Spreadsheet: 9080cdbd-a739-4933-ba4c-644db0e867f4
Sheet: Table-S8

Table S8. [NAME] pathways (RiceCyc) enriched in the clusters DU, DD, E, ED, NE and NEU
S.No | Pathway name | RiceCyc | D | DU | Percent |  | S.No | Pathway name | RiceCyc | D | E | Percent E over D |  | S.No | Pathway name | RiceCyc | D | NE | Percent NE over D
1 | citrulline biosynthesis | 22 | 8 | 8 | 100 |  | 1 | lysine biosynthesis I | 24 | 6 | 6 | 100 |  | 1 | cholesterol biosynthesis I | 17 | 8 | 6 | 75
2 | trehalose biosynthesis I | 21 | 8 | 8 | 100 |  | 2 | lysine biosynthesis II | 24 | 6 | 6 | 100 |  | 2 | cholesterol biosynthesis III (via desmosterol) | 17 | 8 | 6 | 75
3 | proline biosynthesis I | 18 | 7 | 7 | 100 |  | 3 | lysine biosynthesis VI | 24 | 6 | 6 | 100 |  | 3 | suberin biosynthesis | 18 | 6 | 4 | 66.66666666666666
4 | proline biosynthesis II | 18 | 7 | 7 | 100 |  | 4 | sucrose biosynthesis | 25 | 6 | 6 | 100 |  | 4 | methylerythritol phosphate pathway | 13 | 6 | 4 | 66.66666666666666
5 | cytokinins degradation | 45 | 10 | 10 | 100 |  | 5 | heme biosynthesis II | 15 | 6 | 6 | 100 |  | 5 | glycerol degradation I | 24 | 5 | 3 | 60
6 | cholesterol biosynthesis I | 17 | 8 | 8 | 100 |  | 6 | [NAME] biosynthesis II | 22 | 8 | 8 | 100
7 | cholesterol biosynthesis III (via desmosterol) | 17 | 8 | 8 | 100 |  | 7 | folate polyglutamylation I | 18 | 8 | 8 | 100 |  | S.No | Pathway name | RiceCyc | D | NEU | Percent NEU over D
8 | beta;-alanine biosynthesis II | 12 | 7 | 6 | 85.71428571428571 |  | 8 | [NAME] biosynthesis I | 21 | 7 | 7 | 100 |  | 1 | cholesterol biosynthesis I | 17 | 8 | 6 | 75
9 | gamma;-glutamyl cycle | 34 | 6 | 5 | 83.33333333333334 |  | 9 | tryptophan degradation V (side chain pathway) | 15 | 9 | 9 | 100 |  | 2 | cholesterol biosynthesis III (via desmosterol) | 17 | 8 | 6 | 75
10 | D-lactate fermentation to propionate and acetate | 11 | 6 | 5 | 83.33333333333334 |  | 10 | folate transformations | 16 | 6 | 6 | 100
11 | leucine biosynthesis | 17 | 6 | 5 | 83.33333333333334 |  | 11 | methylglyoxal degradation I | 12 | 6 | 6 | 100
12 | tyrosine degradation I | 13 | 6 | 5 | 83.33333333333334 |  | 12 | 13-LOX and 13-HPL pathway | 30 | 14 | 14 | 100
13 | methionine biosynthesis I | 12 | 5 | 4 | 80 |  | 13 | divinyl ether biosynthesis II (13-LOX) | 15 | 7 | 7 | 100
14 | sucrose degradation I | 12 | 5 | 4 | 80 |  | 14 | gamma;-glutamyl cycle | 34 | 6 | 6 | 100
15 | tryptophan biosynthesis | 24 | 12 | 9 | 75 |  | 15 | [NAME] biosynthesis | 42 | 13 | 12 | 92.3076923076923
16 | GDP-L-fucose biosynthesis I (from GDP-D-mannose) | 13 | 8 | 6 | 75 |  | 16 | fatty acid beta;-oxidation I | 29 | 12 | 11 | 91.66666666666666
17 | GDP-D-rhamnose biosynthesis | 12 | 8 | 6 | 75 |  | 17 | reductive TCA cycle I | 33 | 11 | 10 | 90.9090909090909
