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Table 2 Gene ontology annotation enrichment analysis

From: A novel non-invasive method allowing for discovery of pathologically relevant proteins from small airways

Section A: Cellular Component sub-domain (CC)

Description (term)

Enrichment factor

Input and output

N,B,n,b

p value

FDR q value

GO term

Extracellular exosome

1.79

1291,382,194,103

6.80E−14

6.30E−11

GO:0070062

Extracellular vesicle

1.78

1291,384,194,103

1.03E−13

3.19E−11

GO:1903561

Extracellular region

1.39

1291,566,194,118

1.92E−07

2.97E−05

GO:0005576

Blood microparticle

3.43

1291,62,194,32

3.57E−12

8.28E−10

GO:0072562

Platelet alpha granule lumen

3.15

1291,38,194,18

1.53E−06

1.78E−04

GO:0031093

Extracellular matrix

1.82

1291,183,194,50

2.12E−06

2.18E−04

GO:0031012

Collagen-containing extracellular matrix

1.91

1291,150,194,43

3.35E−06

3.11E−04

GO:0062023

Cytoplasmic vesicle lumen

1.92

1291,135,194,39

8.75E−06

6.76E−04

GO:0060205

Endoplasmic reticulum lumen

1.97

1291,91,194,27

1.61E−04

8.27E−03

GO:0005788

Endoplasmic reticulum part

1.71

1291,132,194,34

4.70E−04

2.18E−02

GO:0044432

Section B: Biological Process sub-domain (BP)

Description (term)

Enrichment factor

Input and output

N,B,n,b

p value

FDR q value

GO term

Regulation of extracellular matrix constituent secretion

6.65

1291,5,194,5

7.33E−05

2.23E−02

GO:0003330

Exocytosis

1.80

1291,185,194,50

3.05E−06

1.54E−03

GO:0006887

Vesicle-mediated transport

1.74

1291,276,194,72

3.05E−08

2.78E−05

GO:0016192

Secretion by cell

1.63

1291,224,194,55

2.27E−05

8.63E−03

GO:0032940

Regulation of protein activation cascade

4.50

1291,34,194,23

2.28E−12

2.08E−08

GO:2000257

Regulation of complement activation

4.44

1291,33,194,22

1.13E−11

5.17E−08

GO:0030449

Complement activation, alternative pathway

4.44

1291,12,194,8

6.55E−05

2.14E−02

GO:0006957

Complement activation, classical pathway

3.90

1291,29,194,17

5.25E−08

4.36E−05

GO:0006958

Regulation of humoral immune response

3.64

1291,42,194,23

1.17E−09

1.77E−06

GO:0002920

Innate immune response

1.81

1291,114,194,31

3.04E−04

6.03E−02

GO:0045087

Platelet degranulation

2.80

1291,57,194,24

3.78E−07

2.88E−04

GO:0002576

Fibrinolysis

3.52

1291,17,194,9

2.67E−04

5.41E−02

GO:0042730

Negative regulation of coagulation

3.21

1291,29,194,14

1.86E−05

7.37E−03

GO:0050819

Regulation of coagulation

2.60

1291,41,194,16

1.19E−04

2.72E−02

GO:0050818

Regulation of haemostasis

2.60

1291,41,194,16

1.19E−04

2.86E−02

GO:1900046

Acute-phase response

3.33

1291,24,194,12

4.93E−05

1.67E−02

GO:0006953

Acute inflammatory response

3.21

1291,29,194,14

1.86E−05

8.08E−03

GO:0002526

Neutrophil activation involved in immune response

1.69

1291,126,194,32

9.28E−04

1.69E−01

GO:0002283

Regulation of response to external stimulus

1.48

1291,287,194,64

1.14E−04

2.90E−02

GO:0032101

Defence response

1.40

1291,300,194,63

8.92E−04

1.70E−01

GO:0006952

  1. This table display result from Gene Ontology enrichment analysis using the publicly available “Gene Ontology enrichment analysis and visualization tool” (GOrilla) [28]. A list of 199 uniquely mapped PEx proteins detected with SOMAscan 1.3 K were searched against the Cellular Component sub-domain database (section A) and the Biological Process sub-domain database (section B). A list of 1291 uniquely mapped SOMAscan 1.3 K protein identities was used as reference/background. Enrichment factor was calculated as (b/n)/(B/N), where n—is the total number of PEx protein ID’s, identified by SOMAscan and used as input, b—is the number of PEx/SOMAscan protein ID’s associated with the GO term. p values for enrichment analysis were computed according to the mHG or HG model. FDR q value is the p value corrected for multiple testing using the Benjamini and Hochberg (1995) method