TABLE 2.
Description | Gene markers | COAD | READ | LIHC | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
None | Purity | None | Purity | None | Purity | ||||||||
Cor | P | Cor | P | Cor | P | Cor | P | Cor | P | Cor | P | ||
CD8+ T cell | CD8A | 0.361 | *** | 0.238 | *** | 0.425 | *** | 0.33 | *** | 0.01 | 0.849 | 0.063 | 0.243 |
CD8B | 0.207 | *** | 0.131 | ** | 0.182 | * | 0.158 | 0.0638 | −0.046 | 0.38 | −0.008 | 0.877 | |
T cell (general) | CD3D | 0.362 | *** | 0.229 | *** | 0.332 | *** | 0.215 | * | −0.135 | ** | −0.105 | 0.051 |
CD3E | 0.459 | *** | 0.348 | *** | 0.454 | *** | 0.366 | *** | −0.034 | 0.516 | 0.011 | 0.839 | |
CD2 | 0.418 | *** | 0.292 | *** | 0.412 | *** | 0.307 | *** | −0.034 | 0.51 | 0.007 | 0.903 | |
B cell | CD19 | 0.499 | *** | 0.428 | *** | 0.36 | *** | 0.323 | *** | 0.022 | 0.669 | 0.043 | 0.427 |
CD79A | 0.579 | *** | 0.505 | *** | 0.448 | *** | 0.355 | *** | 0.02 | 0.708 | 0.058 | 0.283 | |
Monocyte | CD86 | 0.435 | *** | 0.294 | *** | 0.424 | *** | 0.339 | *** | −0.059 | 0.253 | −0.035 | 0.522 |
CD115(CSF1R) | 0.517 | *** | 0.401 | *** | 0.568 | *** | 0.532 | *** | 0.027 | 0.599 | 0.054 | 0.319 | |
TAM | CCL2 | 0.407 | *** | 0.294 | *** | 0.493 | *** | 0.414 | *** | 0.082 | 0.114 | 0.127 | * |
CD68 | 0.338 | *** | 0.219 | *** | 0.445 | *** | 0.424 | *** | −0.094 | 0.071 | −0.067 | 0.216 | |
IL10 | 0.328 | *** | 0.226 | *** | 0.256 | *** | 0.193 | * | −0.107 | * | −0.101 | 0.06 | |
M1 Macrophage | INOS(NOS2) | 0.002 | 0.961 | −0.047 | 0.346 | 0.025 | 0.751 | 0.046 | 0.592 | 0.161 | ** | 0.158 | ** |
IRF5 | 0.26 | *** | 0.233 | *** | 0.2 | * | 0.209 | * | 0.019 | 0.709 | 0.01 | 0.859 | |
COX2(PTGS2) | 0.193 | *** | 0.134 | ** | 0.2 | ** | 0.107 | 0.208 | 0.02 | 0.704 | 0.047 | 0.384 | |
M2 Macrophage | CD163 | 0.455 | *** | 0.33 | *** | 0.508 | *** | 0.435 | *** | 0.04 | 0.44 | 0.069 | 0.198 |
VSIG4 | 0.427 | *** | 0.304 | *** | 0.45 | *** | 0.375 | *** | 0.004 | 0.937 | 0.034 | 0.533 | |
MS4A4A | 0.414 | *** | 0.279 | *** | 0.494 | *** | 0.408 | *** | 0.025 | 0.636 | 0.066 | 0.224 | |
Neutrophils | CD66b (CEACAM8) | −0.117 | * | −0.072 | 0.145 | −0.148 | 0.0563 | −0.072 | 0.399 | −0.068 | 0.194 | −0.06 | 0.266 |
CD11b (ITGAM) | 0.427 | *** | 0.322 | *** | 0.482 | *** | 0.392 | *** | −0.07 | 0.176 | −0.084 | 0.117 | |
CCR7 | 0.495 | *** | 0.399 | *** | 0.365 | *** | 0.317 | *** | 0.082 | 0.114 | 0.118 | * | |
Natural killer cell | KIR2DL1 | 0.206 | *** | 0.134 | ** | 0.141 | 0.0707 | 0.077 | 0.365 | 0.03 | 0.568 | 0.031 | 0.569 |
KIR2DL3 | 0.143 | ** | 0.038 | 0.443 | 0.198 | * | 0.144 | 0.0905 | 0.118 | * | 0.141 | ** | |
KIR2DL4 | 0.185 | *** | 0.079 | 0.114 | 0.196 | * | 0.091 | 0.287 | 0.006 | 0.905 | 0.029 | 0.592 | |
KIR3DL1 | 0.168 | *** | 0.053 | 0.290 | 0.148 | 0.0574 | 0.064 | 0.452 | 0.16 | ** | 0.183 | *** | |
KIR3DL2 | 0.26 | *** | 0.172 | *** | 0.304 | *** | 0.232 | ** | 0.074 | 0.157 | 0.125 | * | |
KIR3DL3 | 0.069 | 0.138 | 0.018 | 0.713 | 0.022 | 0.78 | 0.012 | 0.893 | 0.003 | 0.954 | 0.009 | 0.869 | |
KIR2DS4 | 0.137 | ** | 0.082 | 0.097 | 0.123 | 0.114 | 0.057 | 0.502 | 0.128 | * | 0.139 | ** | |
