ArticleNucleic acids research2016
Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Review
- LINC00607 facilitates endothelial VEGF-A receptor FLT1 splicing.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Splicing factor TRA2B enhances synthesis of androgen receptor variant AR-V7 in prostate cancer cells.The Journal of clinical investigation · 2026Article
- RNA Alternative Splicing and Polyadenylation and Regulation of the Glomerular Filtration Barrier.Journal of the American Society of Nephrology : JASN · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Incorporating exon-exon junction reads enhances differential splicing detection.BMC bioinformatics · 2025Article
- Expression Divergence in Response to Sex-biased Selection.Molecular biology and evolution · 2025Article
- Impaired splicing machinery in craniopharyngiomas unveils PRPF8 and RAVER1 as novel biomarkers and therapeutic targets.Acta neuropathologica communications · 2025Article
- The NONO protein regulates nonclassical DNA structure: Effects on circadian genes and DNA damage.iScience · 2025Article
- A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection.Briefings in bioinformatics · 2025Article
- PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites.Nucleic acids research · 2025Article
- Heterozygous mutation in BRCA2 induces accelerated age-dependent decline in sperm quality with male subfertility in rats.Scientific reports · 2025Article
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematodeHorticulture research · 2024Article
- Canine hyper-sociability structural variants associated with altered three-dimensional chromatin state.BMC genomics · 2024Article
- Quantifying transcriptome diversity: a review.Briefings in functional genomics · 2024Review
- betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions.RNA (New York, N.Y.) · 2024Article
- Spliceosome malfunction causes neurodevelopmental disorders with overlapping features.The Journal of clinical investigation · 2024Article
- Multilayer Analysis of RNA Sequencing Data in Alzheimer's Disease to Unravel Molecular Mysteries.Advances in neurobiology · 2024Review
- OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events.BioMedInformatics · 2023Article
32 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differential usage of novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively interpret their results. We tested our method on publicly available data from several experiments performed on the rat pineal gland and Toxoplasma gondii, successfully detecting known and previously validated AIR genes in 19 out of 19 gene-level hypothesis tests. Due to its ability to query novel splice sites, JunctionSeq is still able to detect these differences even when all alternative isoforms for these genes were not included in the transcript annotation. JunctionSeq thus provides a powerful method for detecting alternative isoform regulation even with low-quality annotations. An implementation of JunctionSeq is available as an R/Bioconductor package.
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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.