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Table 1 Results of TCGA data evaluation of candidate cell type markers

From: Gene expression markers of Tumor Infiltrating Leukocytes

Cell type # Candidate genes # Selected markers Mean pairwise similarity statistic in TCGA Selected marker genes
B-cells 34 9 0.59 BLK, CD19, FCRL2, MS4A1, KIAA0125, TNFRSF17, TCL1A, SPIB, PNOC
CD45 1 1 aNA PTRPC
Cytotoxic cells 18 10 0.69 PRF1, GZMA, GZMB, NKG7, GZMH, KLRK1, KLRB1, KLRD1, CTSW, GNLY
DC 7 3 0.46 CCL13, CD209, HSD11B1
Exhausted CD8 5 4 0.44 LAG3, CD244, EOMES, PTGER4
Macrophages 33 4 0.71 CD68, CD84, CD163, MS4A4A
Mast cells 31 5 0.74 TPSB2, TPSAB1, CPA3, MS4A2, HDC
Neutrophils 32 7 0.48 FPR1, SIGLEC5, CSF3R, FCAR, FCGR3B, CEACAM3, S100A12
NK CD56dim cells 14 4 0.40 KIR2DL3, KIR3DL1, KIR3DL2, IL21R
NK cells 36 3 0.47 XCL1, XCL2, NCR1
T-cells 13 6 0.81 CD6, CD3D, CD3E, SH2D1A, TRAT1, CD3G
Th1 cells 27 1 aNA TBX21
Treg 18 2 aNA FOXP3
CD8 T cells 35 2 0.51 CD8A, CD8B
CD4 cells 20 0 bNA  
  1. aOnly one marker gene; quality impossible to assess in expression data alone
  2. bCalculated as the T-cell score minus the CD8 cell score
  3. Cell types lacking acceptable marker genes are omitted. The mean pairwise similarity statistic is a measurement of how well a gene set adheres to the co-expression patterns expected from a set of perfect marker genes, with a score of 1 indicating perfect marker-like behavior