Table 5 List of significant enrichment pathways for specific common DEGs of ZYDH381–1 and DH3732 (P-value ≤0.05)
From: Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation
Pathway term | Pathway ID | DEGs tested | P value | Q value |
|---|---|---|---|---|
Stage I sample | ||||
 Up-regulated DEGs | ||||
  Taurine and hypotaurine metabolism | ko00430 | 3 | 7.34E-05 | 5.29E-03 |
  Nitrogen metabolism | ko00910 | 3 | 7.36E-03 | 2.65E-01 |
  Flavonoid biosynthesis | ko00941 | 3 | 3.51E-02 | 6.46E-01 |
 Down-regulated DEGs | ||||
  Circadian rhythm – plant | ko04712 | 8 | 4.70E-04 | 2.99E-02 |
  Carbon metabolism | ko01200 | 11 | 9.05E-04 | 2.99E-02 |
  Valine, leucine and isoleucine degradation | ko00280 | 4 | 2.98E-03 | 6.56E-02 |
  Plant hormone signal transduction | ko04075 | 11 | 2.11E-02 | 3.22E-01 |
  Caffeine metabolism | ko00232 | 1 | 2.44E-02 | 3.22E-01 |
  Glycolysis / Gluconeogenesis | ko00010 | 5 | 3.87E-02 | 3.74E-01 |
  Propanoate metabolism | ko00640 | 2 | 4.50E-02 | 3.74E-01 |
  Cyanoamino acid metabolism | ko00460 | 3 | 4.86E-02 | 3.74E-01 |
Stage II sample | ||||
 Up-regulated DEGs | ||||
  Fatty acid elongation | ko00062 | 5 | 8.82E-04 | 2.05E-02 |
  Starch and sucrose metabolism | ko00500 | 14 | 9.09E-04 | 2.05E-02 |
  Phenylpropanoid biosynthesis | ko00940 | 11 | 1.02E-03 | 2.05E-02 |
  Glycosaminoglycan degradation | ko00531 | 5 | 1.04E-03 | 2.05E-02 |
  Sphingolipid metabolism | ko00600 | 6 | 3.06E-03 | 3.94E-02 |
  Galactose metabolism | ko00052 | 7 | 3.20E-03 | 3.94E-02 |
  Glycosphingolipid biosynthesis - ganglio series | ko00604 | 4 | 4.14E-03 | 3.94E-02 |
  Phenylalanine metabolism | ko00360 | 4 | 4.35E-03 | 3.94E-02 |
  Other glycan degradation | ko00511 | 6 | 4.49E-03 | 3.94E-02 |
  Taurine and hypotaurine metabolism | ko00430 | 2 | 8.80E-03 | 6.95E-02 |
  Nitrogen metabolism | ko00910 | 3 | 3.07E-02 | 2.13E-01 |
beta-Alanine metabolism | ko00410 | 3 | 3.39E-02 | 2.13E-01 |
  Photosynthesis - antenna proteins | ko00196 | 2 | 3.51E-02 | 2.13E-01 |
  Stilbenoid, diarylheptanoid and gingerol biosynthesis | ko00945 | 4 | 4.49E-02 | 2.53E-01 |
  RNA polymerase | ko03020 | 3 | 4.96E-02 | 2.61E-01 |
 Down-regulated DEGs | ||||
  Circadian rhythm – plant | ko04712 | 10 | 9.18E-05 | 3.84E-03 |
  Valine, leucine and isoleucine degradation | ko00280 | 6 | 9.85E-05 | 3.84E-03 |
  Plant hormone signal transduction | ko04075 | 17 | 4.45E-04 | 1.16E-02 |
  Propanoate metabolism | ko00640 | 3 | 8.61E-03 | 1.13E-01 |
  Glycolysis / Gluconeogenesis | ko00010 | 7 | 8.68E-03 | 1.13E-01 |
