnell	253	31.4	<1 × 10−7
B_D_A-PAR	53	39.3	<1 × 10−7
B_D_A-RIP	28	52.8	<1 × 10−7
Genome-wide	2732	14.8	N/A
B	Total number of WGGA QFMs
Dataset	QFMs	QFMs/Gene	Perm P-value
WGGA
Ascano-PAR	1730	1.43	<1 × 10−7
Ascano-RIP	443	1.58	<1 × 10−7
Brown	166	1.48	<1 × 10−7
Darnell	417	1.65	<1 × 10−7
B_D_A-PAR	83	1.57	<1 × 10−7
B_D_A-RIP	49	1.75	1 × 10−7
Genome-wide	3872	1.42	N/A
C	Genes with ≥1 ACUK cluster
Dataset	Genes	% of Total	Perm P-value
ACUK
Ascano-PAR	69	1.04	<1 × 10−7
Ascano-RIP	8	0.87	0.118
Brown	2	0.56	0.376
Darnell	8	0.99	0.063
B_D_A-PAR	1	0.74	0.204
B_D_A-RIP	0	0.00	0.281
Genome-wide	114	0.62	N/A
D	Total number of ACUK clusters
Dataset	Clusters	Clusters/gene	Perm P-value
ACUK
Ascano-PAR	69	1.00	<1 × 10−7
Ascano-RIP	8	1.00	0.118
Brown	2	1.00	0.376
Darnell	8	1.00	0.063
B_D_A-PAR	1	1.00	0.204
B_D_A-RIP	0	–	0.281
Genome-wide	114	1.00	N/A

Each dataset, including the overlapping genes from all three studies, were analyzed for clusters of each sequence motif. The total number of genes with at least one WGGA QFM/ACUK cluster (A and C, respectively) and the total number of WGGA QFMs/ACUK clusters (B and D, respectively) are shown, as well as the permutation P-values generated by comparison to random sets of genes; n = 10 000 000 permutations of the data. B_D_A-PAR, consensus genes from Brown, Darnell and Ascano PAR-CLIP; B_D_A-RIP, consensus genes from Brown, Darnell and Ascano RIP-Chip.