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Table 1 KEGG and Reactome Pathways revealed by Network enrichment analyses for differentially regulated proteins which were resolved in a STRING subnetwork in the vtg1-KO Experiment. A) proteins down-regulated in vtg1-KO eggs. B) proteins up-regulated in vtg1-KO eggs. Only statistically significant results are reported (χ2, p < 0.05). See Table S5 for full analysis report

From: Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs

A) vtg1-KO Experiment: Network stats for proteins down-regulated in vtg1-KO eggs (Wt; N = 32)

number of nodes:

17

number of edges:

18

average node degree:

2.12

clustering coefficient:

0.64

expected number of edges:

6

PPI enrichment p-value:

2.75E-05

confidence level:

0.15

KEGG Pathways

pathway

description

protein count

FDR

dre00330

Arginine and proline metabolism

2 of 58

0.0074

Reactome Pathways

pathway

description

protein count

FDR

DRE-71288

Creatine metabolism

2 of 10

0.0001

B) vtg1-KO Experiment: Network stats for proteins up-regulated in vtg1-KO eggs (vtg1-KO; N = 94)

number of nodes:

63

number of edges:

107

average node degree:

3.4

clustering coefficient:

0.387

expected number of edges:

58

PPI enrichment p-value:

5.95E-09

confidence level:

0.40

KEGG Pathways

pathway

description

protein count

FDR

dre00270

Cysteine and methionine metabolism

3 of 47

0.0072

dre04260

Cardiac muscle contraction

3 of 89

0.0135

dre04141

Protein processing in endoplasmic reticulum

4 of 176

0.0135

dre01100

Metabolic pathways

10 of 1278

0.0135

dre00790

Folate biosynthesis

2 of 26

0.0135

dre00620

Pyruvate metabolism

2 of 41

0.0244

dre03013

RNA transport

3 of 151

0.0263

dre04261

Adrenergic signaling in cardiomyocytes

3 of 180

0.0368

dre00983

Drug metabolism - other enzymes

2 of 61

0.0368

dre00010

Glycolysis / Gluconeogenesis

2 of 74

0.0439

Reactome Pathways

pathway

description

protein count

FDR

DRE-71182

Phenylalanine and tyrosine catabolism

3 of 14

0.003

DRE-450408

AUF1 (hnRNP D0) binds and destabilizes mRNA

4 of 54

0.003

DRE-3371568

Attenuation phase

3 of 19

0.003

DRE-3371497

HSP90 chaperone cycle for steroid hormone receptors

3 of 21

0.003

DRE-6798695

Neutrophil degranulation

7 of 490

0.0088

DRE-168256

Immune System

11 of 1379

0.0154

DRE-3371453

Regulation of HSF1-mediated heat shock response

3 of 69

0.0238

DRE-1430728

Metabolism

12 of 1751

0.0258

DRE-2262752

Cellular responses to stress

5 of 321

0.0313

DRE-168249

Innate Immune System

8 of 875

0.0313

DRE-140837

Intrinsic Pathway of Fibrin Clot Formation

2 of 19

0.0313

DRE-140875

Common Pathway of Fibrin Clot Formation

2 of 23

0.0365

DRE-901042

Calnexin/calreticulin cycle

2 of 25

0.0387