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miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing

Here, we present the miRMut protocol to annotate mutations found in miRNA genes based on whole-exome sequencing (WES) or whole-genome sequencing (WGS) results. The pipeline assigns mutation characteristics, including miRNA gene IDs (miRBase and MirGeneDB), mutation localization within the miRNA prec...

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Autores principales: Urbanek-Trzeciak, Martyna O., Kozlowski, Piotr, Galka-Marciniak, Paulina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8686061/
https://www.ncbi.nlm.nih.gov/pubmed/34977675
http://dx.doi.org/10.1016/j.xpro.2021.101023
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author Urbanek-Trzeciak, Martyna O.
Kozlowski, Piotr
Galka-Marciniak, Paulina
author_facet Urbanek-Trzeciak, Martyna O.
Kozlowski, Piotr
Galka-Marciniak, Paulina
author_sort Urbanek-Trzeciak, Martyna O.
collection PubMed
description Here, we present the miRMut protocol to annotate mutations found in miRNA genes based on whole-exome sequencing (WES) or whole-genome sequencing (WGS) results. The pipeline assigns mutation characteristics, including miRNA gene IDs (miRBase and MirGeneDB), mutation localization within the miRNA precursor structure, potential RNA-binding motif disruption, the ascription of mutation according to Human Genome Variation Society (HGVS) nomenclature, and miRNA gene characteristics, such as miRNA gene confidence and miRNA arm balance. The pipeline includes creating tabular and graphical summaries. For complete details on the use and execution of this protocol, please refer to Urbanek-Trzeciak et al. (2020).
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spelling pubmed-86860612021-12-30 miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing Urbanek-Trzeciak, Martyna O. Kozlowski, Piotr Galka-Marciniak, Paulina STAR Protoc Protocol Here, we present the miRMut protocol to annotate mutations found in miRNA genes based on whole-exome sequencing (WES) or whole-genome sequencing (WGS) results. The pipeline assigns mutation characteristics, including miRNA gene IDs (miRBase and MirGeneDB), mutation localization within the miRNA precursor structure, potential RNA-binding motif disruption, the ascription of mutation according to Human Genome Variation Society (HGVS) nomenclature, and miRNA gene characteristics, such as miRNA gene confidence and miRNA arm balance. The pipeline includes creating tabular and graphical summaries. For complete details on the use and execution of this protocol, please refer to Urbanek-Trzeciak et al. (2020). Elsevier 2021-12-15 /pmc/articles/PMC8686061/ /pubmed/34977675 http://dx.doi.org/10.1016/j.xpro.2021.101023 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Urbanek-Trzeciak, Martyna O.
Kozlowski, Piotr
Galka-Marciniak, Paulina
miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing
title miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing
title_full miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing
title_fullStr miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing
title_full_unstemmed miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing
title_short miRMut: Annotation of mutations in miRNA genes from human whole-exome or whole-genome sequencing
title_sort mirmut: annotation of mutations in mirna genes from human whole-exome or whole-genome sequencing
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8686061/
https://www.ncbi.nlm.nih.gov/pubmed/34977675
http://dx.doi.org/10.1016/j.xpro.2021.101023
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