Table 4 List of significant enrichment pathways for specific common DEGs of 141 and DH40 (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 | ||||
  Photosynthesis | ko00195 | 12 | 1.89E-13 | 7.54E-12 |
  Ribosome | ko03010 | 18 | 3.53E-09 | 7.06E-08 |
  Porphyrin and chlorophyll metabolism | ko00860 | 6 | 9.85E-05 | 1.31E-03 |
  Photosynthesis - antenna proteins | ko00196 | 3 | 5.89E-04 | 5.89E-03 |
  Oxidative phosphorylation | ko00190 | 5 | 8.53E-03 | 6.83E-02 |
  Glycine, serine and threonine metabolism | ko00260 | 4 | 1.06E-02 | 7.06E-02 |
  Limonene and pinene degradation | ko00903 | 2 | 4.56E-02 | 2.61E-01 |
 Down-regulated DEGs | ||||
  Plant hormone signal transduction | ko04075 | 17 | 1.06E-04 | 6.54E-03 |
  Cutin, suberine and wax biosynthesis | ko00073 | 5 | 9.67E-04 | 3.00E-02 |
  Linoleic acid metabolism | ko00591 | 2 | 2.01E-02 | 3.78E-01 |
  Benzoxazinoid biosynthesis | ko00402 | 2 | 3.05E-02 | 3.78E-01 |
Stage II sample | ||||
 Up-regulated DEGs | ||||
  Porphyrin and chlorophyll metabolism | ko00860 | 8 | 9.28E-06 | 5.94E-04 |
  Ribosome | ko03010 | 14 | 2.46E-04 | 7.89E-03 |
  Photosynthesis | ko00195 | 5 | 9.83E-04 | 2.10E-02 |
  Diterpenoid biosynthesis | ko00904 | 3 | 1.10E-02 | 1.41E-01 |
  C5-Branched dibasic acid metabolism | ko00660 | 2 | 1.41E-02 | 1.50E-01 |
  Ubiquinone and other terpenoid-quinone biosynthesis | ko00130 | 3 | 1.66E-02 | 1.52E-01 |
  Stilbenoid, diarylheptanoid and gingerol biosynthesis | ko00945 | 4 | 2.04E-02 | 1.63E-01 |
  Glycine, serine and threonine metabolism | ko00260 | 4 | 3.17E-02 | 2.26E-01 |
 Down-regulated DEGs | ||||
  Plant hormone signal transduction | ko04075 | 25 | 1.35E-09 | 7.56E-08 |
  Plant-pathogen interaction | ko04626 | 12 | 2.42E-03 | 6.77E-02 |
  Pentose and glucuronate interconversions | ko00040 | 4 | 4.84E-02 | 6.77E-01 |
Stage III sample | ||||
 Up-regulated DEGs | ||||
  Porphyrin and chlorophyll metabolism | ko00860 | 5 | 4.52E-04 | 1.40E-02 |
  Ribosome | ko03010 | 10 | 5.94E-04 | 1.40E-02 |
  Photosynthesis | ko00195 | 4 | 1.25E-03 | 1.96E-02 |
  Stilbenoid, diarylheptanoid and gingerol biosynthesis | ko00945 | 4 | 3.90E-03 | 4.59E-02 |
  Ubiquinone and other terpenoid-quinone biosynthesis | ko00130 | 2 | 4.38E-02 | 3.84E-01 |
  Peroxisome | ko04146 | 3 | 4.90E-02 | 3.84E-01 |
 Down-regulated DEGs | ||||
  Plant hormone signal transduction | ko04075 | 19 | 1.31E-07 | 6.80E-06 |
  Other glycan degradation | ko00511 | 4 | 1.32E-02 | 3.43E-01 |
  Flavonoid biosynthesis | ko00941 | 3 | 3.64E-02 | 3.59E-01 |
  Glycerolipid metabolism | ko00561 | 3 | 3.77E-02 | 3.59E-01 |
  Glycerophospholipid metabolism | ko00564 | 4 | 4.89E-02 | 3.59E-01 |