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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.