Table 1.
Lists of identified potential biomarkers
| CA versus No-CA | Post- versus pre-treatment | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Probe set | Gene | P value | Pre-treatment mean expression ratio | Post-treatment mean expression ratio | Probe set | Gene | P value | No-CA mean fold change | CA mean fold change |
| 210029_at | IDO1 | 9.0E−05 | 7.5 | 5.5 | 206869_at | CHAD | 2.4E−03 | 1.2 | 5.3 |
| 205388_at | TNNC2 | 8.7E−03 | 4.9 | 7.2 | 220423_at | PLA2G2D | 1.2E−07 | −1.0 | 4.7 |
| 202747_s_at | ITM2A | 5.9E−03 | 4.3 | 2.3 | 206641_at | TNFRSF17 | 2.7E−04 | 1.2 | 4.2 |
| 202746_at | ITM2A | 3.4E−03 | 4.0 | 2.4 | 210163_at | CXCL11 | 4.6E−03 | 2.3 | 4.0 |
| 204533_at | CXCL10 | 9.2E−05 | 3.5 | 3.2 | 206666_at | GZMK | 8.2E−06 | 1.8 | 3.8 |
| 211549_s_at | HPGD | 1.0E−02 | 3.5 | 2.5 | 205488_at | GZMA | 6.0E−06 | 2.0 | 3.8 |
| 203290_at | HLA-DQA1 | 7.6E−03 | 3.5 | 3.5 | 210321_at | GZMH | 1.2E−05 | 2.1 | 3.8 |
| 202269_x_at | GBP1 | 9.0E−06 | 3.4 | 3.1 | 207651_at | GPR171 | 8.0E−06 | 1.7 | 3.6 |
| 205295_at | CKMT2 | 7.0E−04 | 3.3 | 7.4 | 211469_s_at | CXCR6 | 5.0E−05 | 1.4 | 3.5 |
| 204834_at | FGL2 | 1.2E−06 | 3.3 | 3.0 | 210164_at | GZMB | 4.4E−04 | 3.2 | 3.5 |
| 210164_at | GZMB | 3.2E−03 | 3.2 | 3.4 | 204438_at | MRC1/MRC1L1 | 1.1E−04 | 1.4 | 3.5 |
| 214617_at | PRF1 | 2.1E−04 | 3.2 | 4.0 | 204891_s_at | LCK | 2.8E−06 | 1.7 | 3.4 |
| 208285_at | OR7A5 | 2.2E−03 | 3.1 | 2.6 | 220832_at | TLR8 | 6.7E−05 | 1.2 | 3.4 |
| 202270_at | GBP1 | 3.2E−06 | 3.1 | 3.3 | 219799_s_at | DHRS9 | 1.2E−04 | 1.3 | 3.4 |
| 211122_s_at | CXCL11 | 1.7E−03 | 3.0 | 4.9 | 206134_at | ADAMDEC1 | 1.8E−03 | 1.1 | 3.3 |
| 221601_s_at | FAIM3 | 7.8E−03 | 3.0 | 2.4 | 210031_at | CD247 | 5.6E−06 | 1.5 | 3.3 |
| 203915_at | CXCL9 | 2.6E−05 | 3.0 | 3.9 | 219812_at | PVRIG | 1.2E−05 | 1.5 | 3.2 |
| 205758_at | CD8A | 5.1E−04 | 2.8 | 3.7 | 204890_s_at | LCK | 2.5E−06 | 1.5 | 3.2 |
| 1405_i_at | CCL5 | 1.0E−04 | 2.7 | 3.7 | 205456_at | CD3E | 1.0E−04 | 1.6 | 3.2 |
| 213915_at | NKG7 | 4.7E−05 | 2.6 | 4.2 | 211122_s_at | CXCL11 | 3.1E−03 | 2.0 | 3.2 |
| 205907_s_at | OMD | 9.7E−03 | 2.6 | 3.4 | 220005_at | P2RY13 | 2.5E−04 | 1.1 | 3.2 |
| 217235_x_at | IGL@ | 5.7E−03 | 2.6 | 3.0 | 217022_s_at | IGH@ | 2.0E−03 | 1.2 | 3.2 |
| 205692_s_at | CD38 | 2.6E−03 | 2.6 | 3.8 | 206974_at | CXCR6 | 8.2E−05 | 1.5 | 3.1 |
| 208609_s_at | TNXB | 6.7E−03 | 2.5 | 2.7 | 207979_s_at | CD8B | 1.5E−05 | 1.5 | 3.1 |
| 221087_s_at | APOL3 | 6.8E−06 | 2.5 | 3.1 | 207419_s_at | RAC2 | 8.0E−06 | 1.4 | 3.1 |
| 204103_at | CCL4 | 7.7E−04 | 2.5 | 2.9 | 211649_x_at | IGH@ | 8.8E−03 | −1.1 | 3.1 |
| 214617_at | PRF1 | 1.7E−05 | 2.5 | 3.1 | |||||
| 205495_s_at | GNLY | 8.2E−03 | 3.6 | 3.1 | |||||
| 220485_s_at | SIRPG | 2.7E−07 | 1.2 | 3.0 | |||||
Left panel: probe sets with ≥2.5-fold higher mean pre-treatment expression in tumor biopsies from patients with CA than those with No-CA. Mean expression ratio in the post-treatment samples as well as P value for the test of a difference in mean expression between CA and No-CA is shown. Right panel: probe sets with ≥threefold increase in mean gene expression after treatment in the CA group. Fold change in the No-CA group as well as P value for the test of a difference between pre- and post-treatment expression is shown. Mean expression ratio gives (mean expression in CA group)/(mean expression in No-CA group). Mean fold change: positive values give mean of (post-treatment expression)/(pre-treatment expression); negative values give negative mean of (pre-treatment expression)/(post-treatment expression)