Annotation of cell types (ACT): a convenient web server for cell type annotation
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Published:2023-11-03
Issue:1
Volume:15
Page:
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ISSN:1756-994X
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Container-title:Genome Medicine
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language:en
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Short-container-title:Genome Med
Author:
Quan Fei, Liang Xin, Cheng Mingjiang, Yang Huan, Liu Kun, He Shengyuan, Sun Shangqin, Deng Menglan, He Yanzhen, Liu Wei, Wang Shuai, Zhao Shuxiang, Deng Lantian, Hou Xiaobo, Zhang Xinxin, Xiao YunORCID
Abstract
Abstract
Background
The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge.
Methods
To address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods.
Results
By integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT (http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified.
Conclusions
We developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification.
Funder
National Natural Science Foundation of China National Science Foundation of Heilongjiang Province HMU Marshal Initiative Funding China Postdoctoral Science Foundation Heilongjiang Postdoctoral Foundation Fundamental Research Funds for the Provincial Universities of Heilongjiang
Publisher
Springer Science and Business Media LLC
Subject
Genetics (clinical),Genetics,Molecular Biology,Molecular Medicine
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