Dendritic cell | HLA−DPB1 | 0.44 | *** | 0.298 | *** | 0.453 | *** | 0.372 | *** | 0.053 | 0.306 | 0.087 | 0.105 |
HLA−DQB1 | 0.308 | *** | 0.181 | *** | 0.18 | * | 0.09 | 0.29 | −0.039 | 0.449 | −0.011 | 0.834 | |
HLA−DRA | 0.355 | *** | 0.204 | *** | 0.366 | *** | 0.244 | ** | 0.034 | 0.516 | 0.064 | 0.239 | |
HLA−DPA1 | 0.424 | *** | 0.283 | *** | 0.456 | *** | 0.36 | *** | 0.058 | 0.267 | 0.089 | 0.101 | |
BDCA−1(CD1C) | 0.466 | *** | 0.381 | *** | 0.538 | *** | 0.468 | *** | 0.018 | 0.726 | 0.034 | 0.534 | |
BDCA−4(NRP1) | 0.446 | *** | 0.323 | *** | 0.571 | *** | 0.505 | *** | 0.139 | ** | 0.152 | ** | |
CD11c (ITGAX) | 0.445 | *** | 0.315 | *** | 0.456 | *** | 0.385 | *** | −0.138 | ** | −0.143 | ** | |
Th1 | T−bet (TBX21) | 0.374 | *** | 0.261 | *** | 0.435 | *** | 0.367 | *** | 0.063 | 0.229 | 0.092 | 0.088 |
STAT4 | 0.417 | *** | 0.303 | *** | 0.422 | *** | 0.334 | *** | −0.044 | 0.397 | −0.026 | 0.628 | |
STAT1 | 0.233 | *** | 0.122 | * | 0.259 | *** | 0.172 | * | 0.027 | 0.607 | 0.043 | 0.422 | |
IFN−γ (IFNG) | 0.126 | ** | 0.023 | 0.645 | 0.148 | 0.0576 | 0.04 | 0.638 | 0.002 | 0.964 | 0.034 | 0.525 | |
TNF−α (TNF) | 0.229 | *** | 0.146 | ** | 0.333 | *** | 0.272 | ** | −0.037 | 0.483 | −0.036 | 0.501 | |
Th2 | GATA3 | 0.488 | *** | 0.397 | *** | 0.465 | *** | 0.399 | *** | 0.011 | 0.834 | 0.043 | 0.421 |
STAT6 | 0.175 | *** | 0.195 | *** | 0.224 | ** | 0.309 | *** | 0.268 | *** | 0.259 | *** | |
STAT5A | 0.3 | *** | 0.242 | *** | 0.163 | * | 0.159 | 0.0609 | 0.171 | *** | 0.198 | *** | |
IL13 | 0.155 | *** | 0.07 | 0.157 | 0.105 | 0.179 | −0.021 | 0.807 | −0.025 | 0.632 | −0.056 | 0.298 | |
Tfh | BCL6 | 0.41 | *** | 0.311 | *** | 0.44 | *** | 0.439 | *** | 0.043 | 0.414 | 0.029 | 0.591 |
IL21 | 0.133 | ** | 0.079 | 0.113 | 0.078 | 0.32 | 0.082 | 0.34 | 0.032 | 0.54 | 0.032 | 0.559 | |
Th17 | STAT3 | 0.312 | *** | 0.239 | *** | 0.398 | *** | 0.383 | *** | 0.037 | 0.477 | 0.042 | 0.435 |
IL17A | −0.063 | 0.179 | −0.08 | 0.106 | −0.078 | 0.316 | −0.062 | 0.472 | −0.032 | 0.541 | −0.006 | 0.91 | |
Treg | FOXP3 | 0.45 | *** | 0.343 | *** | 0.479 | *** | 0.433 | *** | 0.025 | 0.638 | 0.017 | 0.755 |
CCR8 | 0.412 | *** | 0.317 | *** | 0.475 | *** | 0.407 | *** | −0.053 | 0.308 | −0.05 | 0.358 | |
STAT5B | 0.314 | *** | 0.32 | *** | 0.442 | *** | 0.443 | *** | 0.225 | *** | 0.207 | *** | |
TGFβ(TGFB1) | 0.504 | *** | 0.386 | *** | 0.397 | *** | 0.301 | *** | −0.073 | 0.158 | −0.053 | 0.324 | |
T cell exhaustion | PD−1(PDCD1) | 0.366 | *** | 0.26 | *** | 0.382 | *** | 0.297 | *** | −0.067 | 0.199 | −0.031 | 0.566 |
CTLA4 | 0.369 | *** | 0.253 | *** | 0.37 | *** | 0.294 | *** | −0.152 | ** | −0.127 | * | |
LAG3 | 0.351 | *** | 0.235 | *** | 0.363 | *** | 0.303 | *** | −0.073 | 0.16 | −0.044 | 0.412 | |
TIM−3(HAVCR2) | 0.42 | *** | 0.281 | *** | 0.398 | *** | 0.313 | *** | −0.093 | 0.072 | −0.078 | 0.148 | |
GZMB | 0.02 | 0.674 | −0.033 | 0.511 | 0.134 | 0.0848 | 0.077 | 0.37 | 0.041 | 0.433 | 0.067 | 0.212 |
p < 0.05 were considered to be statistically significant (*p < 0.05, **p < 0.01, ***p < 0.001).