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Table 5 Effect of δ-tocotrienol on down-regulation (74) of fold change gene expression in "causal netwworks" section of IPA analysis in hepatitis C patients

From: δ-Tocotrienol feeding modulates gene expression of EIF2, mTOR, protein ubiquitination through multiple-signaling pathways in chronic hepatitis C patients

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Master Regulator

Molecule Type

Part. regulators1

Depth

Pred Acti State2

Act. Z-Score3

P-Value Over4

Network Bi-Corr5

Causal Net6

Target-Con-Re7

B

Down-regulation

         

25

JAK1/2

group

26s Proteasome,Akt,AKT1

3

Inhibited

-7.511

2.54E-14

0.0008

295 (81)

80

26

PPAR ligand-PPAR-Retinoic acid-RXRα

complex

26s Proteasome,Akt,AKT1

3

Inhibited

-4.459

3.31E-13

0.0131

306 (61)

60

27

LXR ligand-LXR-Retinoic acid-RXRα

complex

26s Proteasome,Akt,AR

3

Inhibited

-4.815

4.17E-13

0.0085

290 (58)

57

28

PPARγ ligand-PPARγ-Retinoic acid-RARα

complex

26s Proteasome,Akt,AKT1

3

Inhibited

-4.230

4.23E-13

0.0121

306 (66)

65

29

PXR ligand-PXR-Retinoic acid-RXRα

complex

26s Proteasome,AKT1

3

Inhibited

-4.432

3.33E-12

0.0221

294 (58)

58

30

RAR ligand-RARα-Retinoic acid-RXRα

complex

26s Proteasome,Akt,AKT1

3

Inhibited

-5.396

3.52E-12

0.039

297 (57)

56

31

Vegf Receptor

group

26s Proteasome,ABL1,Akt

3

Inhibited

-5.056

1.56E-11

0.0052

276 (93)

90

32

FXR ligand-FXR-Retinoic acid-RXRα

complex

26s Proteasome,Akt,AKT1

3

Inhibited

-5.100

1.96E-11

0.0484

291 (56)

55

33

hydrogen sulfide

chemical - endogenous mammalian

26s Proteasome,Akt,AKT1

3

Inhibited

-4.222

2.15E-11

0.0013

237 (92)

89

34

NLK

kinase

26s Proteasome,AKT1,Alp

3

Inhibited

-3.429

8.72E-11

0.0375

248 (50)

45

35

CD80

transmembrane receptor

CD28,CD80,IFNG,IL4

2

Inhibited

-6.267

1.32E-10

0.003

132 (8)

8

36

Pdgfra-Pdgfrb

complex

26s Proteasome,AKT1,AR

3

Inhibited

-7.878

1.37E-10

0.0184

285 (93)

89

37

Klra7 (includes others)

transmembrane receptor

26s Proteasome,Akt,AR

3

Inhibited

-7.445

1.44E-10

0.0324

291 (93)

93

38

FLT4

transmembrane receptor

26s Proteasome,Akt,AR

3

Inhibited

-5.020

1.46E-10

0.0177

280 (80)

78

39

Vegfr dimer

complex

26s Proteasome,AKT1,AR

3

Inhibited

-7.071

1.59E-10

0.0178

242 (61)

58

40

lipopolysaccharide

chemical drug

lipopolysaccharide

1

Inhibited

-7.668

2.75E-10

0.0045

120 (1)

1

41

TEK

kinase

26s Proteasome,ADRB2

3

Inhibited

-4.954

3E-10

0.0124

274 (93)

93

42

LATS1

kinase

26s Proteasome,ARID4A

3

Activated

4.680

3.43E-10

0.0322

250 (56)

54

43

NYAP1

other

26s Proteasome,Akt,AKT1

3

Inhibited

-6.264

3.54E-10

0.0304

281 (86)

85

44

MYO16

other

26s Proteasome,Akt,AKT1

3

Inhibited

-6.264

3.54E-10

0.0304

281 (86)

85

45

NYAP2

other

26s Proteasome,Akt,AKT1

3

Inhibited

-6.264

3.54E-10

0.0304

281 (86)

85

46

IRS

group

26s Proteasome,ADRB2

3

Inhibited

-5.548

1.63E-09

0.0456

269 (77)

