Genomic features defining exonic variants that modulate splicing

Table 2 Significance of exon and intron-related features for skipping SAV and HapMap exons

Exon feature	SAV mean	hSNP sampled mean	Z-score	P-value
Exon splice junction strength
Exon 3' SS score (all exons)	7.811	8.489	-1.90	0.057
Exon 5' SS score (all exons)	7.885	8.302	-1.43	0.154
Exon 3' SS score (with ESR)	7.568	8.534	-2.03	0.022
Exon 5' SS score (with ESR)	8.008	8.371	-1.71	0.230
Exon ESR density
ESEfinder density FL	0.126	0.152	-3.78	1.53 × 10^-4
NI-ESE density FL	0.323	0.372	-3.37	7.37 × 10^-4
NI-ESS density FL	0.133	0.093	4.30	1.67 × 10^-5
ESEfinder density W40	0.129	0.153	-3.15	0.0016
NI-ESE density W40	0.324	0.379	-3.47	5.18 × 10^-4
NI-ESS density W40	0.140	0.094	4.50	6.85 × 10^-6
Intronic ESR densities
Upstream NI-ESE density	0.201	0.224	-1.55	0.122
Downstream NI-ESE density	0.235	0.250	-1.06	0.314
Upstream NI-ESS density	0.295	0.241	2.44	0.014
Downstream NI-ESS density	0.258	0.210	2.36	0.018

For each feature, the mean values for non-redundant SAV exons were compared to a bootstrap distribution of sampled means for HapMap exons of similar sizes (hSNP sampled mean). For exon splice junction strength, results marked 'all exons' indicate that the comparison was done using all exons in both datasets and those marked 'with ESR' indicate comparisons using only exons containing a variant with splice-associated ESR changes, that is, ESE loss and/or ESS gain. For exon ESR densities, densities were either measured across the full length of the exon (FL) or in windows of 40 bp at either side of the exon (W40). For exons <80 bp in length, the W40 density is the same as full length density to avoid redundancy. Intronic ESR densities were measured in the first 100 bp upstream and downstream of the exon. SS, splice site.

ISSN: 1474-760X