CellMarker: a manually curated resource of cell markers in human and mouse

Abstract One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substan...

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Bibliographic Details
Published in:Nucleic acids research 2019-01, Vol.47 (D1), p.D721-D728
Main Authors: Zhang, Xinxin, Lan, Yujia, Xu, Jinyuan, Quan, Fei, Zhao, Erjie, Deng, Chunyu, Luo, Tao, Xu, Liwen, Liao, Gaoming, Yan, Min, Ping, Yanyan, Li, Feng, Shi, Aiai, Bai, Jing, Zhao, Tingting, Li, Xia, Xiao, Yun
Format: Article
Language:English
Subjects:
Animals
Database Issue
Databases, Genetic
Humans
Mice
Sequence Analysis - methods
Sequence Analysis - standards
Single-Cell Analysis - methods
Single-Cell Analysis - standards
Software
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Summary:Abstract One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substantial cell markers for distinguishing different cell types in tissues. Here, we developed the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/), aiming to provide a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. By manually curating over 100 000 published papers, 4124 entries including the cell marker information, tissue type, cell type, cancer information and source, were recorded. At last, 13 605 cell markers of 467 cell types in 158 human tissues/sub-tissues and 9148 cell makers of 389 cell types in 81 mouse tissues/sub-tissues were collected and deposited in CellMarker. CellMarker provides a user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Furthermore, a summarized marker prevalence in each cell type is graphically and intuitively presented through a vivid statistical graph. We believe that CellMarker is a comprehensive and valuable resource for cell researches in precisely identifying and characterizing cells, especially at the single-cell level.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gky900