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Cell marker selection #12

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taiwaness opened this issue Dec 3, 2021 · 2 comments

Member

taiwaness commented Dec 3, 2021

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

Member Author

taiwaness commented Dec 29, 2021

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

Collaborator

chiehyujessie commented Jan 5, 2022

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)

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