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Table 3 Results of an overrepresentation analysis on the identified proteins following cytokine stimulation in equine articular chondrocytes carried out using the Reactome resource. The analysis is based on a statistical (hypergeometric distribution) test that determines whether certain Reactome pathways are over-represented (enriched) in the submitted data. This test produces a probability score, which is corrected for false discovery rate using the Benjamani-Hochberg method. The 25 most relevant pathways sorted by p-value are shown. Table extracted from Reactome Pathway Analysis Report

From: Alterations in the chondrocyte surfaceome in response to pro-inflammatory cytokines

Pathway name

Entities

Reactions

found

ratio

p-value

FDRa

found

ratio

Neutrophil degranulation

56 / 480

0.033

1.11e-16

1.27e-13

10 / 10

8.01e-04

Formation of the cornified envelope

28 / 138

0.01

1.94e-14

1.11e-11

13 / 27

0.002

Extracellular matrix organization

42 / 329

0.023

4.09e-14

1.56e-11

183 / 318

0.025

RAB geranylgeranylation

18 / 68

0.005

1.39e-11

3.99e-09

2 / 5

4.00e-04

Integrin cell surface interactions

18 / 86

0.006

5.71e-10

1.31e-07

45 / 54

0.004

Keratinization

28 / 226

0.016

1.55e-09

2.97e-07

20 / 34

0.003

Non-integrin membrane-ECM interactions

15 / 61

0.004

1.88e-09

3.06e-07

19 / 22

0.002

Platelet degranulation

21 / 137

0.009

5.09e-09

7.28e-07

8 / 11

8.81e-04

Response to elevated platelet cytosolic Ca2+

21 / 144

0.01

1.19e-08

1.51e-06

8 / 14

0.001

Cell-Cell communication

20 / 133

0.009

1.61e-08

1.84e-06

46 / 60

0.005

Syndecan interactions

10 / 29

0.002

4.43e-08

4.61e-06

12 / 15

0.001

Axon guidance

45 / 584

0.04

4.92e-08

4.67e-06

147 / 297

0.024

Developmental Biology

73 / 1207

0.084

6.41e-08

5.64e-06

167 / 511

0.041

Post-translational protein phosphorylation

17 / 109

0.008

1.16e-07

9.37e-06

1 / 1

8.01e-05

Cell junction organization

15 / 94

0.007

4.83e-07

3.67e-05

26 / 37

0.003

Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)

17 / 127

0.009

9.31e-07

6.61e-05

1 / 14

0.001

Transport of small molecules

58 / 963

0.067

1.97e-06

1.32e-04

97 / 438

0.035

Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA

6 / 13

9.01e-04

4.45e-06

2.80e-04

2 / 3

2.40e-04

ATF6 (ATF6-alpha) activates chaperone genes

6 / 15

0.001

9.96e-06

5.98e-04

3 / 5

4.00e-04

Vesicle-mediated transport

49 / 824

0.057

1.83e-05

0.001

115 / 251

0.02

Adherens junctions interactions

8 / 35

0.002

1.93e-05

0.001

16 / 16

0.001

ATF6 (ATF6-alpha) activates chaperones

6 / 17

0.001

2.00e-05

0.001

4 / 10

8.01e-04

Transport of inorganic cations/anions and amino acids/oligopeptides

17 / 165

0.011

2.71e-05

0.001

23 / 75

0.006

Platelet activation, signaling and aggregation

24 / 293

0.02

2.78e-05

0.001

33 / 114

0.009

Innate Immune System

69 / 1328

0.092

2.80e-05

0.001

88 / 696

0.056

  1. aFalse Discovery Rate
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BMC Molecular and Cell Biology

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