From: Biomarkers on melanoma patient T Cells associated with ipilimumab treatment
Gene symbol | Gene name | Fold-change | p-value | FDR | Pre-Mean ±SD | Post-Mean ±SD |
---|---|---|---|---|---|---|
a. Genes impacted by ipilimumab in CD4+ T cells | ||||||
Cell cycle related | ||||||
CDC2 | cell division cycle 2, G1 to S and G2 to M | 1.98 | 0.009 | 0.0409 | 18.61 ± 4.41 | 36.92 ± 21.36 |
 |  | 2.78 | 0.0142 | 0.0432 | 66.68 ± 59.31 | 185.59 ± 185.36 |
TYMS | thymidylate synthetase | 2.77 | 0.0075 | 0.0408 | 129.75 ± 58.10 | 358.99 ± 254.47 |
CCNB2 | cyclin B2 | 2.08 | 0.0142 | 0.0434 | 28.17 ± 11.75 | 58.49 ± 45.13 |
CDK7 | cyclin-dependent kinase 7 | 1.26 | 0.0074 | 0.0408 | 214.08 ± 75.01 | 270.13 ± 106.34 |
Cytokines-related | ||||||
PGDS | prostaglandin D2 synthase, hematopoietic | 2.2 | 0.0024 | 0.0393 | 14.20 ± 5.42 | 31.30 ± 14.57 |
 |  | 1.51 | 0.0048 | 0.04044 | 489.68 ± 470.87 | 740.39 ± 581.83 |
TGFBR3 | transforming growth factor β RIII | 1.39 | 0.0111 | 0.0411 | 505.71 ± 304.47 | 701.22 ± 246.45 |
IFNy | interferon, γ | 1.46 | 0.0255 | 0.0751 | 138.35 ± 104.72 | 201.55 ± 120.78 |
IL-7 | interleukin 7 | 1.28 | 0.0169 | 0.0511 | 15.43 ± 10.42 | 19.73 ± 8.89 |
STAT1 | signal transducer and activator of transcription 1 | 1.28 | 0.0081 | 0.0409 | 1141.96 ± 330.11 | 1460.67 ± 577.64 |
SCYE1 | small inducible cytokine subfamily E, member 1 | 1.27 | 0.0103 | 0.041 | 278.24 ± 100.74 | 352.82 ± 149.81 |
 |  | 0.80 | 0.0061 | 0.0406 | 5219.38 ± 1457.55 | 4291.38 ± 1772.32 |
IL-7R | interleukin 7 receptor | 0.74 | 0.0011 | 0.0375 | 3309.89 ± 1296.32 | 2467.81 ± 1094.22 |
IL-2Rα | interleukin 2 receptor, α | 0.69 | 0.01811 | 0.0544 | 113.56 ± 58.89 | 79.12 ± 39.28 |
IL-15 | interleukin 15 | 0.74 | 0.0032 | 0.0398 | 54.76 ± 39.59 | 40.63 ± 31.09 |
TNFSF8 | tumor necrosis factor superfamily, member 8 | 0.73 | 0.0202 | 0.0605 | 248.08 ± 148.25 | 181.53 ± 92.03 |
Chemokines-related | ||||||
ITGB1 | integrin, β1 (antigen CD29) | 1.29 | 0.0055 | 0.0405 | 1449.91 ± 772.02 | 1867.82 ± 802.10 |
 |  | 1.20 | 0.0012 | 0.0375 | 396.68 ± 336.59 | 476.25 ± 376.51 |
CXCR3 | chemokine receptor 3 | 1.29 | 0.0286 | 0.0825 | 47.04 ± 23.35 | 60.53 ± 33.18 |
CXCR7 | chemokine receptor 7 | 0.75 | 0.0205 | 0.0614 | 83.62 ± 25.83 | 63.45 ± 25.78 |
ITGA6 | integrin, α6 | 0.72 | 0.0211 | 0.063 | 1166.8 ± 1046.57 | 837.4 ± 796.19 |
Activation, proliferation and differentiation-related | ||||||
MKI67 | antigen identified by monoclonal antibody Ki-67 | 1.98 | 0.0165 | 0.0498 | 41.58 ± 22.80 | 82.16 ± 62.67 |
 |  | 1.69 | 0.0104 | 0.0410 | 19.37 ± 9.50 | 32.73 ± 20.37 |
ICOS | inducible T-cell costimulator | 1.49 | 0.0011 | 0.0375 | 587.76 ± 294.69 | 874.26 ± 397.84 |
GATA3 | GATA binding protein 3 | 1.43 | 0.0124 | 0.042 | 284.77 ± 189.82 | 406.03 ± 268.34 |
 |  | 1.37 | 0.0023 | 0.0392 | 163.55 ± 83.74 | 224.53 ± 114.73 |
CTLA-4 | cytotoxic T-lymphocyte-associated protein 4 | 1.37 | 0.0249 | 0.0734 | 511.58 ± 260.28 | 700.23 ± 359.54 |
MICA | MHC class I polypeptide-related sequence A | 0.7 | 0.0015 | 0.0379 | 120.33 ± 67.61 | 84.36 ± 51.72 |
BCL family-related | ||||||
