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

By Xinxin Zhang, Yujia Lan, Jinyuan Xu, Fei Quan, E. Zhao, Chunyu Deng, Tao Luo, Liwen Xu, Gaoming Liao, M. Yan and 7 more. Nucleic Acids Res., 2018

1,223 citations recorded by the source corpus.

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.

Subfields: Biophysics, Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b72080e56b86df4a6a646a804838ccba980ee6f9

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In Biophysics

1. Guangchuang Yu

In Molecular Biology

1. Li Zhan
2. Meijun Chen
3. Wenli Tang
4. Tianzhi Wu
5. Erqiang Hu
6. Zehan Dai
7. Shuangbing Xu
8. Tingze Feng

Citations in the corpus

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data (2019, neutral): “At the time when this work was initiated, there was no published database or comprehensive list of genes that can be used for automatic cell-type assignment [CellMarker (41) came out when this manuscript was in preparation].”
• clusterProfiler 4.0: A universal enrichment tool for interpreting omics data (2021, background): “It would be suitable for the timely analysis of gene sets with emerging interests, such as human cell markers 30 and COVID-19-related gene sets.”