clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

Tianzhi Wu; Erqiang Hu; Shuangbin Xu; Meijun Chen; Pingfan Guo; Zehan Dai; Tingze Feng; Lang Zhou; Wenli Tang; Li Zhan; Xiaocong Fu; Shanshan Liu; Xiaochen Bo; Guangchuang Yu

The Innovation (Aug 2021)

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

Tianzhi Wu,
Erqiang Hu,
Shuangbin Xu,
Meijun Chen,
Pingfan Guo,
Zehan Dai,
Tingze Feng,
Lang Zhou,
Wenli Tang,
Li Zhan,
Xiaocong Fu,
Shanshan Liu,
Xiaochen Bo,
Guangchuang Yu

Affiliations

Tianzhi Wu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Erqiang Hu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Shuangbin Xu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Meijun Chen: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Pingfan Guo: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Zehan Dai: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Tingze Feng: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Lang Zhou: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Wenli Tang: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Li Zhan: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Xiaocong Fu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Shanshan Liu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
Xiaochen Bo: Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China; Corresponding author
Guangchuang Yu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China; Corresponding author

Journal volume & issue: Vol. 2, no. 3
p. 100141

Abstract

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Summary: Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible. To meet these requirements, we present here an updated version of our popular Bioconductor package, clusterProfiler 4.0. This package has been enhanced considerably compared with its original version published 9 years ago. The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases. It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization. Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.

Published in The Innovation

ISSN: 2666-6758 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://www.cell.com/the-innovation

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