Cell marker selection

[taiwaness]

@chiehyujessie

Well known markers:

Cell Type	Markers
T cells (CD4+)	PTPRC, CD3D, CD4
T cells (CD8+)	PTPRC, CD3D, CD8A, CD8B
B cells	PTPRC, CD79A
NK cell	PTPRC, NKG7
Myeloid cells	PTPRC, LYZ
Endothelial	PLVAP
Fibroblast	ACTA2
Epithelial	EPCAM, KRT8

[taiwaness]

• tumor vs. normal markers
• our own dataset for showing maker expression

[chiehyujessie]

SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates
(publication in 2020/06)
https://pubmed.ncbi.nlm.nih.gov/32053146/
https://www.cellsurfer.net/surfacegenie
Shiny app -> https://gundrylab.shinyapps.io/surfacegenie/

• extract its surface prediction consensus (SPC) score to update our surface marker list
• use GenieScore to order the results of marker selection instead of p-value
• use the shiny app for marker selection (use small dataset to test first)