18 | TCA cycle variation I | 43 | 15 | 11 | 73.33333333333333 |  | 18 | galactose degradation II | 56 | 22 | 20 | 90.9090909090909
19 | TCA cycle | 35 | 13 | 9 | 69.23076923076923 |  | 19 | photorespiration | 26 | 10 | 9 | 90
20 | methionine biosynthesis II | 31 | 6 | 4 | 66.66666666666666 |  | 20 | UDP-galactose biosynthesis (salvage pathway from galactose using UDP-glucose) | 47 | 17 | 15 | 88.23529411764706
21 | homocysteine and cysteine interconversion | 13 | 6 | 4 | 66.66666666666666 |  | 21 | tRNA charging pathway | 127 | 16 | 14 | 87.5
22 | phenylalanine biosynthesis I | 21 | 6 | 4 | 66.66666666666666 |  | 22 | de novo biosynthesis of pyrimidine ribonucleotides | 29 | 8 | 7 | 87.5
23 | phospholipases | 38 | 9 | 6 | 66.66666666666666 |  | 23 | UDP-glucose conversion | 73 | 24 | 21 | 87.5
24 | mevalonate pathway | 20 | 8 | 5 | 62.5 |  | 24 | beta;-alanine biosynthesis II | 12 | 7 | 6 | 85.71428571428571
25 | [NAME] biosynthesis | 42 | 13 | 8 | 61.53846153846154 |  | 25 | TCA cycle | 35 | 13 | 11 | 84.61538461538461
26 | cytokinins 7-N-glucoside biosynthesis | 1134 | 91 | 56 | 61.53846153846154 |  | 26 | polyisoprenoid biosynthesis | 31 | 6 | 5 | 83.33333333333334
27 | cytokinins 9-N-glucoside biosynthesis | 972 | 78 | 48 | 61.53846153846154 |  | 27 | phospholipid biosynthesis II | 34 | 6 | 5 | 83.33333333333334
28 | cytokinins-O-glucoside biosynthesis | 648 | 52 | 32 | 61.53846153846154 |  | 28 | valine degradation I | 28 | 6 | 5 | 83.33333333333334
29 | phospholipid biosynthesis I | 36 | 5 | 3 | 60 |  | 29 | methionine biosynthesis II | 31 | 6 | 5 | 83.33333333333334
30 | acetyl CoA fermentation to butyrate | 10 | 5 | 3 | 60 |  | 30 | homocysteine and cysteine interconversion | 13 | 6 | 5 | 83.33333333333334
31 | glutaryl-CoA degradation | 10 | 5 | 3 | 60 |  | 31 | D-lactate fermentation to propionate and acetate | 11 | 6 | 5 | 83.33333333333334
 |  |  |  |  |  |  | 32 | UDP-D-xylose biosynthesis | 9 | 5 | 4 | 80
S.No | Pathway name | RiceCyc | D | DD | Percent DD over D |  | 33 | dTDP-L-rhamnose biosynthesis I | 49 | 20 | 16 | 80
1 | lysine biosynthesis I | 24 | 6 | 6 | 100 |  | 34 | phospholipid biosynthesis I | 36 | 5 | 4 | 80
2 | lysine biosynthesis II | 24 | 6 | 6 | 100 |  | 35 | acetyl CoA fermentation to butyrate | 10 | 5 | 4 | 80
3 | lysine biosynthesis VI | 24 | 6 | 6 | 100 |  | 36 | glutaryl-CoA degradation | 10 | 5 | 4 | 80
4 | tRNA charging pathway | 127 | 16 | 16 | 100 |  | 37 | starch biosynthesis | 30 | 10 | 8 | 80
5 | UDP-D-xylose biosynthesis | 9 | 5 | 5 | 100 |  | 38 | TCA cycle variation I | 43 | 15 | 12 | 80
6 | salvage pathways of purine nucleosides | 31 | 9 | 9 | 100 |  | 39 | sucrose degradation III | 47 | 10 | 8 | 80
7 | purine nucleotides de novo biosynthesis II | 44 | 9 | 9 | 100 |  | 40 | methionine biosynthesis I | 12 | 5 | 4 | 80
