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Table 3 GenoMesh analysis of 31 E. coli pathways containing at least 10 genes.

From: A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

Index Pathway name # of genes Average dissimilarity score SD Z value *p-value
1 superpathway of chorismate 50(61) 0.077 0.134 -10.98 0
2 superpathway of histidine, purine, and pyrimidine biosynthesis 42(58) 0.080 0.117 -10.67 2.91E-275
3 superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 35(45) 0.074 0.140 -8.39 3.19E-146
4 aspartate superpathway 26(29) 0.080 0.133 -8.06 2.03E-103
5 respiration (anaerobic) 24(30) 0.086 0.170 -8.57 1.87E-108
6 respiration (anaerobic)-- electron donors reaction list 21(31) 0.209 0.260 -25.72 0
7 mixed acid fermentation 21(28) 0.102 0.171 -10.32 5.00E-138
8 superpathway of glyoxylate bypass and TCA 21(24) 0.123 0.190 -11.86 9.88E-182
9 superpathway of lysine, threonine, methionine, and S-adenosyl-L-methionine biosynthesis 21(23) 0.103 0.140 -10.45 1.71E-141
10 tRNA charging pathway 21(23) 0.073 0.107 -6.21 2.18E-51
11 superpathway of threonine metabolism 20(26) 0.133 0.208 -14.37 8.72E-253
12 superpathway of arginine and polyamine biosynthesis 19(22) 0.124 0.135 -11.32 1.46E-152
13 superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis 18(25) 0.148 0.162 -15.52 1.15E-269
14 superpathway of leucine, valine, and isoleucine biosynthesis 17(30) 0.215 0.247 -23.38 0
15 aerobic respiration -- electron donors reaction list 17(21) 0.270 0.286 -30.45 0
16 TCA cycle 17(20) 0.143 0.209 -14.37 2.47E-221
17 respiration (anaerobic)-- electron acceptors reaction list 16(25) 0.194 0.212 -20.18 0
18 superpathway of lipopolysaccharide biosynthesis 15(26) 0.093 0.127 -7.47 1.20E-54
19 superpathway of glycolysis and Entner-Doudoroff 15(22) 0.114 0.126 -9.92 8.82E-95
20 superpathway of fatty acid biosynthesis 12(24) 0.223 0.221 -19.90 0
21 glycolysis I 12(18) 0.113 0.135 -8.61 1.11E-59
22 formylTHF biosynthesis I 12(15) 0.060 0.079 -3.04 4.90E-09
23 methionine and methyl-donor-molecule biosynthesis 11(13) 0.115 0.145 -8.36 1.92E-52
24 superpathway of sulfate assimilation and cysteine biosynthesis 11(12) 0.176 0.225 -14.26 2.72E-148
25 tetrahydrofolate biosynthesis I 11(12) 0.081 0.153 -4.95 1.13E-19
26 de novo biosynthesis of pyrimidine ribonucleotides 11(12) 0.119 0.142 -8.67 3.51E-56
27 peptidoglycan biosynthesis I 11(11) 0.294 0.225 -25.91 0
28 arginine biosynthesis I 11(11) 0.181 0.156 -14.93 3.35E-162
29 de novo biosynthesis of pyrimidine deoxyribonucleotides 10(18) 0.150 0.220 -11.06 4.00E-83
30 chorismate biosynthesis 10(11) 0.210 0.202 -16.58 7.45E-184
31 colanic acid building blocks biosynthesis 10(11) 0.114 0.135 -7.78 3.94E-42
  1. Note: All permutation p-values are <0.001. * p-valule: 0 means less than 1.00E-323.