Table 4 List of significant pathways.

From: Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD

Outcome

Dysregulated Pathways

# Hits

p-value

FDR

FEV1/FVC

Autophagy

8

0.0008

0.0250

FEV1/FVC

Fat digestion and absorption*

10

0.0001

0.0035

FEV1/FVC

Glycerolipid metabolism*

10

0.0018

0.0512

FEV1/FVC

Glycerophospholipid metabolism

18

<0.0001

<0.0001

FEV1/FVC

Hematopoietic cell lineage*

17

0.0005

0.0375

FEV1/FVC

Lysosome

25

<0.0001

0.0016

FEV1/FVC

Notch signaling pathway

10

0.0021

0.0973

FEV1/FVC

Osteoclast differentiation

23

0.0007

0.0245

FEV1/FVC

Phosphatidylinositol signaling system

14

0.0031

0.0817

FEV1/FVC

Primary immunodeficiency

9

0.0009

0.0530

FEV1/FVC

Ribosome

45

<0.0001

<0.0001

FEV1/FVC

SNARE interactions in vesicular transport

8

0.0026

0.1090

FEV1/FVC

Sphingolipid metabolism

14

<0.0001

<0.0001

FEV1/FVC

Th1 and Th2 cell differentiation

25

<0.0001

<0.0001

FEV1/FVC

Th17 cell differentiation

24

<0.0001

<0.0001

FEV1% predicted

Endocytosis*

39

0.0055

0.0924

FEV1% predicted

Fc gamma R-mediated phagocytosis*

14

0.0017

0.0386

FEV1% predicted

Glycerophospholipid metabolism

17

<0.0001

0.0001

FEV1% predicted

Hippo signaling pathway*

18

0.0041

0.0751

FEV1% predicted

Jak-STAT signaling pathway*

19

0.0085

0.1200

FEV1% predicted

Lysosome

22

0.0013

0.0318

FEV1% predicted

mTOR signaling pathway*

10

0.0045

0.0857

FEV1% predicted

Neurotrophin signaling pathway*

15

0.0070

0.1080

FEV1% predicted

NF-kappa B signaling pathway*

17

0.0054

0.0922

FEV1% predicted

Notch signaling pathway

11

0.0008

0.0247

FEV1% predicted

Osteoclast differentiation

28

<0.0001

0.0003

FEV1% predicted

Peroxisome*

14

0.0037

0.0720

FEV1% predicted

Phagosome

26

0.0009

0.0220

FEV1% predicted

Phosphatidylinositol signaling system

17

0.0019

0.0432

FEV1% predicted

Primary immunodeficiency

7

0.0171

0.1810

FEV1% predicted

Ribosome

47

<0.0001

<0.0001

FEV1% predicted

SNARE interactions in vesicular transport

9

0.0008

0.0247

FEV1% predicted

Sphingolipid metabolism

10

<0.0001

<0.0001

FEV1% predicted

Sphingolipid signaling pathway

19

0.0015

0.0346

FEV1% predicted

T cell receptor signaling pathway*

22

0.0001

0.0042

FEV1% predicted

Th1 and Th2 cell differentiation

29

<0.0001

<0.0001

FEV1% predicted

Th17 cell differentiation

29

<0.0001

<0.0001

Exacerbation Frequency

Aminoacyl-tRNA biosynthesis

3

0.0139

0.1400

Exacerbation Frequency

Antigen processing and presentation*

4

0.0021

0.1130

Exacerbation Frequency

Glycerophospholipid metabolism

3

0.0139

0.1400

Exacerbation Frequency

Mineral absorption

3

0.0183

0.1570

Exacerbation Frequency

Protein digestion and absorption

4

0.0007

0.0195

Exacerbation Frequency

Ribosome

46

<0.0001

<0.0001

Exacerbation Frequency

RNA transport

6

0.0098

0.1090

Exacerbation Severity

ABC transporters*

6

0.0004

0.0056

Exacerbation Severity

Aminoacyl-tRNA biosynthesis

5

0.0013

0.0158

Exacerbation Severity

Arginine and proline metabolism*

4

0.0002

0.0047

Exacerbation Severity

Arginine biosynthesis*

3

0.0025

0.0671

Exacerbation Severity

Autophagy

3

<0.0001

0.0004

Exacerbation Severity

Glycerophospholipid metabolism

6

<0.0001

0.0004

Exacerbation Severity

Glycine, serine and threonine metabolism*

4

0.0019

0.0156

Exacerbation Severity

Insulin resistance*

3

0.0019

0.0566

Exacerbation Severity

Mineral absorption

5

<0.0001

0.0024

Exacerbation Severity

Phenylalanine, tyrosine and tryptophan biosynthesis*

3

0.0030

0.0214

Exacerbation Severity

Protein digestion and absorption

5

0.0002

0.0118

Exacerbation Severity

Purine Metabolism*

4

0.0177

0.0834

Exacerbation Severity

Retrograde endocannabinoid signaling*

3

0.0014

0.0429

Exacerbation Severity

Sphingolipid metabolism

4

0.0001

0.0034

Exacerbation Severity

Sphingolipid signaling pathway

3

0.0008

0.0306

Bronchodilator Response

Lysosome

7

0.0001

0.0386

Bronchodilator Response

Phagosome

9

<0.0001

0.0053

% Emphysema

mRNA surveillance pathway*

8

0.0009

0.1990

% Emphysema

Oxidative phosphorylation*

11

0.0002

0.1130

% Emphysema

RNA transport

12

0.0004

0.1770

  1. The most statistically significant pathways were filtered for KEGG Pathways, FDR ≤ 0.2, p ≤ 0.05, and ≥3 hits and are listed alphabetically. In the dataset column, the data was derived from solely statistically significant metabolites, solely statistically significant transcripts, or from both statistically significant metabolites and gene transcripts. #Hits represent the number of gene transcripts and/or metabolites that are significant in the indicated pathway. *Pathways that are unique to the indicated outcome.
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