ArticleBMC genomics2017
ulfasQTL: an ultra-fast method of composite splicing QTL analysis.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 13 citations in OpenAlex.
- Differentially expressed and alternately spliced genes as a novel tool for genotoxicity: a computerized study in ATT-myc transgenic mice for the recognition of genotoxic and non-genotoxic chemical.Frontiers in genetics · 2025Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- Identification of Candidate mRNA Isoforms for Prostate Cancer-Risk SNPs Utilizing Iso-eQTL and sQTL Methods.International journal of molecular sciences · 2022Article
- Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci.Nature communications · 2022Article
- Quantifying splice-site usage: a simple yet powerful approach to analyze splicing.NAR genomics and bioinformatics · 2021Article
- Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data.American journal of human genetics · 2020Article
- SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data.BMC bioinformatics · 2020Article
- Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes ofFrontiers in plant science · 2019Article
- The Expanding Landscape of Alternative Splicing Variation in Human Populations.American journal of human genetics · 2018Review
- Identification of Splicing Quantitative Trait Loci (sQTL) inFrontiers in genetics · 2017Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundAlternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variations in human traits. Detecting genetic variants that affect splicing phenotypes is essential for understanding the functional impact of genetic variations on alternative splicing. For many situations, the key phenotype is the relative splicing ratios of alternative isoforms rather than the expression values of individual isoforms. Splicing quantitative trait loci (sQTL) analysis methods have been proposed for detecting associations of genetic variants with the vectors of isoform splicing ratios of genes. We call this task as composite sQTL analysis. Existing methods are computationally intensive and cannot scale up for whole genome analysis.
resultsWe developed an ultra-fast method named ulfasQTL for this task based on a previous method sQTLseekeR. It transforms tests of splicing ratios of multiple genes to a matrix form for efficient computation, and therefore can be applied for sQTL analysis at whole-genome scales at the speed thousands times faster than the existing method. We tested ulfasQTL on the data from the GEUVADIS project and compared it with an existing method.
conclusionsulfasQTL is a very efficient tool for composite splicing QTL analysis and can be applied on whole-genome analysis with acceptable time.
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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 OpenQuestion graph.