Gene expression markers of Tumor Infiltrating Leukocytes

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

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

^aOnly one marker gene; quality impossible to assess in expression data alone
^bCalculated as the T-cell score minus the CD8 cell score
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