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Table 1 Pathway level analysis of genes differentially expressed following stimulation with BCG.

From: Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth

 

BCG stimulation

PPD stimulation

Pathway Name

Rank

aImpact Factor

b#Genes in Pathway

c p-value

dgamma p-value

Rank

aImpact Factor

b#Genes in Pathway

c p-value

dgamma p-value

Cell adhesion molecules (CAMs)

1

45.4

4/133

0.153

9.00E-19

-

-

-

-

-

Cytokine-cytokine receptor interaction

2

34.6

34/259

1.31E-12

3.51E-14

15

7.2

27/259

-5.50E-14

0.006

Hematopoietic cell lineage

3

30.6

14/88

8.34E-11

1.57E-12

1

27.3

12/88

2.68E-10

3.86E-11

Toll-like receptor signaling pathway

4

26.4

14/102

6.39E-10

9.56E-11

4

18.3

9/102

2.11E-06

2.14E-07

Fc epsilon RI signaling pathway

5

21.6

2/77

0.336

9.24E-09

11

10.2

2/77

0.211

4.24E-04

Jak-STAT signaling pathway

6

21.3

13/153

8.33E-07

1.22E-08

6

14.0

8/153

3.24E-04

1.21E-05

Graft-versus-host disease

7

20.1

5/42

4.65E-04

4.03E-08

3

18.6

5/42

9.93E-05

1.67E-07

MAPK signaling pathway

8

17.0

13/265

2.78E-04

7.67E-07

5

16.0

9/265

0.003

1.98E-06

TGF-beta signaling pathway

9

16.9

1/89

0.752

8.29E-07

10

10.6

3/89

0.079

3.01E-04

GnRH signaling pathway

10

15.8

1/97

0.781

2.29E-06

2

26.2

1/97

0.662

1.15E-10

Apoptosis

11

14.1

6/84

0.002

1.13E-05

7

13.4

4/84

0.014

2.24E-05

Type I diabetes mellitus

12

13.9

6/44

5.76E-05

1.33E-05

8

12.9

5/44

1.25E-04

3.43E-05

T cell receptor signaling pathway

13

13.1

6/93

0.003

2.84E-05

13

8.8

3/93

0.085

0.001

PPAR signaling pathway

14

12.5

8/69

1.14E-05

5.14E-05

9

12.0

7/69

1.16E-05

8.11E-05

Natural killer cell mediated cytotoxicity

15

11.4

5/131

0.054

1.34E-04

14

7.9

3/131

0.179

0.003

Type II diabetes mellitus

16

9.0

3/44

0.031

0.001

17

6.6

1/44

0.388

0.009

Adipocytokine signaling pathway

17

9.0

4/72

0.026

0.001

-

-

-

-

-

Epithelial cell signaling in Helicobacter pylori infection

18

8.6

4/69

0.022

0.002

12

9.5

3/69

0.041

7.85E-04

Complement and coagulation cascades

19

7.6

6/69

7.06E-04

0.004

-

-

-

-

-

Bladder cancer

20

6.9

3/42

0.027

0.008

16

6.9

3/42

0.011

0.008

Acute myeloid leukemia

21

6.8

5/57

0.002

0.008

-

-

-

-

-

  1. a calculated on basis of proportion of differentially expressed genes in a pathway and gene perturbation factors of all genes in the pathway
  2. b number of genes in a particular pathway
  3. c P value for pathways that contain a proportion of differentially expressed genes that is significantly different from what is expected by chance
  4. d This perturbation factor takes into consideration the (i) normalized fold change of the gene and (ii) the number of genes upstream of its position on a pathway