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. 2019 Jan 8;47(D1):D721-D728.
doi: 10.1093/nar/gky900.

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

Xinxin Zhang  1 , Yujia Lan  1 , Jinyuan Xu  1 , Fei Quan  1 , Erjie Zhao  1 , Chunyu Deng  1 , Tao Luo  1 , Liwen Xu  1 , Gaoming Liao  1 , Min Yan  1 , Yanyan Ping  1 , Feng Li  1 , Aiai Shi  1 , Jing Bai  1 , Tingting Zhao  2 , Xia Li  1 , Yun Xiao  1
Affiliations

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

Xinxin Zhang et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Overview of data collection, annotation and database interface.
Figure 2.
Figure 2.
Statistics of cell markers in CellMarker. (A) Distribution of cell markers for different cell types in human. (B) Distribution of cell markers for different tissue types in human. (C) Distribution of cell markers for different cell types in mouse. (D) Distribution of cell markers for different tissue types in mouse. (E) The numbers of cell marker entries from four different sources. (F) The top 10 widely studied cell types for cell marker research in blood. (G) The top 10 frequently used cell markers in T cell.
Figure 3.
Figure 3.
A schematic workflow of CellMarker. (A) The web images in the home page allow to quick search for cell markers of cells in different tissues. (B) The ‘Browse’ and ‘Search’ pages allow the users to browse and search cell markers.
Figure 4.
Figure 4.
Search result pages of CellMarker. (A) Results of a search for cell markers of Regulatory T (Treg) cell in blood. The cell markers of this cell type are presented in an intuitive statistical graph of cell marker prevalence. An integrative cell marker list for this cell type is provided. The detailed tables of cell marker entries derived from different sources are obtained in the below. (B) The results of the search for cell marker CD133. An interactive bubble chart and a table of comprehensive information of the cell marker are shown.
See this image and copyright information in PMC

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