ArticleNAR genomics and bioinformatics2025
Quantifying annotation-driven bias in alternative splicing from EGAP metadata.
Article in NAR genomics and bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Annotated coding sequences (CDSs) enable genome-wide estimates of alternative splicing. However, the quality and evidence support of these annotations can systematically bias estimates of splicing events across species. Here, we evaluate how annotation-related variables from the NCBI Eukaryotic Genome Annotation Pipeline affect inferred splicing levels. Analyzing 670 multicellular eukaryotes, we find that the percentage of CDSs supported by experimental evidence is the dominant predictor of variation in splicing estimates, whereas assembly quality and raw transcriptomic input play a minor role. To correct this annotation-driven bias, we introduce a normalization procedure based on polynomial regression, yielding an adjusted metric of alternative splicing. This novel metric preserves relative splicing complexity across species while mitigating annotation artifacts, with important implications for comparative genomics.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.