参考内容
single cell marker 基因数据库
https://www.jianshu.com/p/9d7789cc6d97
CellMarker:用来做细胞标记,很nice
https://zhuanlan.zhihu.com/p/300613622
数据库:
- cellMarker(2019年1月08日)
数据库地址: http://bio-bigdata.hrbmu.edu.cn/CellMarker/
关于该数据库的文献的内容发表在《Nucleic Acids Res》上
数据库介绍:
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.
评价:cellmarker数据库是专门用于获得cellmarker的,从100 000篇文献中获得的特征基因数据。
- panglaodb(2019年1月)
数据库地址:https://panglaodb.se/
关于该数据库的文献发表在Database(Oxford)上
数据库介绍:
PanglaoDB contains pre-processed and pre-computed analyses from more than 1054 single-cell experiments covering most major single cell platforms and protocols, based on more than 4 million cells from a wide range of tissues and organs.In addition, we have established a community-curated cell-type marker compendium, containing more than 6000 gene-cell-type associations, as a resource for automatic annotation of cell types.
评价:这个数据库的基因是来源于原始数据后分析得到的结果,通过tSNE降维聚类后,了解到某基因在某个细胞内,因此并不表明,该基因就是该细胞簇的特征基因,但有利于,利用该数据集去给单细胞进行注释。
基因表达的组织细胞特异性:同一基因,在不同组织,不同细胞中表达。
3. CUSABIO
评价:完全不适用。
https://www.cusabio.com/index.php?m=search&c=index&a=init&dosubmit=1&catid=init&typeid=&siteid=1&q=%CE%B3%CE%B4Tcell
- rndsystems
评价:这个数据库的marker是细胞表面分子marker,和转录组的marker还是不一样。因此不使用。
https://www.rndsystems.com/cn/resources/cell-markers/immune-cells
- SCsig:
https://www.gsea-msigdb.org/gsea/msigdb/supplementary_genesets.jsp#SCSig
评价:这是一个基于GSEA分析获得的单细胞测序的marker基因数据集,这个数据集包含的数量比较少。