Table 1.
Immunological gene sets significantly regulated in both TAC and NT in bioreactor. ssGSEA was performed using MSigDB C7 collection of immunological gene sets. Next, differential regulation of these gene sets was examined by using limma. Only corrected p-values < 0.05 were examined further (see Methods). Gene sets significantly regulated in both TAC and NT are presented in the table. Gene sets related to T cell memory are highlighted in yellow
| GeneSet | Description | TAC |
NT |
|---|---|---|---|
| p-value | p-value | ||
| Down-regulated in Bioreactor | |||
| GSE11057_CD4_EFF_MEM_VS_PBMC_UP | Genes up-regulated in comparison of effector memory T cells versus peripheral blood mononuclear cells (PBMC). | 4.93E-02 | 3.51E-02 |
| GSE11057_EFF_MEM_VS_CENT_MEM_CD4_TCELL_UP | Genes up-regulated in comparison of effector memory T cells versus central memory T cells from peripheral blood mononuclear cells (PBMC). | 1.23E-02 | 9.47E-03 |
| GSE11057_NAIVE_VS_EFF_MEMORY_CD4_TCELL_DN | Genes down-regulated in comparison of naive T cells versus effector memory T cells. | 4.93E-02 | 3.80E-02 |
| GSE26928_CENTR_MEMORY_VS_CXCR5_POS_CD4_TCELL_UP | Genes up-regulated in comparison of CD4 central memory T cells versus CD4 CXCR5 + T cells. | 3.51E-02 | 2.21E-02 |
| GSE11924_TH1_VS_TH2_CD4_TCELL_DN | Genes down-regulated in comparison of Th1 cells versus Th2 cells. | 9.46E-03 | 1.4E-02 |
| Up-regulated in Bioreactor | |||
| GSE16522_MEMORY_VS_NAIVE_CD8_TCELL_DN | Genes down-regulated in comparison of rested memory CD8 T cells from pmel-1 mice versus rested naive CD8 T cells from pmel-1 mice. | 1.85E-02 | 1.23E-02 |
| GSE21360_NAIVE_VS_SECONDARY_MEMORY_CD8_TCELL_UP | Genes up-regulated in CD8 T cells: naïve versus 2ʹ memory. | 6.40E-03 | 6.40E-03 |
| GSE21360_SECONDARY_VS_QUATERNARY_MEMORY_CD8_TCELL_DN | Genes down-regulated in memory CD8 T cells: 2ʹ versus 4ʹ. | 6.74E-03 | 6.40E-03 |
| GSE22886_NAIVE_CD4_TCELL_VS_MEMORY_TCELL_UP | Genes up-regulated in comparison of naive CD4 T cells versus unstimulated memory CD4 CD8 T cells. | 9.82E-03 | 6.74E-03 |
| GSE23321_CD8_STEM_CELL_MEMORY_VS_CENTRAL_MEMORY_CD8_TCELL_UP | Genes up-regulated in CD8 T cells: stem cell memory versus central memory. | 6.74E-03 | 6.40E-03 |
| KAECH_DAY8_EFF_VS_MEMORY_CD8_TCELL_DN | Genes down-regulated in effector CD8 T cells at the peak expansion phase (day 8 after LCMV-Armstrong infection) compared to memory CD8 T cells (day 40+ after LCMV-Armstrong infection) | 3.51E-02 | 4.66E-02 |
| GSE24574_BCL6_HIGH_TFH_VS_TCONV_CD4_TCELL_UP | Genes up-regulated in BCL6 [GeneID = 604] high follicular helper T cells versus T conv cells. | 4.1E-02 | 3.5E-02 |
| GSE33425_CD161_INT_VS_NEG_CD8_TCELL_DN | Genes down-regulated in CD8 T cells: KLRB1 int versus KLRB1- . | 2.1E-02 | 3.3E-02 |
| GSE9650_EFFECTOR_VS_EXHAUSTED_CD8_TCELL_DN | Genes down-regulated in comparison of effector CD8 T cells versus exhausted CD8 T cells. | 1.4E-02 | 9.5E-03 |
| GSE9650_GP33_VS_GP276_LCMV_SPECIFIC_EXHAUSTED_CD8_TCELL_UP | Genes up-regulated in comparison of virus specific (gp33) exhausted CD8 T cells versus the virus specific (gp276) cells. | 4.1E-02 | 3.4E-02 |