From: Improved identification of conserved cassette exons using Bayesian networks
Feature subset | Number of features | Motivation | First use |
---|---|---|---|
Exon: length, symmetry, and identity with mouse ortholog | 3 | Alternative exons tend to be shorter, frame-preserving, and more conserved compared to constitutive exons | [7] |
Conservation of intronic flanks: length/identity of the best local and identity of the global alignment | 2 × 3 | Alternative exons tend to have higher conservation in their intronic flanks | |
Conservation in a 12 nucleotide region spanning the 3' and 5'ss | 2 | As alternative exons and their intronic flanks are more conserved, this may in particular concern the exon/intron boundaries | This work |
PPT intensity | 1 | Alternative exons tend to have weaker PPTs | [8] |
Nucleotides at seven positions flanking the 5'ss | 4 × 7 | Alternative exons tend to have specific nucleotide preferences near the 5'ss | [8] |
Frequency of di- and trimers in the exon and flanking introns | 3 × 16 3 × 64 | Motifs which are part of splice regulatory motifs might differ in their abundance in alternative and constitutive exons | [8] (trimers), this work (dimers) |
Splice site strength of 3'and 5'ss | 2 | Alternative exons tend to have weak splice sites | [10] |
Length of flanking introns | 2 | Alternative exons tend to be flanked by long introns | [10] |
GC content of exon and intronic flanks | 3 | GC-poor regions tend to promote alternative splicing | This work |
Features based on NI scores | 24 | Alternative exons tend to have fewer ESEs and more ESSs | This work |
Features based on PU values | 15 | Single-stranded motifs are likelier to bind to regulators | This work |
PTB-binding sites | 6 | PTB is a regulator alternative splicing | This work |
Features based on ISREs | 8 | Alternative exons tend to have more ISREs in their intronic flanks | This work |
Density of various motifs | 22 | Several motifs are known to be associated with alternative splicing | This work |
Combination features | 7 | Combining features can capture more information | This work |