ArticleBioinformatics (Oxford, England)2011
SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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57 citing papers in PubMed, 99 citations in OpenAlex.
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- rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.Nature protocols · 2024Review
- Quantifying transcriptome diversity: a review.Briefings in functional genomics · 2024Review
- The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in neuropsychiatric diseases.Brain, behavior, and immunity · 2023Article
- Advances in alternative splicing identification: deep learning and pantranscriptome.Frontiers in plant science · 2023Article
- Alternative splicing level related to intron size and organism complexity.BMC genomics · 2021Article
- SCISSOR: a framework for identifying structural changes in RNA transcripts.Nature communications · 2021Article
- Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis.Cell reports · 2019Article
- Production of an aberrant splice variant of CCL5 is not caused by genetic mutation in the mammary glands of mastitis‑infected Holstein cows.Molecular medicine reports · 2019Article
- Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs.Frontiers in genetics · 2019Article
- Modeling and analysis of RNA-seq data: a review from a statistical perspective.Quantitative biology (Beijing, China) · 2018Article
- Mechanisms of skeletal muscle wasting in a mouse model for myotonic dystrophy type 1.Human molecular genetics · 2018Article
- Alternative splicing analysis in human monocytes and macrophages reveals MBNL1 as major regulator.Nucleic acids research · 2018Article
- Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1.Neuron · 2018Article
- SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs.Scientific reports · 2018Article
- The Expanding Landscape of Alternative Splicing Variation in Human Populations.American journal of human genetics · 2018Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
motivationAlternative splicing (AS) is a pre-mRNA maturation process leading to the expression of multiple mRNA variants from the same primary transcript. More than 90% of human genes are expressed via AS. Therefore, quantifying the inclusion level of every exon is crucial for generating accurate transcriptomic maps and studying the regulation of AS.
resultsHere we introduce SpliceTrap, a method to quantify exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full-length transcript isoforms, SpliceTrap approaches the expression-level estimation of each exon as an independent Bayesian inference problem. In addition, SpliceTrap can identify major classes of alternative splicing events under a single cellular condition, without requiring a background set of reads to estimate relative splicing changes. We tested SpliceTrap both by simulation and real data analysis, and compared it to state-of-the-art tools for transcript quantification. SpliceTrap demonstrated improved accuracy, robustness and reliability in quantifying exon-inclusion ratios.
conclusionsSpliceTrap is a useful tool to study alternative splicing regulation, especially for accurate quantification of local exon-inclusion ratios from RNA-seq data. AVAILABILITY AND IMPLEMENTATION: SpliceTrap can be implemented online through the CSH Galaxy server http://cancan.cshl.edu/splicetrap and is also available for download and installation at http://rulai.cshl.edu/splicetrap/. CONTACT: michael.zhang@utdallas.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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 OpenQuestion graph.