Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets

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

doi:10.1128/MSYSTEMS.01216-20

Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets

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 MartinoJon 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

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

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.

Original language	English (US)
Article number	e01216-20
Journal	mSystems
Volume	6
Issue number	2
DOIs	https://doi.org/10.1128/MSYSTEMS.01216-20
State	Published - Mar 2021
Externally published	Yes

Keywords

Bioinformatics
Microbial ecology

ASJC Scopus subject areas

Microbiology
Physiology
Biochemistry
Ecology, Evolution, Behavior and Systematics
Modeling and Simulation
Molecular Biology
Genetics
Computer Science Applications

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10.1128/MSYSTEMS.01216-20

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Cantrell, K., Fedarko, M. W., Rahman, G., McDonald, D., Yang, Y., Zaw, T., Gonzalez, A., Janssen, S., Estaki, M., Haiminen, N., Beck, K. L., Zhu, Q., Sayyari, E., Morton, J. T., Armstrong, G., Tripathi, A., Gauglitz, J. M., Marotz, C., Matteson, N. L., ... Knight, R. (2021). Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets. mSystems, 6(2), Article e01216-20. https://doi.org/10.1128/MSYSTEMS.01216-20

Cantrell, K, Fedarko, MW, Rahman, G, McDonald, D, Yang, Y, Zaw, T, Gonzalez, A, Janssen, S, Estaki, M, Haiminen, N, Beck, KL, Zhu, Q, Sayyari, E, Morton, JT, Armstrong, G, Tripathi, A, Gauglitz, JM, Marotz, C, Matteson, NL, Martino, C, Sanders, JG, Carrieri, AP, Song, SJ, Swafford, AD, Dorrestein, PC, Andersen, KG, Parida, L, Kim, HC, Vázquez-Baeza, Y & Knight, R 2021, 'Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets', mSystems, vol. 6, no. 2, e01216-20. https://doi.org/10.1128/MSYSTEMS.01216-20

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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.",

keywords = "Bioinformatics, Microbial ecology",

author = "Kalen Cantrell and Fedarko, {Marcus W.} and Gibraan Rahman and Daniel McDonald and Yimeng Yang and Thant Zaw and Antonio Gonzalez and Stefan Janssen and Mehrbod Estaki and Niina Haiminen and Beck, {Kristen L.} and Qiyun Zhu and Erfan Sayyari and Morton, {James T.} and George Armstrong and Anupriya Tripathi and Gauglitz, {Julia M.} and Clarisse Marotz and Matteson, {Nathaniel L.} and Cameron Martino and Sanders, {Jon G.} and Carrieri, {Anna Paola} and Song, {Se Jin} and Swafford, {Austin D.} and Dorrestein, {Pieter C.} and Andersen, {Kristian G.} and Laxmi Parida and Kim, {Ho Cheol} and Yoshiki V{\'a}zquez-Baeza and Rob Knight",

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year = "2021",

month = mar,

doi = "10.1128/MSYSTEMS.01216-20",

language = "English (US)",

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AU - Yang, Yimeng

AU - Zaw, Thant

AU - Gonzalez, Antonio

AU - Janssen, Stefan

AU - Estaki, Mehrbod

AU - Haiminen, Niina

AU - Beck, Kristen L.

AU - Zhu, Qiyun

AU - Sayyari, Erfan

AU - Morton, James T.

AU - Armstrong, George

AU - Tripathi, Anupriya

AU - Gauglitz, Julia M.

AU - Marotz, Clarisse

AU - Matteson, Nathaniel L.

AU - Martino, Cameron

AU - Sanders, Jon G.

AU - Carrieri, Anna Paola

AU - Song, Se Jin

AU - Swafford, Austin D.

AU - Dorrestein, Pieter C.

AU - Andersen, Kristian G.

AU - Parida, Laxmi

AU - Kim, Ho Cheol

AU - Vázquez-Baeza, Yoshiki

AU - Knight, Rob

PY - 2021/3

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N2 - 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.

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Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets

Abstract

Keywords

ASJC Scopus subject areas

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