8 | salvage pathways of purine nucleosides II (plant) | 24 | 6 | 6 | 100 |  | 41 | sucrose degradation I | 12 | 5 | 4 | 80
9 | de novo biosynthesis of pyrimidine deoxyribonucleotides | 35 | 7 | 7 | 100 |  | 42 | salvage pathways of purine nucleosides | 31 | 9 | 7 | 77.77777777777779
10 | cellulose biosynthesis | 30 | 9 | 8 | 88.88888888888889 |  | 43 | cellulose biosynthesis | 30 | 9 | 7 | 77.77777777777779
11 | purine nucleotides de novo biosynthesis I | 77 | 17 | 15 | 88.23529411764706 |  | 44 | phospholipases | 38 | 9 | 7 | 77.77777777777779
12 | phenylpropanoid biosynthesis | 22 | 8 | 7 | 87.5 |  | 45 | salvage pathways of pyrimidine ribonucleotides | 38 | 9 | 7 | 77.77777777777779
13 | sucrose biosynthesis | 25 | 6 | 5 | 83.33333333333334 |  | 46 | triacylglycerol degradation | 99 | 22 | 17 | 77.27272727272727
14 | heme biosynthesis II | 15 | 6 | 5 | 83.33333333333334 |  | 47 | salvage pathways of purine and pyrimidine nucleotides | 71 | 22 | 17 | 77.27272727272727
15 | flavonoid biosynthesis | 18 | 6 | 5 | 83.33333333333334 |  | 48 | UDP-N-acetylgalactosamine biosynthesis | 37 | 13 | 10 | 76.92307692307693
16 | aspartate degradation II | 14 | 6 | 5 | 83.33333333333334 |  | 49 | purine nucleotides de novo biosynthesis I | 77 | 17 | 13 | 76.47058823529412
17 | suberin biosynthesis | 18 | 6 | 5 | 83.33333333333334 |  | 50 | phenylpropanoid biosynthesis | 22 | 8 | 6 | 75
18 | fatty acid elongation -- saturated | 28 | 10 | 8 | 80 |  | 51 | phospholipid desaturation | 16 | 8 | 6 | 75
19 | mixed acid fermentation | 84 | 19 | 15 | 78.94736842105263 |  | 52 | [NAME] biosynthesis | 60 | 12 | 9 | 75
20 | [NAME] biosynthesis II | 22 | 8 | 6 | 75 |  | 53 | tetrapyrrole biosynthesis I | 33 | 8 | 6 | 75
21 | folate polyglutamylation I | 18 | 8 | 6 | 75 |  | 54 | glycogen biosynthesis I (from ADP-D-Glucose) | 21 | 8 | 6 | 75
22 | fatty acid biosynthesis - initial steps | 27 | 8 | 6 | 75 |  | 55 | mevalonate pathway | 20 | 8 | 6 | 75
23 | fatty acid  elongation -- unsaturated II | 22 | 8 | 6 | 75 |  | 56 | GDP-L-fucose biosynthesis I (from GDP-D-mannose) | 13 | 8 | 6 | 75
24 | phospholipid desaturation | 16 | 8 | 6 | 75 |  | 57 | GDP-D-rhamnose biosynthesis | 12 | 8 | 6 | 75
25 | fructose degradation to pyruvate and lactate (anaerobic) | 117 | 34 | 25 | 73.52941176470588 |  | 58 | starch degradation | 67 | 24 | 18 | 75
26 | glycolysis IV (plant cytosol) | 110 | 30 | 22 | 73.33333333333333 |  | 59 | citrulline biosynthesis | 22 | 8 | 6 | 75
27 | [NAME] biosynthesis I | 21 | 7 | 5 | 71.42857142857143 |  | 60 | trehalose biosynthesis I | 21 | 8 | 6 | 75
28 | photorespiration | 26 | 10 | 7 | 70 |  | 61 | brassinosteroid biosynthesis II | 101 | 38 | 28 | 73.68421052631578
