From: Coordinations between gene modules control the operation of plant amino acid metabolic networks
Coordination | Enrichment (Log2) | # of genes in a group | # of genes in the genome | Biological process (GO) |
---|---|---|---|---|
Asp-family Met met. Group | ||||
Positive (920 genes) | 3.04 | 4 | 10 | syncytium formation |
 | 2.88 | 5 | 14 | protein targeting to mitochondrion |
 | 2.86 | 6 | 17 | microtubule-based process |
 | 2.77 | 31 | 94 | ribosome biogenesis and assembly |
 | 2.69 | 5 | 16 | cellular protein metabolic process |
 | 2.67 | 4 | 13 | nucleocytoplasmic transport |
 | 2.56 | 12 | 42 | chromosome organization and biogenesis |
 | 2.47 | 91 | 340 | translation |
 | 2.44 | 5 | 19 | response to UV |
 | 2.42 | 7 | 27 | translational elongation |
 | 2.31 | 13 | 54 | nucleosome assembly |
 | 2.23 | 5 | 22 | sterol biosynthetic process |
 | 1.73 | 9 | 56 | fatty acid biosynthetic process |
 | 1.44 | 17 | 129 | transmembrane receptor protein tyrosine kinase signaling pathway |
 | -1.62 | 12 | 762 | regulation of transcription, DNA-dependent |
Negative (1780 genes) | 2.76 | 7 | 11 | heat acclimation |
 | 2.66 | 16 | 27 | response to hydrogen peroxide |
 | 2.57 | 5 | 9 | response to water |
 | 2.51 | 15 | 28 | response to high light intensity |
 | 2.41 | 9 | 18 | cold acclimation |
 | 2.26 | 9 | 20 | trehalose biosynthetic process |
 | 2.24 | 8 | 18 | response to desiccation |
 | 2.05 | 19 | 49 | response to osmotic stress |
 | 2.03 | 33 | 86 | response to heat |
 | 1.98 | 36 | 97 | response to water deprivation |
 | 1.9 | 55 | 157 | response to abscisic acid stimulus |
 | 1.89 | 8 | 23 | fatty acid beta-oxidation |
 | 1.87 | 25 | 73 | response to wounding |
 | 1.86 | 16 | 47 | response to cadmium ion |
 | 1.79 | 11 | 34 | abscisic acid mediated signaling |
 | 1.76 | 14 | 44 | toxin catabolic process |
 | 1.68 | 47 | 156 | response to salt stress |
 | 1.57 | 25 | 90 | response to ethylene stimulus |
 | 1.47 | 36 | 139 | response to cold |
 | 1.34 | 19 | 80 | response to stress |
 | 1.29 | 23 | 100 | response to jasmonic acid stimulus |
 | 1.26 | 20 | 89 | response to salicylic acid stimulus |
Asp-family Catabolic group | ||||
Positive (536 genes) | 3.21 | 6 | 23 | fatty acid beta-oxidation |
 | 2.75 | 4 | 21 | tryptophan biosynthetic process |
 | 2.71 | 5 | 27 | response to hydrogen peroxide |
 | 2.66 | 13 | 73 | response to wounding |
 | 2.27 | 6 | 44 | toxin catabolic process |
 | 2.27 | 6 | 44 | aging |
 | 2.15 | 6 | 48 | defense response to fungus |
 | 2.13 | 12 | 97 | response to water deprivation |
 | 2.1 | 19 | 157 | response to abscisic acid stimulus |
 | 1.92 | 13 | 122 | multicellular organismal development |
 | 1.89 | 9 | 86 | response to heat |
 | 1.77 | 15 | 156 | response to salt stress |
 | 1.62 | 13 | 150 | response to oxidative stress |
 | 1.61 | 12 | 139 | response to cold |
Negative (2451 genes) | 2.69 | 5 | 6 | purine nucleotide biosynthetic process |
 | 2.54 | 6 | 8 | pentose-phosphate shunt, non-oxidative branch |
 | 2.44 | 66 | 94 | ribosome biogenesis and assembly |
