Figure 2

Network Analysis for TR/ER, TR/MR, MR/ER comparative groups. The network diagrams include boxes (the top-10pathways), dots (enzymes), rounded rectangles (compounds), and lines. The lines between these rounded rectangles and dots or boxes indicate their confirmed interactions (no lines are shown for unconfirmed interactions). The rounded rectangles represent the bioprocesses, cellular localization and molecular functions, or signaling pathways; lines between the dots and the rounded rectangles represent associations or participation; red represents an increasing quantity; green represents a decreasing quantity; and the yellow-to-blue gradient represents significance going from low to high. The numbers below the dots represent Enzyme Commission (EC) numbers. (a) Network Analysis for the TR/ER comparative group: benzoate O-methyltransferase (2.1.1.273), dodecanoyl-[acyl-carrier-protein] hydrolase (3.1.2.21), cinnamoyl-CoA reductas (1.2.1.44), cinnamyl-alcohol dehydrogenase (1.1.1.195), nitrilase (3.5.5.1), amidase (3.5.1.4), (R)-2-methylmalate dehydratase (4.2.1.35), 4-hydroxybenzoate polyprenyltransferase (2.5.1.39), beta-galactosidase (3.2.1.23), galactinol–sucrose galactosyltransferase (2.4.1.82), galactinol–raffinosegalactosyltransferase (2.4.1.67), Arginase (3.5.3.1), tyrosine decarboxylase (4.1.1.25), primary-amine oxidase (1.4.3.21), tryptophan synthase (4.2.1.20), oleoyl-[acyl-carrier-protein] hydrolase (3.1.2.14), dihydrolipoyl dehydrogenase (1.8.1.4), oxoglutarate dehydrogenase (succinyl-transferring) (1.2.4.2), palmitoyl-CoA hydrolase (3.1.2.2), plant seed peroxygenase (1.11.2.3), isocitrate dehydrogenase (NADP+) (1.1.1.42), isocitrate dehydrogenase (NAD+) (1.1.1.41), glutamate N-acetyltransferase (2.3.1.35), ornithine carbamoyltransferase (2.1.3.3), 4-hydroxyphenylpyruvate dioxygenase (1.13.11.27), Peroxidase (1.11.1.7) histidine decarboxylase (4.1.1.22), histidinol dehydrogenase (1.1.1.23), L-tryptophan–pyruvate aminotransferase (2.6.1.99), L-aspartate oxidase (1.4.3.16), tryptophan N-monooxygenase (1.14.13.125), nitric-oxide synthase (NADPH) (1.14.13.39), glutamate dehydrogenase [NAD(P)+] (1.4.1.3), L-glutamate gamma-semialdehyde dehydrogenase (1.2.1.88), aspartate transaminase (2.6.1.1), arogenate dehydrogenase (NADP+) (1.3.1.78), phenylalanine N-monooxygenase (1.14.14.40) and aspartate carbamoyltransferase (2.1.3.2). (b) Network Analysis for the TR/MR comparative group: polyamine oxidase (propane-1,3-diamine-forming) (1.5.3.14), aldehyde dehydrogenase (NAD+) (1.2.1.3), choline monooxygenase (1.14.15.7), alcohol dehydrogenase (1.1.1.1), galactinol–sucrose galactosyltransferase (2.4.1.82), sucrose synthase (2.4.1.13), anthraniloyl-CoA monooxygenase (1.14.13.124)and Peroxidase (1.11.1.7). (c) Network Analysis for the MR/ER comparative group: NAD + –protein-arginine ADP-ribosyltransferase (2.4.2.31), NAD + ADP-ribosyltransferase (2.4.2.30), hypoxanthine phosphoribosyltransferase (2.4.2.8), Dihydropyrimidinase (3.5.2.2), dihydropyrimidine dehydrogenase (NADP+) (1.3.1.2), adenine phosphoribosyltransferase (2.4.2.7), cytokinin dehydrogenase (1.5.99.12), choline kinase (2.7.1.32), phosphoethanolamine N-methyltransferase (2.1.1.103), 5′-nucleotidase (3.1.3.5), galactinol–sucrose galactosyltransferase (2.4.1.82), sucrose synthase (2.4.1.13), caffeate O-methyltransferase (2.1.1.68), coniferyl-aldehyde dehydrogenase (1.2.1.68), oleoyl-[acyl-carrier-protein] hydrolase (3.1.2.14), tyrosine decarboxylase (4.1.1.25), palmitoyl-CoA hydrolase (3.1.2.2), plant seed peroxygenase (1.11.2.3), (R)-mandelonitrilelyase (4.1.2.10), tryptophan synthase (4.2.1.20), Amidase (3.5.1.4), Arginase (3.5.3.1), primary-amine oxidase (1.4.3.21), 4-hydroxybenzoate polyprenyltransferase (2.5.1.39), benzoate O-methyltransferase (2.1.1.273), aspartate transaminase (2.6.1.1), 4-hydroxyphenylpyruvate dioxygenase (1.13.11.27), nitric-oxide synthase (NADPH) (1.14.13.39), aspartate carbamoyltransferase (2.1.3.2), Nitrilase (3.5.5.1), L-aspartate oxidase (1.4.3.16), L-tryptophan–pyruvate aminotransferase (2.6.1.99) and tryptophan N-monooxygenase (1.14.13.125).