Table 1 Exonic splicing regulatory elements datasets used in this study
From: Genomic features defining exonic variants that modulate splicing
ESR dataset | Format | Method | Reference |
|---|---|---|---|
ESEFinder | 4 ESE PWMs | Set of four experimentally derived ESE binding site matrices for four SR proteins (SF2, SC35, SRp40, SRp55) identified by an in vitro SELEX approach with specific SR protein complementation | [14] |
Fas- (hex3)ESS | 176 ESS hexamers | Set of experimentally derived ESSs identified in vivo through cloning of random decamers into fluorescence activated minigene reporter by selecting those sequences that cause exon skipping. Unique candidates were clustered and represented by non-degenerate hexamers | [15] |
RESCUE-ESE | 238 ESE hexamers | Set of putative ESEs derived from overrepresented hexamer motifs in exons versus introns and exons with weak splice sites versus exons with strong splice sites | [17] |
PESX | 2,096 ESE/974 ESS octomers | Set of putative ESEs (PESE) and ESSs (PESS) overrepresented and underrepresented in internal non-coding exons versus unspliced pseudoexons and 5' UTRs of intronless genes | [18] |
NI-ESR | 979 ESE/496 ESS hexamers | Uses the neighborhood inference (NI) algorithm to identify new candidate ESEs and ESSs using a set of previously identified ESEs/ESSs. The NI algorithm searches the sequence neighborhood of a particular hexamer and scores it by whether the surrounding sequences contain mostly known ESEs, ESSs or neither. Predicted candidates were verified by cross-validation and a subset was experimentally validated | [19] |
Ast-ESR | 285 hexamers | Motifs based on computational analysis of overrepresented and conserved dicodons in orthologous human-mouse exons. Putative ESRs are not labeled as ESEs or ESSs as a number were found to act as both enhancers and silencers in minigene assays depending on sequence context. | [16] |
Composite-ESR | 400 ESE/217 ESS hexamers | Combined set of ESE/ESS based on RESCUE-ESE, PESE, PESS and Fas-ESS datasets | [60] |