Coexpression of Neighboring Genes in the Genome of Arabidopsis thaliana

Table 3.

Degree of Coexpression of Genes Within the Same Pathway as Defined by the KEGG Database

Pathway no.
Pathway id
Pathway description
Total comparisons
R
No. genes
1 ath03050 Proteasome 946 0.436 47
2 ath03010 Ribosome 24504 0.385 249
3 ath00580 Phospholipid degradation 25 0.378 9
4 ath03030 DNA polymerase 89 0.360 16
5 ath00960 Alkaloid biosynthesis II 10 0.349 5
6 ath03032 Replication complex 36 0.300 10
7 ath00020 Citrate cycle (TCA cycle) 670 0.264 39
8 ath00860 Porphyrin and chlorophyll metabolism 190 0.254 22
9 ath00061 Fatty acid biosynthesis (path 1) 78 0.240 13
10 ath03020 RNA polymerase 491 0.214 37
11 ath00720 Reductive carboxylate cycle (CO2 fixation) 170 0.213 20
12 ath00195 Photosynthesis 1646 0.198 63
13 ath00510 N-Glycans biosynthesis 262 0.189 25
14 ath00521 Streptomycin biosynthesis 21 0.189 7
15 ath00193 ATP synthesis 525 0.184 37
16 ath03022 Basal transcription factors 326 0.175 34
17 ath00970 Aminoacyl-tRNA biosynthesis 629 0.174 38
18 ath03014 Other translation factors 15 0.171 7
19 ath00150 Androgen and estrogen metabolism 10 0.167 6
20 ath03034 Other replication, recombination and repair factors 66 0.158 14
21 ath00300 Lysine biosynthesis 66 0.143 13
22 ath00360 Phenylalanine metabolism 2502 0.138 78
23 ath00760 Nicotinate and nicotinamide metabolism 2894 0.136 86
24 ath00400 Phenylalanine, tyrosine and tryptophan biosynthesis 629 0.135 40
25 ath00632 Benzoate degradation via CoA ligation 3208 0.132 89
75 ath00750 Vitamin B6 metabolism 10 0.050 5
76 ath00561 Glycerolipid metabolism 1032 0.049 48
77 ath00511 N-Glycan degradation 35 0.048 9
78 ath00252 Alanine and aspartate metabolism 494 0.045 36
79 ath00330 Arginine and proline metabolism 560 0.041 36
80 ath00910 Nitrogen metabolism 378 0.037 29
81 ath00220 Urea cycle and metabolism of amino groups 136 0.036 20
82 ath00410 β-Alanine metabolism 120 0.034 17
83 ath00670 One carbon pool by folate 78 0.034 16
84 ath00362 Benzoate degradation via hydroxylation 36 0.033 10
85 ath00340 Histidine metabolism 91 0.029 15
86 ath00472 D-Arginine and D-ornithine metabolism 21 0.027 8
87 ath00251 Glutamate metabolism 818 0.025 43
88 ath00351 1,1,1-Trichloro-2.2-bis(4-chlorophenyl)ethane (DDT) degradation 21 0.022 8
89 ath00361 γ-Hexachlorocyclohexane degradation 587 0.021 40
90 ath00053 Ascorbate and aldarate metabolism 836 0.020 47
91 ath00100 Sterol biosynthesis 449 0.018 34
92 ath03060 Protein export 377 0.018 31
93 ath00530 Aminosugars metabolism 153 0.018 20
94 ath00628 Fluorene degradation 587 0.017 40
95 ath04710 Circadian rhythm 496 0.014 32
96 ath00120 Bile acid biosynthesis 91 0.006 14
97 ath00900 Terpenoid biosynthesis 95 0.002 17
98 ath00460 Cyanoamino acid metabolism 65 -0.007 15
99 ath02052 Other ion-coupled transporters 45 -0.074 10
100
ath00550
Peptidoglycan biosynthesis
10
-0.172
5

  • This table excludes pathways with less than five genes defined. Only top 25 and bottom 25 pathways are shown in this table. Those in bold are those known to involve multiprotein complexes.

This Article

  1. Genome Res. 14: 1060-1067

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