 | 2.18 | 199 | 340 | translation |
 | 2.04 | 9 | 17 | microtubule-based process |
 | 2.01 | 14 | 27 | translational elongation |
 | 1.95 | 8 | 16 | cellular protein metabolic process |
 | 1.95 | 21 | 42 | chromosome organization and biogenesis |
 | 1.89 | 11 | 23 | tRNA aminoacylation for protein translation |
 | 1.83 | 11 | 24 | chlorophyll biosynthetic process |
 | 1.72 | 23 | 54 | nucleosome assembly |
 | 1.32 | 18 | 56 | fatty acid biosynthetic process |
 | 1.11 | 36 | 129 | transmembrane receptor protein tyrosine kinase signaling pathway |
 | 1.02 | 52 | 199 | protein folding |
 | -0.74 | 66 | 851 | protein amino acid phosphorylation |
 | -0.93 | 36 | 530 | regulation of transcription |
 | -1.08 | 22 | 359 | N-terminal protein myristoylation |
 | -1.19 | 43 | 762 | regulation of transcription, DNA-dependent |
 | -1.82 | 12 | 329 | defense response |
 | -2.37 | 5 | 200 | ubiquitin-dependent protein catabolic process |
Aromatic amino acids (AAA) group | ||||
Positive (498 genes) | 4.96 | 4 | 5 | negative regulation of programmed cell death |
 | 4.14 | 5 | 11 | phenylpropanoid biosynthetic process |
 | 4.11 | 4 | 9 | phenylpropanoid metabolic process |
 | 3.47 | 4 | 14 | aromatic amino acid family biosynthetic process |
 | 3.35 | 5 | 19 | response to fungus |
 | 3.21 | 5 | 21 | tryptophan biosynthetic process |
 | 3.14 | 5 | 22 | cell wall catabolic process |
 | 3 | 15 | 73 | response to wounding |
 | 2.86 | 9 | 48 | defense response to fungus |
 | 2.65 | 5 | 31 | lignin biosynthetic process |
 | 2.37 | 6 | 45 | defense response to bacterium |
 | 2.14 | 5 | 44 | toxin catabolic process |
 | 1.86 | 14 | 150 | response to oxidative stress |
 | 1.74 | 12 | 139 | response to cold |
 | 1.3 | 54 | 851 | protein amino acid phosphorylation |
Negative (2466 genes) | 2.94 | 6 | 6 | glycine decarboxylation via glycine cleavage system |
 | 2.94 | 5 | 5 | protein import into chloroplast thylakoid membrane |
 | 2.94 | 4 | 4 | water transport |
 | 2.94 | 4 | 4 | photosynthesis, light harvesting |
 | 2.94 | 4 | 4 | cellulose and pectin-containing primary cell wall biogenesis |
 | 2.94 | 4 | 4 | amylopectin biosynthetic process |
 | 2.75 | 7 | 8 | photosystem II assembly |
 | 2.68 | 5 | 6 | protein import into chloroplast stroma |
 | 2.68 | 5 | 6 | isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway |
 | 2.68 | 5 | 6 | carotene biosynthetic process |
 | 2.65 | 9 | 11 | starch catabolic process |
 | 2.53 | 6 | 8 | thylakoid membrane organization and biogenesis |
 | 2.48 | 8 | 11 | reductive pentose-phosphate cycle |
 | 2.36 | 16 | 24 | chlorophyll biosynthetic process |
 | 1.88 | 11 | 23 | ATP-dependent proteolysis |
 | 1.77 | 12 | 27 | chloroplast organization and biogenesis |
 | 1.51 | 20 | 54 | photosynthesis |
 | 1.31 | 18 | 56 | fatty acid biosynthetic process |
 | -0.62 | 72 | 851 | protein amino acid phosphorylation |
 | -0.99 | 50 | 762 | regulation of transcription, DNA-dependent |
 | -1.22 | 20 | 359 | N-terminal protein myristoylation |
 | -1.72 | 13 | 329 | defense response |