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
| 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 |