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CoVennTree: a new method for the comparative analysis of large datasets
The visualization of massive datasets, such as those resulting from comparative metatranscriptome analyses or the analysis of microbial population structures using ribosomal RNA sequences, is a challenging task. We developed a new method called CoVennTree (Comparative weighted Venn Tree) that simult...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335276/ https://www.ncbi.nlm.nih.gov/pubmed/25750651 http://dx.doi.org/10.3389/fgene.2015.00043 |
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author | Lott, Steffen C. Voß, Björn Hess, Wolfgang R. Steglich, Claudia |
author_facet | Lott, Steffen C. Voß, Björn Hess, Wolfgang R. Steglich, Claudia |
author_sort | Lott, Steffen C. |
collection | PubMed |
description | The visualization of massive datasets, such as those resulting from comparative metatranscriptome analyses or the analysis of microbial population structures using ribosomal RNA sequences, is a challenging task. We developed a new method called CoVennTree (Comparative weighted Venn Tree) that simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. With the introduction of weighted Venn structures, the contents and relationships of various datasets can be correlated and simultaneously aggregated without losing information. We demonstrate the suitability of this approach using a dataset of 16S rDNA sequences obtained from microbial populations at three different depths of the Gulf of Aqaba in the Red Sea. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance. |
format | Online Article Text |
id | pubmed-4335276 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-43352762015-03-06 CoVennTree: a new method for the comparative analysis of large datasets Lott, Steffen C. Voß, Björn Hess, Wolfgang R. Steglich, Claudia Front Genet Genetics The visualization of massive datasets, such as those resulting from comparative metatranscriptome analyses or the analysis of microbial population structures using ribosomal RNA sequences, is a challenging task. We developed a new method called CoVennTree (Comparative weighted Venn Tree) that simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. With the introduction of weighted Venn structures, the contents and relationships of various datasets can be correlated and simultaneously aggregated without losing information. We demonstrate the suitability of this approach using a dataset of 16S rDNA sequences obtained from microbial populations at three different depths of the Gulf of Aqaba in the Red Sea. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance. Frontiers Media S.A. 2015-02-20 /pmc/articles/PMC4335276/ /pubmed/25750651 http://dx.doi.org/10.3389/fgene.2015.00043 Text en Copyright © 2015 Lott, Voß, Hess and Steglich. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Lott, Steffen C. Voß, Björn Hess, Wolfgang R. Steglich, Claudia CoVennTree: a new method for the comparative analysis of large datasets |
title | CoVennTree: a new method for the comparative analysis of large datasets |
title_full | CoVennTree: a new method for the comparative analysis of large datasets |
title_fullStr | CoVennTree: a new method for the comparative analysis of large datasets |
title_full_unstemmed | CoVennTree: a new method for the comparative analysis of large datasets |
title_short | CoVennTree: a new method for the comparative analysis of large datasets |
title_sort | covenntree: a new method for the comparative analysis of large datasets |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335276/ https://www.ncbi.nlm.nih.gov/pubmed/25750651 http://dx.doi.org/10.3389/fgene.2015.00043 |
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