29 | sucrose degradation to ethanol and lactate (anaerobic) | 198 | 50 | 35 | 70 |  | 62 | respiration (anaerobic) | 65 | 22 | 16 | 72.72727272727273
30 | oxidative ethanol degradation I | 57 | 10 | 7 | 70 |  | 63 | gluconeogenesis | 80 | 28 | 20 | 71.42857142857143
31 | methionine degradation III | 55 | 10 | 7 | 70 |  | 64 | histidine biosynthesis I | 29 | 7 | 5 | 71.42857142857143
32 | glycolysis I | 113 | 32 | 22 | 68.75 |  | 65 | arginine degradation I (arginase pathway) | 17 | 7 | 5 | 71.42857142857143
33 | glucose fermentation to lactate II | 94 | 31 | 21 | 67.74193548387096 |  | 66 | proline biosynthesis I | 18 | 7 | 5 | 71.42857142857143
34 | tryptophan degradation V (side chain pathway) | 15 | 9 | 6 | 66.66666666666666 |  | 67 | proline biosynthesis II | 18 | 7 | 5 | 71.42857142857143
35 | folate transformations | 16 | 6 | 4 | 66.66666666666666 |  | 68 | cysteine biosynthesis I | 22 | 10 | 7 | 70
36 | valine degradation I | 28 | 6 | 4 | 66.66666666666666 |  | 69 | cytokinins 7-N-glucoside biosynthesis | 1134 | 91 | 63 | 69.23076923076923
37 | polyisoprenoid biosynthesis | 31 | 6 | 4 | 66.66666666666666 |  | 70 | cytokinins 9-N-glucoside biosynthesis | 972 | 78 | 54 | 69.23076923076923
38 | removal of superoxide radicals | 75 | 6 | 4 | 66.66666666666666 |  | 71 | cytokinins-O-glucoside biosynthesis | 648 | 52 | 36 | 69.23076923076923
39 | isoleucine degradation II | 62 | 12 | 8 | 66.66666666666666 |  | 72 | sucrose degradation to ethanol and lactate (anaerobic) | 198 | 50 | 34 | 68
40 | aerobic respiration -- electron donor II | 107 | 6 | 4 | 66.66666666666666 |  | 73 | purine nucleotides de novo biosynthesis II | 44 | 9 | 6 | 66.66666666666666
41 | respiration (anaerobic)-- electron donors reaction list | 38 | 6 | 4 | 66.66666666666666 |  | 74 | salvage pathways of purine nucleosides II (plant) | 24 | 6 | 4 | 66.66666666666666
42 | aerobic respiration -- electron donors reaction list | 36 | 6 | 4 | 66.66666666666666 |  | 75 | flavonoid biosynthesis | 18 | 6 | 4 | 66.66666666666666
43 | glutathione-mediated detoxification | 47 | 6 | 4 | 66.66666666666666 |  | 76 | aspartate degradation II | 14 | 6 | 4 | 66.66666666666666
44 | methylerythritol phosphate pathway | 13 | 6 | 4 | 66.66666666666666 |  | 77 | aerobic respiration -- electron donor II | 107 | 6 | 4 | 66.66666666666666
45 | NAD salvage pathway II | 29 | 9 | 6 | 66.66666666666666 |  | 78 | respiration (anaerobic)-- electron donors reaction list | 38 | 6 | 4 | 66.66666666666666
46 | glycolipid desaturation | 100 | 50 | 33 | 66 |  | 79 | aerobic respiration -- electron donors reaction list | 36 | 6 | 4 | 66.66666666666666
47 | gluconeogenesis | 80 | 28 | 18 | 64.28571428571429 |  | 80 | chlorophyllide a biosynthesis | 32 | 12 | 8 | 66.66666666666666
48 | ethanol fermentation to acetate | 64 | 14 | 9 | 64.28571428571429 |  | 81 | tryptophan biosynthesis | 24 | 12 | 8 | 66.66666666666666
