miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data

Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework fo...

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Autores principales:	Ilias Glogovitis, Galina Yahubyan, Thomas Würdinger, Danijela Koppers-Lalic, Vesselin Baev
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	miRNAs isomiRs NGS Galaxy bioinformatics tools Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
Acceso en línea:	https://doaj.org/article/1d73c6f8936e4e44bf3e6653643b4ac3
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spelling	oai:doaj.org-article:1d73c6f8936e4e44bf3e6653643b4ac32021-11-25T17:02:22ZmiRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data10.3390/cancers132256632072-6694https://doaj.org/article/1d73c6f8936e4e44bf3e6653643b4ac32021-11-01T00:00:00Zhttps://www.mdpi.com/2072-6694/13/22/5663https://doaj.org/toc/2072-6694Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework for comprehensive analysis of miRs and their sequence variants—miR isoforms (isomiRs). Though isomiRs are commonly reported in deep-sequencing experiments, their detailed structure complexity and specific differential expression (DE) remain not fully examined by the majority of the available analysis tools. miRGalaxy encompasses biologist-user-friendly tools and workflows dedicated to the analysis of the isomiR-ome and its complex behavior in various biological samples. miRGalaxy is developed as a modular, accessible, redistributable, shareable, and user-friendly framework for scientists working with small RNA (sRNA)-seq data. Due to its modular workflow, advanced users can customize the steps and tools for their needs. In addition, the framework provides an analysis report where the significant output results are summarized in charts and visualizations. miRGalaxy can be accessed via preconfigured Docker image flavor and a Toolshed installation if the user already has a running Galaxy instance. Over the last decade, studies on the expression of miRs and isomiRs in normal and deregulated tissues have led to the discovery of their potential as diagnostic biomarkers. The detection of miRs in biofluids further expanded the exploration of the miR repertoire as a source of liquid biopsy biomarkers. Here we show the miRGalaxy framework application for in-depth analysis of the sRNA-seq data from two different biofluids, milk and plasma, to identify, annotate, and discover specific differentially expressed miRs and isomiRs.Ilias GlogovitisGalina YahubyanThomas WürdingerDanijela Koppers-LalicVesselin BaevMDPI AGarticlemiRNAsisomiRsNGSGalaxybioinformatics toolsNeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENCancers, Vol 13, Iss 5663, p 5663 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	miRNAs isomiRs NGS Galaxy bioinformatics tools Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
spellingShingle	miRNAs isomiRs NGS Galaxy bioinformatics tools Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Ilias Glogovitis Galina Yahubyan Thomas Würdinger Danijela Koppers-Lalic Vesselin Baev miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
description	Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework for comprehensive analysis of miRs and their sequence variants—miR isoforms (isomiRs). Though isomiRs are commonly reported in deep-sequencing experiments, their detailed structure complexity and specific differential expression (DE) remain not fully examined by the majority of the available analysis tools. miRGalaxy encompasses biologist-user-friendly tools and workflows dedicated to the analysis of the isomiR-ome and its complex behavior in various biological samples. miRGalaxy is developed as a modular, accessible, redistributable, shareable, and user-friendly framework for scientists working with small RNA (sRNA)-seq data. Due to its modular workflow, advanced users can customize the steps and tools for their needs. In addition, the framework provides an analysis report where the significant output results are summarized in charts and visualizations. miRGalaxy can be accessed via preconfigured Docker image flavor and a Toolshed installation if the user already has a running Galaxy instance. Over the last decade, studies on the expression of miRs and isomiRs in normal and deregulated tissues have led to the discovery of their potential as diagnostic biomarkers. The detection of miRs in biofluids further expanded the exploration of the miR repertoire as a source of liquid biopsy biomarkers. Here we show the miRGalaxy framework application for in-depth analysis of the sRNA-seq data from two different biofluids, milk and plasma, to identify, annotate, and discover specific differentially expressed miRs and isomiRs.
format	article
author	Ilias Glogovitis Galina Yahubyan Thomas Würdinger Danijela Koppers-Lalic Vesselin Baev
author_facet	Ilias Glogovitis Galina Yahubyan Thomas Würdinger Danijela Koppers-Lalic Vesselin Baev
author_sort	Ilias Glogovitis
title	miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
title_short	miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
title_full	miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
title_fullStr	miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
title_full_unstemmed	miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
title_sort	mirgalaxy: galaxy-based framework for interactive analysis of microrna and isomir sequencing data
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/1d73c6f8936e4e44bf3e6653643b4ac3
work_keys_str_mv	AT iliasglogovitis mirgalaxygalaxybasedframeworkforinteractiveanalysisofmicrornaandisomirsequencingdata AT galinayahubyan mirgalaxygalaxybasedframeworkforinteractiveanalysisofmicrornaandisomirsequencingdata AT thomaswurdinger mirgalaxygalaxybasedframeworkforinteractiveanalysisofmicrornaandisomirsequencingdata AT danijelakopperslalic mirgalaxygalaxybasedframeworkforinteractiveanalysisofmicrornaandisomirsequencingdata AT vesselinbaev mirgalaxygalaxybasedframeworkforinteractiveanalysisofmicrornaandisomirsequencingdata
_version_	1718412762755891200

miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data

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