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Table 3 MetaCore pathway analysis of differentially expressed genes of the treatment comparison IR versus OUT.

From: Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

Day 5 IR vs OUT

P-value

Significant*

Total**

Cholesterol Biosynthesis

5.574E-13

15

21

Oxidative phosphorylation

0.00002

21

99

Vitamin B6 metabolism

0.00412

3

5

Cell adhesion_Gap junctions

0.00536

6

22

Regulation of lipid metabolism_Insulin regulation of fatty acid methabolism

0.00770

9

46

Regulation of lipid metabolism_Regulation of lipid metabolism via LXR, NF-Y and SREBP

0.00820

7

31

Cytoskeleton remodeling_Neurofilaments

0.01043

6

25

Ubiquinone metabolism

0.01169

9

49

Immune response_Antigen presentation by MHC class I

0.0127

6

26

Cell adhesion_Endothelial cell contacts by junctional mechanisms

0.0127

6

26

Day 28 IR vs OUT

P -value

Significant*

Total**

Cholesterol Biosynthesis

0.00000

10

21

Immune response_Antigen presentation by MHC class I

0.00001

10

26

Immune response_Classic complement pathway

0.00003

12

40

Immune response_IFN alpha/beta signalling pathway

0.00005

9

24

Regulation of lipid metabolism_Regulation of lipid metabolism via LXR, NF-Y and SREBP

0.00209

8

31

Immune response_Antiviral actions of Interferons

0.00209

8

31

CFTR folding and maturation (norm and CF)

0.00320

5

14

Immune response_IL-22 signalling pathway

0.00321

8

33

Neurodisease_Parkin disorder under Parkinson's disease

0.00592

7

29

Immune response_Antigen presentation by MHC class II

0.00790

4

11

Day 56 IR vs OUT

P -value

Significant*

Total**

Immune response_NFAT in immune response

0.00027

15

42

Immune response_Bacterial infections in normal airways

0.00040

14

39

Bacterial infections in CF airways

0.00048

15

44

Immune response_IL-12-induced IFN-gamma production

0.00066

12

32

Immune response_ICOS pathway in T-helper cell

0.00082

13

37

Immune response_CD28 signalling

0.00123

14

43

Cell adhesion_Integrin-mediated cell adhesion and migration

0.00201

14

45

Development_Angiopoietin - Tie2 signalling

0.00250

11

32

Apoptosis and survival_HTR1A signalling

0.00362

12

38

Sphingolipid metabolism/Human version

0.00362

12

38

  1. Differentially expressed genes (P < 0.05) were imported into GeneGo MetaCore analytical software to determine the significantly enriched canonical pathways in the treatment comparison IR vs OUT. The top ten pathways for each comparison are shown, with the number of genes assigned to each pathway, and the corresponding P-value.
  2. * The number of genes on each map that are differentially expressed in the specific treatment comparison
  3. ** The total number of genes on each map
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BMC Biology

ISSN: 1741-7007

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