49 | betanidin degradation | 189 | 41 | 26 | 63.41463414634146 |  | 82 | proline degradation I | 16 | 6 | 4 | 66.66666666666666
50 | tetrapyrrole biosynthesis I | 33 | 8 | 5 | 62.5 |  | 83 | proline degradation II | 16 | 6 | 4 | 66.66666666666666
51 | xylulose-monophosphate cycle | 17 | 8 | 5 | 62.5 |  | 84 | 4-hydroxyproline degradation I | 15 | 6 | 4 | 66.66666666666666
52 | leucine degradation III | 66 | 13 | 8 | 61.53846153846154 |  | 85 | phenylalanine biosynthesis I | 21 | 6 | 4 | 66.66666666666666
53 | valine degradation II | 66 | 13 | 8 | 61.53846153846154 |  | 86 | leucine biosynthesis | 17 | 6 | 4 | 66.66666666666666
54 | cysteine biosynthesis I | 22 | 10 | 6 | 60 |  | 87 | glycolipid desaturation | 100 | 50 | 33 | 66
55 | purine degradation | 11 | 5 | 3 | 60 |  | 88 | fructose degradation to pyruvate and lactate (anaerobic) | 117 | 34 | 22 | 64.70588235294117
56 | ureide biosynthesis | 9 | 5 | 3 | 60 |  | 89 | ethanol fermentation to acetate | 64 | 14 | 9 | 64.28571428571429
57 | pentose phosphate pathway (partial) | 6 | 5 | 3 | 60 |  | 90 | mixed acid fermentation | 84 | 19 | 12 | 63.1578947368421
58 | glycerol degradation I | 24 | 5 | 3 | 60 |  | 91 | xylulose-monophosphate cycle | 17 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 92 | glycolysis I | 113 | 32 | 20 | 62.5
 |  |  |  |  |  |  | 93 | fatty acid biosynthesis - initial steps | 27 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 94 | fatty acid  elongation -- unsaturated II | 22 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 95 | leucine degradation III | 66 | 13 | 8 | 61.53846153846154
 |  |  |  |  |  |  | 96 | valine degradation II | 66 | 13 | 8 | 61.53846153846154
 |  |  |  |  |  |  | 97 | phenylalanine degradation III | 61 | 13 | 8 | 61.53846153846154
 |  |  |  |  |  |  | 98 | purine degradation | 11 | 5 | 3 | 60
 |  |  |  |  |  |  | 99 | ureide biosynthesis | 9 | 5 | 3 | 60
 |  |  |  |  |  |  | 100 | pentose phosphate pathway (partial) | 6 | 5 | 3 | 60
 |  |  |  |  |  |  | 101 | oxidative ethanol degradation I | 57 | 10 | 6 | 60
 |  |  |  |  |  |  | 102 | methionine degradation III | 55 | 10 | 6 | 60
 |  |  |  |  |  |  | 103 | enterobactin biosynthesis | 86 | 15 | 9 | 60
 |  |  |  |  |  |  | S.No | Pathway name | RiceCyc | D | EU | Percent EU over D
 |  |  |  |  |  |  | 1 | gamma;-glutamyl cycle | 34 | 6 | 5 | 83.33333333333334
 |  |  |  |  |  |  | 2 | citrulline biosynthesis | 22 | 8 | 6 | 75
 |  |  |  |  |  |  | 3 | trehalose biosynthesis I | 21 | 8 | 6 | 75
 |  |  |  |  |  |  | 4 | beta;-alanine biosynthesis II | 12 | 7 | 5 | 71.42857142857143
 |  |  |  |  |  |  | 5 | proline biosynthesis I | 18 | 7 | 5 | 71.42857142857143
 |  |  |  |  |  |  | 6 | proline biosynthesis II | 18 | 7 | 5 | 71.42857142857143
