Table 3.
Top 20 enriched biological pathways
| Worms grown with Chryseobacterium sp. CHNTR56 MYb120 | Worms grown with Comamonas sp. 12022 MYb131 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Pathway | Total | Expected | Hits | P.Value | FDR | Pathway | Total | Expected | Hits | P.Value | FDR |
| DNA replication | 33 | 4.83 | 17 | 5.32E-07 | 6.64E-05 | Circadian rhythm - mammal | 23 | 1.43 | 10 | 3.49E-07 | 4.36E-05 |
| TGF-beta signaling pathway | 33 | 4.83 | 14 | 9.06E-05 | 0.00383 | TGF-beta signaling pathway | 33 | 2.05 | 11 | 2.09E-06 | 0.000131 |
| Glutathione metabolism* | 38 | 5.56 | 15 | 0.000136 | 0.00383 | Drug metabolism - cytochrome P450* | 32 | 1.99 | 10 | 1.21E-05 | 0.000505 |
| Circadian rhythm - mammal | 23 | 3.37 | 11 | 0.000144 | 0.00383 | Metabolism of xenobiotics by cytochrome P450* | 29 | 1.81 | 9 | 3.63E-05 | 0.00113 |
| Wnt signaling pathway | 64 | 9.37 | 21 | 0.000153 | 0.00383 | Wnt signaling pathway | 64 | 3.98 | 13 | 9.65E-05 | 0.00241 |
| Fatty acid metabolism | 56 | 8.2 | 17 | 0.00177 | 0.0357 | Peroxisome | 64 | 3.98 | 12 | 0.000403 | 0.00731 |
| Taurine and hypotaurine metabolism | 5 | 0.732 | 4 | 0.002 | 0.0357 | Cysteine and methionine metabolism | 31 | 1.93 | 8 | 0.00042 | 0.00731 |
| Drug metabolism - cytochrome P450* | 32 | 4.69 | 11 | 0.004 | 0.0625 | Fatty acid metabolism | 56 | 3.49 | 11 | 0.000468 | 0.00731 |
| Calcium signaling pathway | 42 | 6.15 | 13 | 0.00508 | 0.0706 | Glutathione metabolism* | 38 | 2.37 | 8 | 0.0018 | 0.0225 |
| Metabolism of xenobiotics by cytochrome P450* | 29 | 4.25 | 10 | 0.00587 | 0.0734 | Taurine and hypotaurine metabolism | 5 | 0.311 | 3 | 0.00215 | 0.0225 |
| Mismatch repair | 18 | 2.64 | 7 | 0.01 | 0.114 | Arginine and proline metabolism | 39 | 2.43 | 8 | 0.00215 | 0.0225 |
| Biosynthesis of unsaturated fatty acids | 16 | 2.34 | 6 | 0.0206 | 0.215 | Biosynthesis of unsaturated fatty acids | 16 | 0.996 | 5 | 0.00216 | 0.0225 |
| Fatty acid elongation in mitochondria | 13 | 1.9 | 5 | 0.0306 | 0.285 | Limonene and pinene degradation | 17 | 1.06 | 5 | 0.00291 | 0.0279 |
| Pyrimidine metabolism | 68 | 9.96 | 16 | 0.0319 | 0.285 | Phenylalanine metabolism | 18 | 1.12 | 5 | 0.00383 | 0.0342 |
| Phenylalanine metabolism | 18 | 2.64 | 6 | 0.037 | 0.307 | Ubiquitin mediated proteolysis | 84 | 5.23 | 12 | 0.00474 | 0.0395 |
| Neuroactive ligand-receptor interaction | 23 | 3.37 | 7 | 0.0404 | 0.307 | Nitrogen metabolism | 21 | 1.31 | 5 | 0.00781 | 0.0611 |
| Cyanoamino acid metabolism | 6 | 0.879 | 3 | 0.0442 | 0.307 | Tyrosine metabolism | 22 | 1.37 | 5 | 0.00962 | 0.0707 |
| Sulfur metabolism | 6 | 0.879 | 3 | 0.0442 | 0.307 | ECM-receptor interaction | 8 | 0.498 | 3 | 0.0105 | 0.0727 |
| Progesterone-mediated oocyte maturation | 39 | 5.71 | 10 | 0.0487 | 0.315 | Lysosome | 76 | 4.73 | 10 | 0.0172 | 0.113 |
| – | alpha-Linolenic acid metabolism | 11 | 0.685 | 3 | 0.0269 | 0.168 | |||||
Enriched biological pathways (KEGG) ranked by P-value are shown. Cellular detoxification related pathways are enriched in the worms grown with Chryseobacterium sp. CHNTR56 MYb120 or Comamonas sp. 12022 MYb131, in comparison with E. coli OP50. These pathways are indicated with asterisk (*)