Table 2

Summary of identified miRNA-mRNA regulatory modules

mRNA expression in HCV+ vs. HCV-b

Module p-valuec


Module

identifier

No. of mRNA

No. of

miRNA

miRNA

miRNA

gene family

% of overlapped targetsa

log2 ratio

p-value

adj.

p-value

P_score

P_Nt

Selected GO terms (BP)d


miRNA down-regulated, and mRNA up-regulated in HCV+ vs. HCV-


7

48

1

hsa-miR-320

mir-320

56.2 (12.5)

0.6

4.8E-09

0.001

1.1E-25

0

cell cycle checkpoint


8

34

1

hsa-miR-92

mir-25

44.1 (20.6)

0.6

5.6E-10

0

1.3E-33

0

actin cytoskeleton organization and biogenesis


10

77

1

hsa-miR-296

mir-296

62.3 (2.6)

0.8

4.3E-15

0

5.5E-37

0

T cell receptor signaling pathway


29

37

1

hsa-miR-193b

mir-193

43.2 (2.7)

0.6

3.9E-08

0

3.3E-33

0

regulation of apoptosis


30

39

1

hsa-miR-181b

mir-181

59 (5.1)

1.0

5.8E-24

0

2.8E-22

0.03

cell cycle checkpoint


37

46

1

hsa-miR-422b

mir-378

39.1 (2.2)

0.5

6.4E-07

0

8.1E-26

0

B cell differentiation


39

74

1

hsa-miR-122a

mir-122

51.4 (1.4)

0.5

1.7E-05

0.011

1.4E-44

0.01

DNA repair


50

11

2

hsa-miR-122a,

hsa-miR-320

mir-122,

mir-320

54.5 (0)

0.8

4.9E-13

0

1.3E-56

0

MAPKKK cascade


87

11

2

hsa-miR-193b,

hsa-miR-320

mir-193,

mir-320

31.8 (0)

0.5

2.1E-06

0.001

2.8E-53

0

cell cycle checkpoint


miRNA up-regulated, and mRNA down-regulated in HCV+ vs. HCV-


1

52

1

hsa-miR-130a

mir-130

46.2 (19.2)

-0.5

2.3E-05

0.016

6.5E-15

0.02

regulation of Rho protein signal transduction


2

66

1

hsa-miR-26b

mir-26

60.6 (13.6)

-0.7

3.6E-08

0

7.9E-32

0

actin cytoskeleton organization and biogenesis


4

191

1

hsa-miR-16

mir-15

54.5 (18.3)

-0.8

2.5E-09

0

2.6E-46

0

insulin receptor signaling pathway


13

51

1

hsa-miR-21

mir-21

49 (5.9)

-0.6

7.6E-07

0.002

3.8E-33

0

inactivation of MAPK activity


15

170

1

hsa-miR-26a

mir-26

62.4 (17.1)

-0.6

6.4E-07

0.002

4.8E-50

0

insulin receptor signaling pathway


16

22

1

hsa-miR-155

mir-155

54.5 (4.5)

-0.6

7.7E-10

0

4.7E-17

0.02

B cell differentiation


18

59

2

hsa-miR-26a,

hsa-miR-26b

mir-26

62.7 (15.3)

-0.6

3.2E-07

0.001

7.8E-85

0

innate immune response


27

86

1

hsa-miR-215

mir-192

43 (1.2)

-0.7

1.8E-07

0.002

8.2E-32

0

insulin receptor signaling pathway


28

21

2

hsa-miR-16,

hsa-miR-215

mir-15,

mir-192

38.1 (9.5)

-0.7

7.0E-09

0

2.2E-51

0

apoptotic program


36

37

1

hsa-miR-324-3p

mir-324

45.9 (0)

-0.6

2.9E-08

0

2.6E-07

0

cAMP-mediated signaling


43

88

1

hsa-miR-202

mir-202

43.2 (13.6)

-0.6

2.3E-04

0.036

5.6E-52

0

apoptotic program


52

82

1

hsa-miR-509

mir-509

50 (1.2)

-0.6

1.6E-11

0

4.8E-60

0

transforming growth factor beta receptor signaling pathway


55

48

1

hsa-miR-424

mir-322

60.4 (20.8)

