-AbSplice is a method that predicts aberrant splicing across human tissues, as described in Wagner, -Çelik et al., 2023. This track displays precomputed AbSplice scores for all possible -single-nucleotide variants genome-wide. The scores represent the probability that a given variant -causes aberrant splicing in a given tissue. -AbSplice scores -can be computed from VCF files and are based on quantitative tissue-specific splice site annotations -(SpliceMaps). -While SpliceMaps can be generated for any tissue of interest from a cohort of RNA-seq samples, this -track includes 49 tissues available from the -Genotype-Tissue -Expression (GTEx) dataset. -
- --The AbSplice score is a probability estimate of how likely aberrant splicing of some sort takes -place in a given tissue. The authors suggest three cutoffs which are represented by color in the track.
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-Mouseover on items shows the gene name, maximum score, and tissues that had this score. Clicking on -any item brings up a table with scores for all 48 GTEX tissues. -
- --The raw data can be explored interactively with the -Table Browser, or the -Data Integrator -For automated analysis, the data may be queried from our -REST API. -Please refer to our -mailing list archives -for questions, or our -Data Access FAQ -for more information. -
AbSplice scores are also available at the -public repository created by the authors. -
- --Data was converted from the files (AbSplice_DNA_hg38_snvs_high_scores.zip) provided by the authors -at zenodo.org. Files in the -score_cutoff=0.01 directory were concatenated. To convert the data to bigBed format, scores and -their tissues were selected from the AbSplice_DNA fields and maximum scores calculated using -a custom -script. -
- --Thanks to Nils Wagner for helpful comments and suggestions.
- --Wagner N, Çelik MH, Hölzlwimmer FR, Mertes C, Prokisch H, Yépez VA, Gagneur J. - -Aberrant splicing prediction across human tissues. -Nat Genet. 2023 May;55(5):861-870. -PMID: 37142848 -