ArticleNucleic acids research2016
NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.
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 72 papers.
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Who cites it
72 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
- The molecular axis hnRNPU/circKCNK2/EDC4/IL-11 aggravates osteolytic bone metastasis of RCC.Oncogene · 2025Article
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia.Cancer cell international · 2025Review
- Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications.Molecular psychiatry · 2025Review
- Article
- Circular RNAs in cancer stem cells: Insights into their roles and mechanisms (Review).International journal of molecular medicine · 2025Review
- Circular RNAs: Biogenesis and Functions : Circular RNA detection and bioinformatic analysis.Advances in experimental medicine and biology · 2025Review
- Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.ACS pharmacology & translational science · 2024Review
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Biological role and regulation of circular RNA as an emerging biomarker and potential therapeutic target for cancer.Molecular biology reports · 2024Review
- An accretive detection method for in silico identification and validation of circular RNAs in wheat (Triticum aestivum L.) using RT-qPCR.Molecular biology reports · 2024Article
- The clinical perspective of circular RNAs in neurodegenerative diseases: potential diagnostic tools and therapeutic targets.Frontiers in cellular neuroscience · 2024Review
- State-of-the-Art Circular RNA Analytics Using the Circtools Software Suite.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- New insight into circRNAs: characterization, strategies, and biomedical applications.Experimental hematology & oncology · 2023Review
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.Nature methods · 2023Article
- Computational approaches for circRNAs prediction and in silico characterization.Briefings in bioinformatics · 2023Review
- Assessing the impacts of various factors on circular RNA reliability.Life science alliance · 2023Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Analysis of RNA-seq data often detects numerous 'non-co-linear' (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method ('NCLscan'), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
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