GeneTrail: A Framework for the Analysis of High-Throughput Profiles
Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are req...
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2021-09-01
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doaj-d22b154b8f9e4316bd346f6623ee1e962021-09-16T05:03:20ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2021-09-01810.3389/fmolb.2021.716544716544GeneTrail: A Framework for the Analysis of High-Throughput ProfilesNico Gerstner0Tim Kehl1Kerstin Lenhof2Lea Eckhart3Lara Schneider4Daniel Stöckel5Christina Backes6Eckart Meese7Andreas Keller8Andreas Keller9Andreas Keller10Hans-Peter Lenhof11Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyHealthcare Digital & Data, Merck Healthcare KGaA, Darmstadt, GermanyCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyDepartment of Human Genetics, Saarland University, Homburg, GermanyCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyChair for Clinical Bioinformatics, Saarland University, Saarbrücken, GermanyDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, United StatesCenter for Bioinformatics, Saarland Informatics Campus, Saarbrücken, GermanyExperimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms.GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de.https://www.frontiersin.org/articles/10.3389/fmolb.2021.716544/fullCOVID-19enrichment analysisgene regulationweb servertime-serie analysissingle-cell analysis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nico Gerstner Tim Kehl Kerstin Lenhof Lea Eckhart Lara Schneider Daniel Stöckel Christina Backes Eckart Meese Andreas Keller Andreas Keller Andreas Keller Hans-Peter Lenhof |
spellingShingle |
Nico Gerstner Tim Kehl Kerstin Lenhof Lea Eckhart Lara Schneider Daniel Stöckel Christina Backes Eckart Meese Andreas Keller Andreas Keller Andreas Keller Hans-Peter Lenhof GeneTrail: A Framework for the Analysis of High-Throughput Profiles Frontiers in Molecular Biosciences COVID-19 enrichment analysis gene regulation web server time-serie analysis single-cell analysis |
author_facet |
Nico Gerstner Tim Kehl Kerstin Lenhof Lea Eckhart Lara Schneider Daniel Stöckel Christina Backes Eckart Meese Andreas Keller Andreas Keller Andreas Keller Hans-Peter Lenhof |
author_sort |
Nico Gerstner |
title |
GeneTrail: A Framework for the Analysis of High-Throughput Profiles |
title_short |
GeneTrail: A Framework for the Analysis of High-Throughput Profiles |
title_full |
GeneTrail: A Framework for the Analysis of High-Throughput Profiles |
title_fullStr |
GeneTrail: A Framework for the Analysis of High-Throughput Profiles |
title_full_unstemmed |
GeneTrail: A Framework for the Analysis of High-Throughput Profiles |
title_sort |
genetrail: a framework for the analysis of high-throughput profiles |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Molecular Biosciences |
issn |
2296-889X |
publishDate |
2021-09-01 |
description |
Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms.GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de. |
topic |
COVID-19 enrichment analysis gene regulation web server time-serie analysis single-cell analysis |
url |
https://www.frontiersin.org/articles/10.3389/fmolb.2021.716544/full |
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