circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging
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Le résumé fourni par la source
MOTIVATION: Circular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. RESULTS: We developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. AVAILABILITY: https://github.com/biomedbigdata/circRNA-sponging Contact: markus.daniel.hoffmann@tum.de; markus.list@tum.de Supplementary Material: Supplementary data are available at Bioinformatic Advances online.
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging
- Date Crossref
- 20/01/2023
- Éditeur
- openRxiv
- Type
- posted-content
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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National Institute of Diabetes and Digestive and Kidney Diseases pays non établi dans la noticeStructure de recherche
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Technical University of Munich Institute for Advanced Study (Lichtenbergstrasse 2a pays non établi dans la noticeUniversité ou école supérieure
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Universität Hamburg pays non établi dans la noticeUniversité ou école supérieure
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University of Southern Denmark Computational BioMedicine Lab pays non établi dans la noticeUniversité ou école supérieure
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Georgetown University Departments of Oncology & Medicine pays non établi dans la noticeUniversité ou école supérieure
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TUM School of Life Sciences Chair of Experimental Bioinformatics pays non établi dans la noticeUniversité ou école supérieure
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University of Hamburg Chair of Computational Systems Biology pays non établi dans la noticeUniversité ou école supérieure
National Institute of Diabetes and Digestive and Kidney Diseases, Institute for Advanced Study (Lichtenbergstrasse 2a — Technical University of Munich et Universität Hamburg, avec 4 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.