Table II. Gene identifications and annotations of discussed genes of the subnetworks with Padj < 0.05

The fold-change value is positive and negative when the gene expression is up-regulated in lignin-forming conditions and in non-lignin-forming conditions, respectively.

AnnotationGene IdentifierLignin-Forming versus Non-Lignin-Forming
Fold ChangePadj
Shikimate pathway
 3-Deoxy-d-arabino-heptulosonate 7-phosphate synthaseMA_6189912g00102.74.6E-02
 3-Deoxy-d-arabino-heptulosonate 7-phosphate synthaseMA_10142969g00101.42.6E-03
 3-Dehydroquinate dehydratase/shikimate dehydrogenaseMA_10436080g00102.38.0E-12
 Chorismate synthaseMA_2539599g00102.41.1E-03
 Putative prephenate aminotransferaseMA_17674g00101.59.8E-03
 Arogenate dehydratase/prephenate dehydrataseMA_7514745g001039.31.9E-18
 Arogenate dehydratase/prephenate dehydrataseMA_864553g001027.22.1E-20
 Arogenate dehydratase/prephenate dehydrataseMA_387748g00101.84.3E-07
 Arogenate dehydrataseMA_864553g002032.44.3E-19
 Arogenate dehydrogenaseMA_42232g00106.87.5E-08
Phenylpropanoid pathway
 Phe ammonia lyaseMA_5862513g00104.84.1E-05
 Cinnamate 4-hydroxylaseMA_10159692g00105.01.6E-04
 Cinnamate 4-hydroxylaseMA_10435536g001061.72.9E-38
 4-Coumarate-CoA ligase-likeMA_166573g00102.93.3E-05
 Cinnamoyl-CoA reductaseMA_137109g00102.73.3E-02
 Caffeate/5-hydroxyconiferaldehyde O-methyltransferaseMA_10430251g0010−4.16.8E-08
 Caffeate/5-hydroxyconiferaldehyde O-methyltransferaseMA_10375504g00104.73.2E-03
 Caffeate/5-hydroxyconiferaldehyde O-methyltransferaseMA_630428g0010−5.15.7E-03
 Caffeate/5-hydroxyconiferaldehyde O-methyltransferaseMA_10426580g001017.04.1E-07
 Caffeate/5-hydroxyconiferaldehyde O-methyltransferaseMA_86438g00109.13.1E-04
Flavonoid pathway
 Flavonoid 3′-hydroxylaseMA_10434848g001012.82.6E-06
 Flavonoid 3′-hydroxylaseMA_158072g00104.08.6E-05
 Dihydroflavonol-4-reductaseMA_110462g00103.29.2E-06
 Leucoanthocyanidin dioxygenaseMA_169203g001033.59.0E-21
 Anthocyanidin 3-O-glucosyltransferaseMA_156209g00102.53.3E-08
Transcription factors
 Abscisic stress-ripening protein, ASRMA_60383g00102.42.2E-02
 Abscisic stress-ripening protein, ASRaMA_773806g00103.81.7E-03
 Abscisic stress-ripening protein, ASRMA_89246g00107.74.7E-05
 bHLH transcription factorMA_895755g00102.62.4E-08
 C2H2 zinc finger transcription factorMA_756968g00108.27.5E-06
 Ethylene-responsive transcription factorMA_4072g0020−2.74.3E-11
 Ethylene-responsive transcription factorMA_98464g00108.27.1E-09
 GRAS transcriptional regulatorMA_99004g0010−2.12.7E-02
 MYB family transcription factoraMA_139448g001020.31.5E-13
 MYB family transcription factorMA_937875g00109.33.3E-04
 MYB family transcription factorMA_10225049g00108.31.7E-04
 MYB family transcription factorMA_51173g00102.51.5E-05
 MYB family transcription factorMA_37058g00102.72.0E-03
 MYB family transcription factorMA_316475g001034.11.5E-28
 NAC transcription factorMA_139896g00101.91.3E-06
 NAC transcription factorMA_18958g00106.53.0E-08
 NAC transcription factorMA_16595g00101.94.9E-04
 Probable WRKY transcription factorMA_76002g001017.18.1E-07
 Tify family transcription factoraMA_10427283g003011.71.0E-08
 Tify family transcription factoraMA_10436587g00204.71.3E-02
 Two-component response regulator ARRMA_8059983g001054.92.8E-17
Other
 ABC transporter G family memberMA_18507g0010−3.26.1E-04
 Cys-rich receptor-like protein kinaseMA_874084g0010−2.13.7E-02
 Cys-rich receptor-like protein kinaseMA_9111704g00103.98.8E-22
 Gal oxidaseMA_812690g00105.62.1E-03
 Dirigent proteinMA_10428143g002019.55.9E-12
 Dirigent proteinMA_6385864g001010.58.2E-06
 Dirigent proteinMA_10428143g00108.51.4E-05
 Dirigent proteinMA_362458g001030.96.1E-21
 LaccaseMA_414479g001011.23.2E-12
 LaccaseMA_67291g001010.41.1E-20
 PeroxidaseMA_10432865g00208.12.2E-23
 PeroxidaseMA_10433564g001030.84.2E-64
 PeroxidaseMA_179122g001023.54.3E-17
 Pinoresinol reductase homologMA_445017g001018.56.2E-16
 Pinoresinol reductase homologMA_222809g001010.93.4E-09
  • a Switch or regulation position in the subnetwork.