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EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a co...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602470/ https://www.ncbi.nlm.nih.gov/pubmed/31106358 http://dx.doi.org/10.1093/nar/gkz398 |
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author | Krainer, Julie Weinhäusel, Andreas Hanak, Karel Pulverer, Walter Özen, Seza Vierlinger, Klemens Pabinger, Stephan |
author_facet | Krainer, Julie Weinhäusel, Andreas Hanak, Karel Pulverer, Walter Özen, Seza Vierlinger, Klemens Pabinger, Stephan |
author_sort | Krainer, Julie |
collection | PubMed |
description | DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/. |
format | Online Article Text |
id | pubmed-6602470 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-66024702019-07-05 EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies Krainer, Julie Weinhäusel, Andreas Hanak, Karel Pulverer, Walter Özen, Seza Vierlinger, Klemens Pabinger, Stephan Nucleic Acids Res Web Server Issue DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/. Oxford University Press 2019-07-02 2019-05-20 /pmc/articles/PMC6602470/ /pubmed/31106358 http://dx.doi.org/10.1093/nar/gkz398 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Krainer, Julie Weinhäusel, Andreas Hanak, Karel Pulverer, Walter Özen, Seza Vierlinger, Klemens Pabinger, Stephan EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
title | EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
title_full | EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
title_fullStr | EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
title_full_unstemmed | EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
title_short | EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
title_sort | epic-tabsat: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602470/ https://www.ncbi.nlm.nih.gov/pubmed/31106358 http://dx.doi.org/10.1093/nar/gkz398 |
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