Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies. It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome da...

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Bibliographic Details
Published in:Nature protocols Vol. 15; no. 3; pp. 799 - 821
Main Authors: Chong, Jasmine, Liu, Peng, Zhou, Guangyan, Xia, Jianguo
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 01.03.2020
Nature Publishing Group
Subjects:
631/114/2398
631/114/794
631/1647/48
631/326/2565
Analysis
Analytical Chemistry
Bioinformatics
Biological Techniques
Biomedical and Life Sciences
Computational biology
Computational Biology/Bioinformatics
Correlation analysis
Data analysis
Data processing
Databases, Genetic
DNA, Bacterial
Functional analysis
Interfaces
Life Sciences
Meta-analysis
Meta-Analysis as Topic
Metagenomics - methods
Methods
Microarrays
Microbial colonies
Microbiomes
Microbiota - genetics
Microbiota - physiology
Microorganisms
Models, Statistical
Modules
Online databases
Organic Chemistry
Performance prediction
Protocol
Researchers
RNA, Bacterial
Shotguns
Software
Statistical analysis
Statistics
User interfaces
Web analytics
Websites
Canada
ISSN:1754-2189, 1750-2799, 1750-2799
Online Access:Get full text
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Description
Summary:MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies. It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome data processing, statistical analysis, functional profiling and comparison with public datasets or known microbial signatures. MicrobiomeAnalyst currently contains four modules: Marker-gene Data Profiling (MDP), Shotgun Data Profiling (SDP), Projection with Public Data (PPD), and Taxon Set Enrichment Analysis (TSEA). This protocol will first introduce the MDP module by providing a step-wise description of how to prepare, process and normalize data; perform community profiling; identify important features; and conduct correlation and classification analysis. We will then demonstrate how to perform predictive functional profiling and introduce several unique features of the SDP module for functional analysis. The last two sections will describe the key steps involved in using the PPD and TSEA modules for meta-analysis and visual exploration of the results. In summary, MicrobiomeAnalyst offers a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces. The complete protocol can be executed in ~70 min. This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data.
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ISSN:1754-2189
1750-2799
1750-2799
DOI:10.1038/s41596-019-0264-1