Table 3 Summary of features investigated in this study
From: MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing
Feature | Type | Description |
|---|---|---|
Distance to nearest splice site | SNP-based | Distance between a given variant and the nearest 5′ or 3′ splice site in the target exon. |
ESR change | SNP-based | Change in the frequency of ESR elements subsequent to a single base substitution. This includes: |
ESE to neutral (ESE loss) | ||
ESE to ESE (no change) | ||
Neutral to ESE (ESE gain) | ||
ESE to ESS (ESE loss and ESS gain) | ||
Neutral to neutral (no change) | ||
ESS to ESS | ||
Neutral to ESS (ESS gain) | ||
ESS to neutral (ESS loss) | ||
ESS to ESE (ESS loss and ESE gain) | ||
In ESE | SNP-based | Frequency of ESE binding sites (in the wild-type) that overlap with the location of the variant |
In ESS | SNP-based | Frequency of ESS binding sites (in the wild-type) that overlap with the variant |
ESR hexamer score (ESR-HS) | SNP-based | Hexamer scoring function to express the relationship between disease and neutral variants and their differential distributions with respect to loss or gain of an ESE or ESS |
Spectrum kernel | SNP-based | Frequency of 3-mers and 4-mers over an 11 bp window (wild type and mutant) |
Change in natural splice site strength | SNP-based | MaxEnt splice site score of natural splice site in mutant allele minus MaxEnt splice site score of wild-type allele |
Maximum cryptic splice site | SNP-based | Maximum cryptic splice site (5′ and 3′) score (outside of the natural splice site) found overlapping the variant on the mutant allele |
Evolutionarily conserved element | SNP-based | PhastCons conserved element probability for substitution site, based on multiple alignments of 46 placental mammals |
Base-wise evolutionary conservation | SNP-based | PhyloP base-wise sequence conservation score at site of single base substitution based on multiple sequence alignment of 46 placental mammals |
Natural wild-type splice site strength | Exon-based | MaxEntScan score of the natural 5′ and 3′ splice site of the wild-type target exon |
Flanking intron size | Exon-based | Length in base-pairs of the upstream and downstream introns flanking the target exon |
Intronic ESS density | Exon-based | Intronic ESS density was calculated for 100 bp upstream and 100 bp downstream of the target exon |
Exonic ESS density | Exon-based | ESS density was calculated across the first 50 bp and the last 50 bp of the target exon. If the length of the exon was less than 100 bp, then the full length of the exon was used to calculate the ESS density |
Exonic ESE density | Exon-based | Same as above but for ESEs |
Internal coding exon | Exon-based | {true, false}, Is the target exon an internal coding exon (that is, the target exon is not the first or last coding exon) |
Exonic GC content | Exon-based | Percentage of nucleotides that are either guanine or cytosine in the target exon |
Exon size | Exon-based | Size of the target exon |
Constitutive exon | Exon-based | Is the target exon constitutively spliced |
Exon number | Gene-based | Number of exons in the transcript |
Transcript number | Gene-based | Number of different reported isoforms that the target gene encodes |