-0.7

1.2E-09

0

1.3E-13

0.02

nuclear import


56

30

2

hsa-miR-16,

hsa-miR-424

mir-15,

mir-322

53.3 (23.3)

-0.7

1.5E-09

0

1.1E-58

0

transforming growth factor beta receptor signaling pathway


57

12

1

hsa-miR-191

mir-191

66.7 (0)

-0.6

4.0E-07

0.002

7.8E-51

0

positive regulation of peptidyl-serine phosphorylation


58

15

2

hsa-miR-26a,

hsa-miR-424

mir-26,

mir-322

66.7 (23.3)

-0.7

2.1E-10

0

1.4E-44

0

transforming growth factor beta receptor signaling pathway


59

19

2

hsa-miR-16,

hsa-miR-26a

mir-15,

mir-26

60.5 (26.3)

-0.7

4.4E-11

0

2.4E-62

0

transforming growth factor beta receptor signaling pathway


60

11

3

hsa-miR-16,

hsa-miR-26a,

hsa-miR-424

mir-15,

mir-26,

mir-322

54.5 (33.3)

-0.7

5.3E-12

0

2.5E-67

0

transforming growth factor beta receptor signaling pathway


63

28

1

hsa-miR-199a*

mir-199

0 (0)

-0.8

5.0E-07

0.002

2.1E-04

0.03

negative regulation of MAP kinase activity


73

12

2

hsa-miR-16,

hsa-miR-509

mir-15,

mir-509

66.7 (25)

-0.6

2.0E-09

0

4.2E-55

0

negative regulation of translational initiation


76

28

2

hsa-miR-215,

hsa-miR-26a

mir-192,

mir-26

57.1 (12.5)

-0.6

6.7E-07

0

1.0E-66

0

transforming growth factor beta receptor signaling pathway


78

23

2

hsa-miR-130a,

hsa-miR-16

mir-130,

mir-15

47.8 (10.9)

-0.4

1.3E-07

0.001

9.6E-63

0

RNA-mediated gene silencing


79

35

1

hsa-miR-146b

mir-146

68.6 (2.9)

-0.3

5.5E-08

0

4.7E-14

0

complement activation, alternative pathway


81

23

1

hsa-miR-15b

mir-15

30.4 (8.7)

-0.3

2.3E-04

0.019

6.7E-05

0.03

telomere maintenance via telomerase


94

23

2

hsa-miR-202,

hsa-miR-509

mir-202,

mir-509

56.5 (6.5)

-0.4

4.3E-06

0.005

2.0E-89

0

transforming growth factor beta receptor signaling pathway


96

15

2

hsa-miR-21,

hsa-miR-26a

mir-21,

mir-26

53.3 (23.3)

-0.5

1.7E-08

0.001

1.6E-51

0

MAPKKK cascade


101

11

3

hsa-miR-21,

hsa-miR-26a,

hsa-miR-26b

mir-21,

mir-26

54.5 (21.2)

-0.4

1.0E-05

0.005

8.8E-72

0

innate immune response


102

10

3

hsa-miR-215,

hsa-miR-26a,

hsa-miR-26b

mir-192,

mir-26

53.3 (20)

-0.6

5.9E-07

0.003

1.4E-75

0

endothelial cell migration


170

10

2

hsa-miR-202,

hsa-miR-324-3p

mir-202,

mir-324

50 (10)

-0.5

1.0E-07

0.001

1.1E-32

0

response to dsRNA


aThe overlap (%) is with the TargetScan prediction. The number in parenthesis is the overlap (%) with TargetScan conserved predicted targets, i.e. those targets with a conserved site as predicted by TargetScan.

bDifferential expression of target mRNAs in HCV+ vs. HCV- was assessed together as one group for each module. adj. p-value: adjusted p-value, estimated based on 1000 permutations.

cModule p-value was estimated based on 100 simulations. P_score: the scoring method. P_Nt: the counting method.

dOne representative GO term was manually selected for each module. See text for details.

Peng et al. BMC Genomics 2009 10:373   doi:10.1186/1471-2164-10-373

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