  Alanine, aspartate and glutamate metabolism | ko00250 | 4 | 1.04E-02 | 1.16E-01 |
  Fatty acid degradation | ko00071 | 3 | 1.78E-02 | 1.48E-01 |
  Cyanoamino acid metabolism | ko00460 | 4 | 1.91E-02 | 1.48E-01 |
  Nitrogen metabolism | ko00910 | 3 | 2.06E-02 | 1.48E-01 |
  Glycerolipid metabolism | ko00561 | 4 | 2.21E-02 | 1.48E-01 |
  Arginine biosynthesis | ko00220 | 3 | 2.27E-02 | 1.48E-01 |
  Tyrosine metabolism | ko00350 | 3 | 2.67E-02 | 1.60E-01 |
  Carbon metabolism | ko01200 | 9 | 3.64E-02 | 2.03E-01 |
Stage III sample | ||||
 Up-regulated DEGs | ||||
  Phenylpropanoid biosynthesis | ko00940 | 22 | 3.77E-08 | 3.54E-06 |
  Sphingolipid metabolism | ko00600 | 9 | 3.48E-04 | 1.45E-02 |
  Starch and sucrose metabolism | ko00500 | 19 | 5.78E-04 | 1.45E-02 |
  Other glycan degradation | ko00511 | 9 | 6.18E-04 | 1.45E-02 |
  Glycosaminoglycan degradation | ko00531 | 6 | 1.17E-03 | 2.21E-02 |
  Glycosphingolipid biosynthesis - ganglio series | ko00604 | 5 | 3.28E-03 | 4.67E-02 |
  Phenylalanine metabolism | ko00360 | 5 | 3.48E-03 | 4.67E-02 |
  Cutin, suberine and wax biosynthesis | ko00073 | 6 | 4.27E-03 | 4.71E-02 |
  Porphyrin and chlorophyll metabolism | ko00860 | 7 | 4.51E-03 | 4.71E-02 |
  Galactose metabolism | ko00052 | 8 | 9.75E-03 | 8.64E-02 |
  Cyanoamino acid metabolism | ko00460 | 6 | 1.01E-02 | 8.64E-02 |
  Stilbenoid, diarylheptanoid and gingerol biosynthesis | ko00945 | 6 | 1.69E-02 | 1.33E-01 |
  Taurine and hypotaurine metabolism | ko00430 | 2 | 1.99E-02 | 1.43E-01 |
  Terpenoid backbone biosynthesis | ko00900 | 6 | 2.13E-02 | 1.43E-01 |
  Fatty acid elongation | ko00062 | 4 | 2.74E-02 | 1.72E-01 |
  Brassinosteroid biosynthesis | ko00905 | 3 | 2.96E-02 | 1.74E-01 |
  Flavonoid biosynthesis | ko00941 | 5 | 4.07E-02 | 2.25E-01 |
 Down-regulated DEGs | ||||
  Plant hormone signal transduction | ko04075 | 20 | 8.00E-05 | 5.92E-03 |
  Circadian rhythm – plant | ko04712 | 10 | 2.52E-04 | 9.31E-03 |
  Glycolysis / Gluconeogenesis | ko00010 | 9 | 1.26E-03 | 2.82E-02 |
  Valine, leucine and isoleucine degradation | ko00280 | 5 | 1.52E-03 | 2.82E-02 |
  Propanoate metabolism | ko00640 | 3 | 1.20E-02 | 1.36E-01 |
  Carbon metabolism | ko01200 | 11 | 1.29E-02 | 1.36E-01 |
  Fatty acid degradation | ko00071 | 3 | 2.45E-02 | 1.98E-01 |
  Nitrogen metabolism | ko00910 | 3 | 2.81E-02 | 1.98E-01 |
  Cyanoamino acid metabolism | ko00460 | 4 | 2.83E-02 | 1.98E-01 |
  Caffeine metabolism | ko00232 | 1 | 3.42E-02 | 1.98E-01 |
  Pyruvate metabolism | ko00620 | 5 | 3.45E-02 | 1.98E-01 |
  Anthocyanin biosynthesis | ko00942 | 2 | 3.48E-02 | 1.98E-01 |