6種細胞特徵數據庫 (Cell type annotation database)-查詢細胞類型的好幫手!

前言

SingleR (2.2.0)自動化判別細胞類型的文章中不難看出,使用不同數據庫當作細胞註釋的參考,會得到相似但卻不太一樣的結果。因此,這類自動化判別細胞的套件,只能用於初步判斷細胞類型。如果想要更進一步確認細胞的類型,則需要仰賴研究人員的知識和經驗進行判斷。以下是一些單細胞數據分析常用的特徵數據庫(cell marker database),使用方法都很簡單,只需要輸入特徵基因名稱,就能從數據庫找尋到可能的對應細胞,提供大家參考。

1. PanglaoDB

數據庫網址: https://panglaodb.se/

參考文獻: Oscar Franzén, Li-Ming Gan, Johan L M Björkegren, PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data, Database, Volume 2019, 2019, baz046.

PanglaoDB

2. CellMarker 2.0

數據庫網址: http://117.50.127.228/CellMarker/index.html

參考文獻: Congxue Hu, Tengyue Li, Yingqi Xu, Xinxin Zhang et al., CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D870–D876.

3. The Human Protein Atlas

數據庫網址: https://www.proteinatlas.org/

參考文獻: Peter J. Thul and Cecilia Lindskog, The human protein atlas: A spatial map of the human proteome, Protein Sci. 2018 Jan; 27(1): 233–244.

4. Mouse Cell Atlas (MCA)

數據庫網址: https://bis.zju.edu.cn/MCA/index.html

參考文獻: Huiyu Sun, Yincong Zhou, Lijiang Fei, Haide Chen, Guoji Guo, scMCA: A Tool to Define Mouse Cell Types Based on Single-Cell Digital Expression, Methods Mol Biol. 2019;1935:91-96.

5. SingleCellBase

數據庫網址: http://cloud.capitalbiotech.com/SingleCellBase/index.jsp

參考文獻: Fanlin Meng, Wenyan Qin, Kunbang Liu, Yan Wang et al., singleCellBase: a high-quality manually curated database of cell markers for single cell annotation across multiple species, https://doi.org/10.21203/rs.3.rs-2039534/v1.

6. Single Cell Portal

數據庫網址: https://singlecell.broadinstitute.org/single_cell

您的分享,我非常感激!!!
MillionQuesn
MillionQuesn

一個旅居台灣的異鄉人,分享突然靈光一現的亮點。

文章: 46

發佈留言

發佈留言必須填寫的電子郵件地址不會公開。 必填欄位標示為 *

error: Alert: Content selection is disabled!!