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Table 2 Overrepresented pathways in upregulated (UP) and downregulated (DOWN) genes across growth conditions and genotypes

From: Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure

Patterna Pathway id Pathway name In group In all genes Bh_p_val
D1_COLD_UP PWY-2902 cytokinins-O-glucoside biosynthesis 37 72 0.0002
  PWY-3781 aerobic respiration -- electron donor IIa 7 106 0.0012
D1_CG60_DOWN PWY-695 abscisic acid biosynthesis 9 12 0.0013
  PWY-6299 aldehyde oxidation I 6 8 0.0354
  PWY-6446 benzoate biosynthesis III (CoA-dependent, non- β -oxidative) 8 15 0.0354
  PWY-6444 benzoate biosynthesis II (CoA-independent, non- β -oxidative) 8 15 0.0354
  PWYQT-4429 CO2 fixation into oxaloacetate 4 4 0.0354
D4_COLD_DOWN PWY-282 cuticular wax biosynthesisb 0 5 0.0057
D4_COLD_UP PWY-282 cuticular wax biosynthesis 3 5 0.0115
D4_CG60_DOWN PWY-6446 benzoate biosynthesis III (CoA-dependent, non- β -oxidative) 10 15 0.0091
  PWY-6444 benzoate biosynthesis II (CoA-independent, non- β -oxidative) 10 15 0.0091
  PWY-724 superpathway of lysine, threonine and methionine biosynthesis II 23 59 0.0168
  PWY-6457 trans-cinnamoyl-CoA biosynthesis 6 7 0.0220
  PWY-5156 superpathway of fatty acid biosynthesis II (plant) 18 44 0.0332
  PWY-1081 homogalacturonan degradation 18 45 0.0332
  TRPSYN-PWY tryptophan biosynthesis 11 22 0.0332
  PWY1F-467 phenylpropanoid biosynthesis, initial reactions 6 8 0.0332
  PWY-5172 acetyl-CoA biosynthesis (from citrate) 6 8 0.0332
  PWY0–162 pyrimidine ribonucleotides de novo biosynthesis 14 33 0.0391
  PWY-5670 epoxysqualene biosynthesis 4 4 0.0429
  1. aThe code for the gene expression pattern is “day”, main effect factor level, direction of the main effect. D1 refers to samples harvested during cold exposure and their controls. D4 refers to samples harvested 24 h after cold exposure and their controls. CG60_UP indicates a significant, positive effect of CG60. CG60_DOWN indicates a significant, negative effect of CG60
  2. bPathways with b at the end of the description were underrepresented amongst the gene set