Table 3.
T-cell activation signatures in tumors at baseline that correlated with PFS.*
| Gene Signature Name | Genes | Category | Original P value | PPV | FDR Q value |
|---|---|---|---|---|---|
|
| |||||
| GSE26928_EFF_MEMORY_VS_CXCR5_POS_CD4_TCELL_DN | 153 | C7 | 0.001 | 0 | 0 |
| LYMPHOCYTE_DIFFERENTIATION | 19 | C5 | 0.001 | 0.001 | 0.06 |
| GSE22045_TREG_VS_TCONV_DN | 159 | C7 | 0.001 | 0.002 | 0.08 |
| GSE14308_TH1_VS_INDUCED_TREG_UP | 178 | C7 | 0.003 | 0.01 | 0.08 |
| ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN | 32 | C2 | 0.004 | 0.01 | 0.09 |
| BIOCARTA_IL7_PATHWAY | 16 | C2 | 0.004 | 0.01 | 0.09 |
| IMMUNE_SYSTEM_DEVELOPMENT | 58 | C5 | 0.004 | 0.01 | 0.09 |
| T_CELL_DIFFERENTIATION | 11 | C5 | 0.004 | 0.01 | 0.09 |
| GSE13306_TREG_VS_TCONV_SPLEEN_DN | 156 | C7 | 0.01 | 0.01 | 0.08 |
| POSITIVE_REGULATION_OF_IMMUNE_SYSTEM_PROCESS | 39 | C5 | 0.01 | 0.02 | 0.09 |
| GSE3982_MEMORY_CD4_TCELL_VS_TH1_UP | 173 | C7 | 0.01 | 0.02 | 0.08 |
| GSE7852_TREG_VS_TCONV_LN_DN | 140 | C7 | 0.01 | 0.03 | 0.08 |
| LYMPHOCYTE_ACTIVATION | 49 | C5 | 0.01 | 0.03 | 0.09 |
| BIOCARTA_TCR_PATHWAY | 42 | C2 | 0.01 | 0.03 | 0.09 |
| GSE10239_MEMORY_VS_KLRG1HIGH_EFF_CD8_TCELL_UP | 143 | C7 | 0.02 | 0.03 | 0.08 |
| GSE22886_NAIVE_CD8_TCELL_VS_MEMORY_TCELL_DN | 191 | C7 | 0.01 | 0.03 | 0.08 |
| GSE17580_TREG_VS_TEFF_S_MANSONI_INF_DN | 172 | C7 | 0.02 | 0.03 | 0.08 |
| GSE7852_TREG_VS_TCONV_DN | 166 | C7 | 0.02 | 0.03 | 0.08 |
| POSITIVE_REGULATION_OF_IMMUNE_RESPONSE | 20 | C5 | 0.02 | 0.03 | 0.09 |
| GSE7460_TREG_VS_TCONV_ACT_DN | 145 | C7 | 0.02 | 0.04 | 0.08 |
| GSE20366_TREG_VS_TCONV_DN | 163 | C7 | 0.02 | 0.04 | 0.08 |
| MARSON_FOXP3_TARGETS_DN | 49 | C2 | 0.02 | 0.05 | 0.10 |
Listed are selected gene signatures whose expression levels in gene expression profiles of pretreatment tumor biopsies from 18 patients were found to correlate significantly and positively with PFS by univariate Cox regression. Candidate signatures were drawn from the C2, C5, and C7 categories of the Molecular Signatures Database (http://www.broadinstitute.org/gsea/msigdb). The p value for each signature tested in isolation is shown, as well as its position (PPV, permutation p value) in the distribution of p values of 1000 signatures of randomly-selected genes similarly tested for correlation with PFS. A false discovery rate (FDR) control for multiple comparisons is used, based on the number of candidate signatures with isolated p values ≤ 0.05.