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Table 2 Microarray data for immune related genes from CD4 + T cells (Table 2a) and CD8 + T cells (Table 2b) with fold increases over baseline control samples, p-values for the differences indicated, FDR for the false discovery rate, and the mean ± SD of pre and post samples for the gene expression ranges

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
  1. Increases of greater than 1.2 fold and decreases of 0.8 fold or less are shown. Multiple values refer to different expressed sequence tags from the same gene.