EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

ABSTRACT Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 node...

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Autores principales:	Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	bioinformatics microbial ecology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/642607271af34b37a0d4e6c0fe02b930
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spelling	oai:doaj.org-article:642607271af34b37a0d4e6c0fe02b9302021-12-02T19:36:40ZEMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets10.1128/mSystems.01216-202379-5077https://doaj.org/article/642607271af34b37a0d4e6c0fe02b9302021-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.01216-20https://doaj.org/toc/2379-5077ABSTRACT Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of ‘omic data. IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.Kalen CantrellMarcus W. FedarkoGibraan RahmanDaniel McDonaldYimeng YangThant ZawAntonio GonzalezStefan JanssenMehrbod EstakiNiina HaiminenKristen L. BeckQiyun ZhuErfan SayyariJames T. MortonGeorge ArmstrongAnupriya TripathiJulia M. GauglitzClarisse MarotzNathaniel L. MattesonCameron MartinoJon G. SandersAnna Paola CarrieriSe Jin SongAustin D. SwaffordPieter C. DorresteinKristian G. AndersenLaxmi ParidaHo-Cheol KimYoshiki Vázquez-BaezaRob KnightAmerican Society for Microbiologyarticlebioinformaticsmicrobial ecologyMicrobiologyQR1-502ENmSystems, Vol 6, Iss 2 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	bioinformatics microbial ecology Microbiology QR1-502
spellingShingle	bioinformatics microbial ecology Microbiology QR1-502 Kalen Cantrell Marcus W. Fedarko Gibraan Rahman Daniel McDonald Yimeng Yang Thant Zaw Antonio Gonzalez Stefan Janssen Mehrbod Estaki Niina Haiminen Kristen L. Beck Qiyun Zhu Erfan Sayyari James T. Morton George Armstrong Anupriya Tripathi Julia M. Gauglitz Clarisse Marotz Nathaniel L. Matteson Cameron Martino Jon G. Sanders Anna Paola Carrieri Se Jin Song Austin D. Swafford Pieter C. Dorrestein Kristian G. Andersen Laxmi Parida Ho-Cheol Kim Yoshiki Vázquez-Baeza Rob Knight EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
description	ABSTRACT Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of ‘omic data. IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.
format	article
author	Kalen Cantrell Marcus W. Fedarko Gibraan Rahman Daniel McDonald Yimeng Yang Thant Zaw Antonio Gonzalez Stefan Janssen Mehrbod Estaki Niina Haiminen Kristen L. Beck Qiyun Zhu Erfan Sayyari James T. Morton George Armstrong Anupriya Tripathi Julia M. Gauglitz Clarisse Marotz Nathaniel L. Matteson Cameron Martino Jon G. Sanders Anna Paola Carrieri Se Jin Song Austin D. Swafford Pieter C. Dorrestein Kristian G. Andersen Laxmi Parida Ho-Cheol Kim Yoshiki Vázquez-Baeza Rob Knight
author_facet	Kalen Cantrell Marcus W. Fedarko Gibraan Rahman Daniel McDonald Yimeng Yang Thant Zaw Antonio Gonzalez Stefan Janssen Mehrbod Estaki Niina Haiminen Kristen L. Beck Qiyun Zhu Erfan Sayyari James T. Morton George Armstrong Anupriya Tripathi Julia M. Gauglitz Clarisse Marotz Nathaniel L. Matteson Cameron Martino Jon G. Sanders Anna Paola Carrieri Se Jin Song Austin D. Swafford Pieter C. Dorrestein Kristian G. Andersen Laxmi Parida Ho-Cheol Kim Yoshiki Vázquez-Baeza Rob Knight
author_sort	Kalen Cantrell
title	EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
title_short	EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
title_full	EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
title_fullStr	EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
title_full_unstemmed	EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
title_sort	empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/642607271af34b37a0d4e6c0fe02b930
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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

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