CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data

• Published in: Nucleic acids research 2023-01, Vol.51 (D1), p.D870-D876
• Main Authors: Hu, Congxue, Li, Tengyue, Xu, Yingqi, Zhang, Xinxin, Li, Feng, Bai, Jing, Chen, Jing, Jiang, Wenqi, Yang, Kaiyue, Ou, Qi, Li, Xia, Wang, Peng, Zhang, Yunpeng
• Format: Article
• Language: English
• Subjects: Animals; Cells - cytology; Database Issue; Databases, Genetic; Databases, Nucleic Acid; Humans; Mice; Neoplasms - genetics; Sequence Analysis; Single-Cell Gene Expression Analysis
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkac947

CellMarker 2.0 (http://bio-bigdata.hrbmu.edu.cn/CellMarker or http://117.50.127.228/CellMarker/) is an updated database that provides a manually curated collection of experimentally supported markers of various cell types in different tissues of human and mouse. In addition, web tools for analyzing single cell sequencing data are described. We have updated CellMarker 2.0 with more data and several new features, including (i) Appending 36 300 tissue-cell type-maker entries, 474 tissues, 1901 cell types and 4566 markers over the previous version. The current release recruits 26 915 cell markers, 2578 cell types and 656 tissues, resulting in a total of 83 361 tissue-cell type-maker entries. (ii) There is new marker information from 48 sequencing technology sources, including 10X Chromium, Smart-Seq2 and Drop-seq, etc. (iii) Adding 29 types of cell markers, including protein-coding gene lncRNA and processed pseudogene, etc. Additionally, six flexible web tools, including cell annotation, cell clustering, cell malignancy, cell differentiation, cell feature and cell communication, were developed to analysis and visualization of single cell sequencing data. CellMarker 2.0 is a valuable resource for exploring markers of various cell types in different tissues of human and mouse.