Bcl3 | B-cell CLL/lymphoma 3 | 1.56 | 0.0036 | 0.0400 | 199.55 ± 112.65 | 311.36 ± 120.66 |
BAK1 | Bcl2-antagonist/killer 1 | 1.26 | 2.00E-04 | 0.0365 | 130.50 ± 27.61 | 164.92 ± 33.45 |
 |  | 1.24 | 0.0067 | 0.0407 | 314.36 ± 77.54 | 388.54 ± 79.60 |
Bcl2L11 | Bcl2-like 11 | 1.21 | 0.0369 | 0.1053 | 442.48 ± 299.18 | 536.88 ± 388.57 |
BCLAF1 | Bcl2-associated transcription factor 1 | 1.21 | 0.0234 | 0.0695 | 61.14 ± 14.91 | 73.89 ± 26.64 |
 |  | 0.72 | 0.0158 | 0.0479 | 189.15 ± 81.00 | 137.91 ± 40.11 |
Bcl2 | B-cell CLL/lymphoma 2 | 0.63 | 0.0050 | 0.0404 | 427.68 ± 327.43 | 272.97 ± 207.62 |
Apoptosis, MAP kinase and protein kinase-related | ||||||
ANXA5 | annexin 5 | 1.32 | 0.0271 | 0.0794 | 599.68 ± 269.08 | 793.89 ± 425.06 |
MAPK6 | mitogen-activated protein kinase 6 | 1.31 | 0.0261 | 0.0768 | 209.49 ± 142.30 | 273.63 ± 202.36 |
PPP1CC | protein phosphatase 1, catalytic subunit, γ isoform | 1.23 | 0.0152 | 0.0462 | 998.56 ± 432.59 | 1225.87 ± 571.01 |
CASP7 | caspase 7, apoptosis-related cysteine peptidase | 1.22 | 0.0145 | 0.0441 | 141.11 ± 41.72 | 171.83 ± 48.77 |
MAP2K6 | mitogen-activated protein kinase kinase kinase 6 | 0.77 | 0.0105 | 0.0410 | 77.3 ± 41.24 | 59.77 ± 33.17 |
ANXA11 | annexin 11 | 0.75 | 0.0003 | 0.0368 | 93.23 ± 20.45 | 70.21 ± 31.98 |
ATF7 | activating transcription factor 7 | 0.75 | 0.0252 | 0.0743 | 170.44 ± 120.64 | 128.30 ± 107.21 |
MAP4K4 | mitogen-activated protein kinase kinase kinase 4 | 0.63 | 0.0095 | 0.041 | 137.49 ± 51.60 | 86.97 ± 29.96 |
b. Genes impacted by ipilimumab in CD8+ T cells | ||||||
Cell cycle-related | ||||||
CDC2 | cell division cycle 2, G1 to S and G2 to M | 1.81 | 0.03 | 0.0897 | 18.37 ± 6.09 | 33.23 ± 21.15 |
CDCA7 | Cell division cycle associated 7 | 1.67 | 0.0113 | 0.0647 | 87.63 ± 93.37 | 146.50 ± 111.23 |
Cytokines-related | ||||||
TNFSF4 | tumor necrosis factor superfamily, member 4 | 0.58 | 0.0082 | 0.0647 | 40.88 ± 27.10 | 23.93 ± 14.71 |
Chemokines-related | ||||||
ITGAV | integrin, αV (antigen CD51) | 0.80 | 5.00E-04 | 0.0647 | 114.65 ± 54.10 | 91.78 ± 42.91 |
Activation, Differentiation and Interaction-related | ||||||
HLA-DRB4 | major histocompatibility complex, class II, DR β4 | 1.4 | 0.0163 | 0.0647 | 28.04 ± 26.29 | 39.18 ± 37.40 |
 |  | 1.39 | 0.0100 | 0.0647 | 178.84 ± 104.07 | 248.93 ± 148.36 |
GATA3 | GATA binding protein 3 | 1.35 | 0.0026 | 0.0647 | 139.84 ± 44.14 | 188.83 ± 75.51 |
HLA-DRA | major histocompatibility complex, class II, DR α | 1.38 | 0.0193 | 0.0647 | 540.53 ± 402.57 | 745.47 ± 350.32 |
CD6 | CD6 molecule (CD166 receptor) | 1.32 | 0.0248 | 0.0754 | 179.47 ± 95.79 | 236.58 ± 157.76 |
CD5 | CD5 molecule | 1.22 | 0.0181 | 0.0647 | 103.58 ± 38.21 | 126.47 ± 45.17 |
EOMES | Eomesodermin | 0.69 | 0.0292 | 0.0877 | 1063.26 ± 642.42 | 738.05 ± 445.38 |
Apoptosis, MAP Kinases-related | ||||||
TIAM1 | T-cell lymphoma invasion and metastasis 1 | 1.68 | 0.0105 | 0.0647 | 83.63 ± 67.00 | 140.61 ± 116.68 |
ANXA5 | annexin 5 | 1.31 | 0.0114 | 0.0647 | 576.93 ± 278.33 | 747.53 ± 316.78 |
API5 | apoptosis inhibitor 5 | 1.24 | 0.0088 | 0.0647 | 187.92 ± 118.48 | 233.04 ± 151.93 |