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