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Table 2 Significantly enriched GO terms in AGCN modules (I = 1.8)

From: Arabidopsis gene co-expression network and its functional modules

module # annotated genes1 GO term2 genes in GO term3 p value4
1 1208 photosynthesis 97/107 1.38E-52
2 684 response to oxidative stress 30/88 1.43E-07
3 438 protein biosynthesis 95/204 5.68E-52
4 256 DNA metabolism 59/107 9.07E-52
5 104 defense response 18/205 4.79E-08
6 87 reproductive structure development 15/100 3.16E-11
7 78 protein ubiquitination 5/14 1.00E-06
8 59 defense response 19/205 1.65E-13
9 48 establishment and/or maintenance of chromatin architecture 6/43 1.71E-06
11 39 cell wall modification 5/32 2 64E-06
15 36 response to wounding 7/54 4.50E-08
18 33 cuticle biosynthesis 5/8 3.45E-10
21 29 toxin metabolism 5/25 1.54E-07
27 23 glucosinolate biosynthesis 4/9 3.12E-08
28 18 RNA processing 5/65 1.65E-06
31 20 monosaccharide metabolism 5/47 5.67E-07
33 17 response to heat 10/47 1.69E-17
34 18 secondary cell wall biosynthesis (sensu Magnoliophyta) 6/8 1.51E-14
35 17 protein biosynthesis 11/204 1.75E-12
41 16 enzyme linked receptor protein signaling pathway 5/51 2.49E-07
42 15 organic acid metabolism 9/186 2.38E-10
43 13 response to auxin stimulus 7/69 6.62E-11
46 14 lipid metabolism 7/194 1.93E-07
50 12 cellular respiration 6/15 1.34E-13
56 11 leaf development 4/28 1.87E-07
67 10 starch metabolism 8/20 3.18E-19
79 9 indoleacetic acid metabolism 3/4 1.28E-08
80 8 phenylpropanoid metabolism 6/44 5.71E-12
119 6 response to heat 6/47 3.14E-13
122 6 lipid transport 4/47 7.49E-08
140 5 nitrogen compound metabolism 5/129 7.23E-09
154 4 wax biosynthesis 2/7 8.65E-06
165 4 glutamate biosynthesis 2/2 4 12E-07
170 4 electron transport 4/219 2.64E-06
173 4 fatty acid beta-oxidation 2/9 1.48E-05
180 4 purine transport 2/3 1.24E-06
190 4 response to water deprivation 4/41 2.87E-09
201 2 Glycolysis 2/16 8.24E-06
205 3 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 2/5 2.06E-06
213 4 response to heat 4/47 5.05E-09
224 3 fatty acid beta-oxidation 2/9 7.41E-06
238 3 sulfolipid biosynthesis 2/2 2.06E-07
266 3 ovule development 2/12 1.36E-05
273 3 phenylpropanoid metabolism 3/44 5.06E-07
311 3 Proteolysis 3/130 1.37E-05
315 3 response to iron ion 2/3 6.18E-07
  1. 1. The number of genes which were assigned with biological process GO terms in a module.
  2. 2. Only the most over-represented GO term was listed for each module.
  3. 3. The two values listed in this column refer to the number of genes associated with the over-represented GO term in the module and the number of genes associated with the same GO term in the network.
  4. 4. The p value indicated the probability that a module contains equal or larger number of genes associated with the GO term under a hypergeometric distribution.