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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