74

47

FAK-Src

complex

26s Proteasome,ABL1,Akt

3

Inhibited

-6.839

2.41E-09

0.043

273 (90)

86

48

Plk

group

26s Proteasome,Akt,AKT1

3

Inhibited

-2.500

2.77E-09

0.0425

219 (55)

50

49

G-protein beta

group

26s Proteasome,ADORA2A

3

Inhibited

-5.647

3.22E-09

0.0309

283 (103)

99

50

ADRA1B

G-protein coupled receptor

26s Proteasome,ADRA1B

3

Inhibited

-6.238

4.49E-09

0.0406

278 (86)

85

51

IL2

cytokine

IL2

1

Inhibited

-4.619

8.23E-09

0.0004

48 (1)

1

52

propolis

biologic drug

26s Proteasome,AKT1

3

Inhibited

-2.829

1.78E-08

0.0482

231 (76)

73

53

exenatide

biologic drug

26s Proteasome,Akt,AMPK

3

 

-1.432

2.36E-08

0.0088

236 (88)

88

54

imidazole

chemical - endogenous mammalian

26s Proteasome,ADORA2A

3

 

1.091

2.79E-08

0.05

243 (75)

70

55

LETM1

other

Akt,AMPK,APP,AR

3

 

-1.023

0.000000069

0.036

215 (64)

63

56

IL-2R

complex

IL-2R,IL2RA,IL2RG,JAK1

2

Inhibited

-3.491

0.00000012

0.0103

84 (14)

13

57

IL23

complex

IL12B,IL23,JAK2,MTOR

2

Inhibited

-7.155

0.000000165

0.0112

80 (9)

9

58

IL15

cytokine

IL15

1

Inhibited

-2.121

0.000000551

0.0009

32 (1)

1

59

TH17 Cytokine

group

IL17A,IL21,IL22,TH17

2

Inhibited

-4.323

0.000000813

0.0037

39 (4)

4

60

IL4R

transmembrane receptor

IL4,IL4R,IRS1,IRS2,JAK

2

Inhibited

-4.503

0.00000102

0.0252

75 (13)

12

61

IL21

cytokine

IL21

1

Inhibited

-2.985

0.00000527

0.0028

22 (1)

1

62

SATB1

transcription regulator

SATB1

1

 

1.528

0.00000669

0.0011

21 (1)

1

63

cyclosporin A

biologic drug

cyclosporin A

1

 

1.441

0.0000108

0.0163

39 (1)

1

64

IL12RB2

transmembrane receptor

IL12 (family),IL12RB2

2

Inhibited

-4.116

0.0000233

0.0103

34 (4)

3

65

mir-26

microRNA

Akt,mir-26

2

 

0.192

0.0000247

0.0126

27 (2)

2

66

mir-221

microRNA

Akt,mir-221

2

 

-0.192

0.0000247

0.0129

27 (2)

2

67

IL5

cytokine

IL5

1

Inhibited

-4.914

0.0000541

0.0136

28 (1)

1

68

ropivacaine

chemical drug

Akt,NOS3,Pkc(s)

2

 

-1.029

0.0000544

0.0289

34 (5)

4

69

UCP3

transporter

IRS1,IRS2,PI3K

2

 

-1.961

0.0000657

0.0231

26 (4)

3

70

AIF1

other

AIF1,Akt,BAD

2

 

-1.177

0.0000657

0.0211

26 (3)

3

71

IFN Beta

group

IFN Beta

1

Inhibited

-2.138

0.00082

0.043

14 (1)

1

72

PDGFD

growth factor

PDGFD

1

 

-0.577

0.000838

0.0044

3 (1)

1

73

PARP9

enzyme

PARP9

1

Inhibited

-2.236

0.00123

0.0073

5 (1)

1

74

PPP1R14B

phosphatase

PPP1R14B

1

 

-1.732

0.00162

0.005

3 (1)

1

  1. 1Part. Regulators = Paticipating Regulators; 2Pred Acti state = Predicted Acitivation State; 3Act. Z-Score = Activation Z-Score; 4P-Value Over. = P-Value Overlap; 5Network Bi-Corr = Network Bias-Corrected P-Values; 7Target-Con-Re. = Target Connected regulators