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Table 2 KEGG and Reactome Pathways revealed by Network enrichment analyses for differentially regulated proteins which were resolved in a STRING subnetwork in the vtg3-KO Experiment. A) proteins down-regulated in vtg3-KO eggs. B) proteins up-regulated in vtg3-KO eggs. Only statistically significant results are reported (χ2, p < 0.05). See Table S6 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) vtg3-KO Experiment: Network stats for proteins down-regulated in vtg3-KO eggs (Wt; N = 21)
number of nodes: 11
number of edges: 7
average node degree: 1.27
clustering coefficient: 0.394
expected number of edges: 1
PPI enrichment p-value: 6.99E-06
confidence level: 0.4
KEGG Pathways
pathway Description Protein counts FDR
dre01200 Carbon metabolism 2 of 125 0.0147
B) vtg3-KO Experiment: Network stats for proteins up-regulated in vtg3-KO eggs (vtg3-KO; N = 53)
number of nodes: 36
number of edges: 46
average node degree: 2.56
clustering coefficient: 0.417
expected number of edges: 36
PPI enrichment p-value: 0.0517
confidence level: 0.4
KEGG Pathways
pathway description protein count FDR
dre04141 Protein processing in endoplasmic reticulum 6 of 176 3.04E-06
dre00270 Cysteine and methionine metabolism 4 of 47 6.54E-06
dre00620 Pyruvate metabolism 3 of 41 0.00019
dre00330 Arginine and proline metabolism 3 of 58 0.00037
dre04260 Cardiac muscle contraction 3 of 89 0.001
dre01100 Metabolic pathways 8 of 1278 0.001
dre03040 Spliceosome 3 of 131 0.0022
dre00640 Propanoate metabolism 2 of 31 0.0022
dre04261 Adrenergic signaling in cardiomyocytes 3 of 180 0.0041
dre00010 Glycolysis / Gluconeogenesis 2 of 74 0.0091
dre04144 Endocytosis 3 of 293 0.013
dre04010 MAPK signaling pathway 3 of 359 0.0206
dre03010 Ribosome 2 of 126 0.0206
Reactome Pathways
pathway description protein count FDR
DRE-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA 5 of 54 5.35E-06
DRE-3371568 Attenuation phase 4 of 19 5.35E-06
DRE-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) 4 of 21 5.35E-06
DRE-71288 Creatine metabolism 3 of 10 3.53E-05
DRE-3371453 Regulation of HSF1-mediated heat shock response 4 of 69 0.00014
DRE-2262752 Cellular responses to stress 6 of 321 0.0002
DRE-71406 Pyruvate metabolism and Citric Acid (TCA) cycle 3 of 55 0.002
DRE-189085 Digestion of dietary carbohydrate 2 of 11 0.0037
DRE-71291 Metabolism of amino acids and derivatives 4 of 249 0.0076
DRE-901042 Calnexin/calreticulin cycle 2 of 25 0.0111
DRE-70268 Pyruvate metabolism 2 of 31 0.0157
DRE-168256 Immune System 7 of 1379 0.0343
DRE-390522 Striated Muscle Contraction 2 of 54 0.0372
DRE-5358346 Hedgehog ligand biogenesis 2 of 58 0.0408