 |  |  |  |  |  |  | 7 | D-lactate fermentation to propionate and acetate | 11 | 6 | 4 | 66.66666666666666
 |  |  |  |  |  |  | 8 | GDP-L-fucose biosynthesis I (from GDP-D-mannose) | 13 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 9 | GDP-D-rhamnose biosynthesis | 12 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 10 | [NAME] biosynthesis | 42 | 13 | 8 | 61.53846153846154
 |  |  |  |  |  |  | 11 | TCA cycle | 35 | 13 | 8 | 61.53846153846154
 |  |  |  |  |  |  | 12 | phospholipid biosynthesis I | 36 | 5 | 3 | 60
 |  |  |  |  |  |  | 13 | acetyl CoA fermentation to butyrate | 10 | 5 | 3 | 60
 |  |  |  |  |  |  | 14 | glutaryl-CoA degradation | 10 | 5 | 3 | 60
 |  |  |  |  |  |  | 15 | TCA cycle variation I | 43 | 15 | 9 | 60
 |  |  |  |  |  |  | 16 | methionine biosynthesis I | 12 | 5 | 3 | 60
 |  |  |  |  |  |  | 17 | sucrose degradation I | 12 | 5 | 3 | 60
 |  |  |  |  |  |  | S.No | Pathway name | RiceCyc | D | ED | Percent ED over D
 |  |  |  |  |  |  | 1 | lysine biosynthesis I | 24 | 6 | 6 | 100
 |  |  |  |  |  |  | 2 | lysine biosynthesis II | 24 | 6 | 6 | 100
 |  |  |  |  |  |  | 3 | lysine biosynthesis VI | 24 | 6 | 6 | 100
 |  |  |  |  |  |  | 4 | tRNA charging pathway | 127 | 16 | 14 | 87.5
 |  |  |  |  |  |  | 5 | sucrose biosynthesis | 25 | 6 | 5 | 83.33333333333334
 |  |  |  |  |  |  | 6 | heme biosynthesis II | 15 | 6 | 5 | 83.33333333333334
 |  |  |  |  |  |  | 7 | UDP-D-xylose biosynthesis | 9 | 5 | 4 | 80
 |  |  |  |  |  |  | 8 | salvage pathways of purine nucleosides | 31 | 9 | 7 | 77.77777777777779
 |  |  |  |  |  |  | 9 | [NAME] biosynthesis II | 22 | 8 | 6 | 75
 |  |  |  |  |  |  | 10 | folate polyglutamylation I | 18 | 8 | 6 | 75
 |  |  |  |  |  |  | 11 | [NAME] biosynthesis I | 21 | 7 | 5 | 71.42857142857143
 |  |  |  |  |  |  | 12 | purine nucleotides de novo biosynthesis I | 77 | 17 | 12 | 70.58823529411765
 |  |  |  |  |  |  | 13 | photorespiration | 26 | 10 | 7 | 70
 |  |  |  |  |  |  | 14 | tryptophan degradation V (side chain pathway) | 15 | 9 | 6 | 66.66666666666666
 |  |  |  |  |  |  | 15 | folate transformations | 16 | 6 | 4 | 66.66666666666666
 |  |  |  |  |  |  | 16 | valine degradation I | 28 | 6 | 4 | 66.66666666666666
 |  |  |  |  |  |  | 17 | cellulose biosynthesis | 30 | 9 | 6 | 66.66666666666666
 |  |  |  |  |  |  | 18 | purine nucleotides de novo biosynthesis II | 44 | 9 | 6 | 66.66666666666666
 |  |  |  |  |  |  | 19 | salvage pathways of purine nucleosides II (plant) | 24 | 6 | 4 | 66.66666666666666
 |  |  |  |  |  |  | 20 | phenylpropanoid biosynthesis | 22 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 21 | fatty acid biosynthesis - initial steps | 27 | 8 | 5 | 62.5
 |  |  |  |  |  |  | 22 | fatty acid  elongation -- unsaturated II | 22 | 8 | 5 | 62.5