ArticleBMC bioinformatics2016
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Recent advances in the detection and functional analysis of circRNAs with short-read RNA sequencing-based methods.Molecular biology reports · 2026Review
- Differential Expression of Circular RNAs in Rat Brain Regions with Various Degrees of Damage After Ischemia-Reperfusion.International journal of molecular sciences · 2025Article
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- Article
- Deconvolution of the tumor-educated platelet transcriptome reveals activated platelet and inflammatory cell transcript signatures.JCI insight · 2024Article
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Early-stage idiopathic Parkinson's disease is associated with reduced circular RNA expression.NPJ Parkinson's disease · 2024Article
- Computational approaches for circRNAs prediction and in silico characterization.Briefings in bioinformatics · 2023Review
- Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis.PloS one · 2022Article
- A Brief Review of circRNA Biogenesis, Detection, and Function.Current genomics · 2021Review
- Article
- The bioinformatics toolbox for circRNA discovery and analysis.Briefings in bioinformatics · 2021Review
- Roles for RNA export factor, Nxt1, in ensuring muscle integrity and normal RNA expression in Drosophila.G3 (Bethesda, Md.) · 2021Article
- Insights Into the Role of CircRNAs: Biogenesis, Characterization, Functional, and Clinical Impact in Human Malignancies.Frontiers in cell and developmental biology · 2021Review
- Role of Circular RNA in Kidney-Related Diseases.Frontiers in pharmacology · 2021Article
- A genome-wide circular RNA transcriptome in rat.Biology methods & protocols · 2021Article
- Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation.Development (Cambridge, England) · 2020Review
- Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood.BMC medical genomics · 2020Article
- circRNAs expressed in human peripheral blood are associated with human aging phenotypes, cellular senescence and mouse lifespan.GeroScience · 2020Article
Corrections and comments
- Erratum issuedErratum to: PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.2016 · Elliot, David J [corrected to Elliott, David J]
Authors and funding
7 authors.
Funding
Abstract
backgroundTranscripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues and cell types from many eukaryotes, and are now known to be mostly circular, cytoplasmic, and non-coding. Although there is no uniformly ascribed function, several have been shown to be involved in gene regulation. Accurate identification of these transcripts can, however, be difficult due to artefacts from a wide variety of sources.
resultsHere, we present a computational method, PTESFinder, to identify these transcripts from high throughput RNAseq data. Uniquely, it systematically excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outputs both PTES and canonical exon junction counts to facilitate comparative analyses. In comparison with four existing methods, PTESFinder achieves highest specificity and comparable sensitivity at a variety of read depths. PTESFinder also identifies between 13 % and 41.6 % more structures, compared to publicly available methods recently used to identify human circular RNAs.
conclusionsWith high sensitivity and specificity, user-adjustable filters that target known sources of false positives, and tailored output to facilitate comparison of transcript levels, PTESFinder will facilitate the discovery and analysis of these poorly understood transcripts.
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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.